3CA8

Crystal structure of Escherichia coli YdcF, an S-adenosyl-L-methionine utilizing enzyme

PDB DOI: https://doi.org/10.2210/pdb3CA8/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-02-19 Released: 2008-05-06
Deposition Author(s): Lim, K., Chao, K., Lehmann, C., Herzberg, O., Structure 2 Function Project (S2F)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.238 (Depositor), 0.250 (DCC)
R-Value Work:
0.195 (Depositor), 0.200 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The Escherichia coli YdcF binds S-adenosyl-L-methionine and adopts an alpha/beta-fold characteristic of nucleotide-utilizing enzymes.

Chao, K.L., Lim, K., Lehmann, C., Doseeva, V., Howard, A.J., Schwarz, F.P., Herzberg, O.

(2008) Proteins 72: 506-509

PubMed: 18393394 Search on PubMed
DOI: https://doi.org/10.1002/prot.22046
Primary Citation of Related Structures:
3CA8

Organizational Affiliation

Center for Advanced Research in Biotechnology, W.M. Keck Laboratory for Structural Biology, University of Maryland Biotechnology Institute, Rockville, Maryland, USA.

Macromolecule Content

Total Structure Weight: 61.89 kDa
Atom Count: 5,031
Modelled Residue Count: 520
Deposited Residue Count: 532
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein ydcF	A, B	266	Escherichia coli K-12	Mutation(s): 0 Gene Names: ydcF, b1414, JW1411
UniProt
Find proteins for P34209 (Escherichia coli (strain K12)) Explore P34209 Go to UniProtKB: P34209
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P34209
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain S [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain H [auth A] SDF format, chain M [auth A] SDF format, chain R [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain S [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain H [auth A] MOL2 format, chain M [auth A] MOL2 format, chain R [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain S [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain H [auth A] mmCIF format, chain M [auth A] mmCIF format, chain R [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	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], L [auth A], M [auth A], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-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 L [auth A] Focus chain M [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] 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 L [auth A] Focus chain M [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain F [auth A] SDF format, chain N [auth B] SDF format, chain Q [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain F [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain F [auth A] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] N [auth B] C [auth A], D [auth A], E [auth A], F [auth A], N [auth B], O [auth B], P [auth B], Q [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.238 (Depositor), 0.250 (DCC)
R-Value Work: 0.195 (Depositor), 0.200 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.795	α = 90
b = 39.71	β = 96.34
c = 122.645	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHELXD	phasing
SOLVE	phasing
RESOLVE	model building
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
RESOLVE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-05-06

Deposition Author(s):

Structure 2 Function Project (S2F)

Revision History (Full details and data files)

Version 1.0: 2008-05-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations
Version 1.3: 2024-04-03
Changes: Refinement description