4ZFM | pdb_00004zfm

Structure of Gan1D-E170Q in complex with cellobiose-6-phosphate

PDB DOI: https://doi.org/10.2210/pdb4ZFM/pdb

Classification: HYDROLASE
Organism(s): Geobacillus stearothermophilus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2015-04-21 Released: 2016-06-29
Deposition Author(s): Lansky, S., Zehavi, A., Dvir, H., Shoham, Y., Shoham, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.158 (Depositor), 0.158 (DCC)
R-Value Work:
0.130 (Depositor), 0.131 (DCC)
R-Value Observed:
0.132 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Structure of Gan1D-E170Q in complex with cellobiose-6-phosphate

Lansky, S., Zehavi, A., Dvir, H., Shoham, Y., Shoham, G.

To be published.

Macromolecule Content

Total Structure Weight: 227.5 kDa
Atom Count: 18,396
Modeled Residue Count: 1,844
Deposited Residue Count: 1,940
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative 6-phospho-beta-galactobiosidase	A, B, C, D	485	Geobacillus stearothermophilus	Mutation(s): 1 Gene Names: gan1D EC: 3.2.1.85
UniProt
Find proteins for W8QF82 (Geobacillus stearothermophilus) Explore W8QF82 Go to UniProtKB: W8QF82
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	W8QF82
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
1,5-anhydro-6-O-phosphono-D-glucitol-(1-4)-beta-D-glucopyranose	E	2		N/A	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G15380AW GlyCosmos: G15380AW

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BG6 Query on BG6 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B]	F [auth A], M [auth B]	6-O-phosphono-beta-D-glucopyranose C₆ H₁₃ O₉ P NBSCHQHZLSJFNQ-VFUOTHLCSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain M [auth B]
0WK Query on 0WK Download:Ideal Coordinates CCD File SDF format, chain U [auth C] MOL2 format, chain U [auth C] mmCIF format, chain U [auth C]	U [auth C]	1,5-anhydro-6-O-phosphono-D-glucitol C₆ H₁₃ O₈ P KAJAXXUCVJFKFM-SLPGGIOYSA-N		Interactions Focus chain U [auth C] Interactions & Density Focus chain U [auth C]
BGC Query on BGC Download:Ideal Coordinates CCD File SDF format, chain V [auth C] MOL2 format, chain V [auth C] mmCIF format, chain V [auth C]	V [auth C]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain V [auth C] Interactions & Density Focus chain V [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D] mmCIF format, chain I [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], P [auth C], Q [auth C], R [auth C], S [auth C], W [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain T [auth C] SDF format, chain X [auth D] MOL2 format, chain L [auth A] MOL2 format, chain T [auth C] MOL2 format, chain X [auth D] mmCIF format, chain L [auth A] mmCIF format, chain T [auth C] mmCIF format, chain X [auth D]	L [auth A], T [auth C], X [auth D]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain L [auth A] Focus chain T [auth C] Focus chain X [auth D] Interactions & Density Focus chain L [auth A] Focus chain T [auth C] Focus chain X [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.158 (Depositor), 0.158 (DCC)
R-Value Work: 0.130 (Depositor), 0.131 (DCC)
R-Value Observed: 0.132 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.59	α = 90
b = 97.47	β = 97.66
c = 105.27	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-06-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-06-29
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary