3TOZ

2.2 Angstrom Crystal Structure of Shikimate 5-dehydrogenase from Listeria monocytogenes in Complex with NAD.

PDB DOI: https://doi.org/10.2210/pdb3TOZ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Listeria monocytogenes EGD-e
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2011-09-06 Released: 2011-09-21
Deposition Author(s): Minasov, G., Light, S.H., Halavaty, A., Shuvalova, L., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.256
R-Value Work: 0.195
R-Value Observed: 0.199

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

2.2 Angstrom Crystal Structure of Shikimate 5-dehydrogenase from Listeria monocytogenes in Complex with NAD.

Minasov, G., Light, S.H., Halavaty, A., Shuvalova, L., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 285.78 kDa
Atom Count: 19,603
Modelled Residue Count: 2,315
Deposited Residue Count: 2,520
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Shikimate dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	315	Listeria monocytogenes EGD-e	Mutation(s): 0 Gene Names: aroE, lmo0490 EC: 1.1.1.25
UniProt
Find proteins for Q8Y9N5 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y9N5 Go to UniProtKB: Q8Y9N5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8Y9N5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain S [auth D] SDF format, chain T [auth E] SDF format, chain V [auth F] SDF format, chain X [auth G] SDF format, chain Z [auth H] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth E] MOL2 format, chain V [auth F] MOL2 format, chain X [auth G] MOL2 format, chain Z [auth H] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D] mmCIF format, chain T [auth E] mmCIF format, chain V [auth F] mmCIF format, chain X [auth G] mmCIF format, chain Z [auth H]	I [auth A] L [auth B] P [auth C] S [auth D] T [auth E] I [auth A], L [auth B], P [auth C], S [auth D], T [auth E], V [auth F], X [auth G], Z [auth H]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Z [auth H] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Z [auth H]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain W [auth F] SDF format, chain Y [auth G] MOL2 format, chain BA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain W [auth F] MOL2 format, chain Y [auth G] mmCIF format, chain BA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain W [auth F] mmCIF format, chain Y [auth G]	BA [auth H] J [auth A] K [auth A] M [auth B] N [auth B] BA [auth H], J [auth A], K [auth A], M [auth B], N [auth B], O [auth B], W [auth F], Y [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain W [auth F] Focus chain Y [auth G] Interactions & Density Focus chain BA [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain W [auth F] Focus chain Y [auth G]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain U [auth E] MOL2 format, chain AA [auth H] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain U [auth E] mmCIF format, chain AA [auth H] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain U [auth E]	AA [auth H], Q [auth C], R [auth C], U [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth H] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth E] Interactions & Density Focus chain AA [auth H] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.256
R-Value Work: 0.195
R-Value Observed: 0.199
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/m33toz

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.13	α = 90
b = 78.434	β = 90.49
c = 214.829	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
BALBES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-09-21

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2011-09-21
Type: Initial release
Version 1.1: 2017-11-08
Changes: Refinement description
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description