3GVD | pdb_00003gvd

Crystal Structure of Serine Acetyltransferase CysE from Yersinia pestis

PDB DOI: https://doi.org/10.2210/pdb3GVD/pdb

Classification: TRANSFERASE
Organism(s): Yersinia pestis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-03-30 Released: 2009-05-12
Deposition Author(s): Kim, Y., Zhou, M., Peterson, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.265 (Depositor), 0.256 (DCC)
R-Value Work:
0.199 (Depositor), 0.191 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Serine Acetyltransferase CysE from Yersinia pestis

Kim, Y., Zhou, M., Peterson, S., Anderson, W.F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 356.66 kDa
Atom Count: 25,003
Modeled Residue Count: 3,162
Deposited Residue Count: 3,312
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine acetyltransferase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	276	Yersinia pestis	Mutation(s): 0 Gene Names: cysE, YPO0070 EC: 2.3.1.30
UniProt
Find proteins for A0A2U2H3H7 (Yersinia pestis) Explore A0A2U2H3H7 Go to UniProtKB: A0A2U2H3H7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2U2H3H7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG5 Query on PG5 Download:Ideal Coordinates CCD File SDF format, chain S [auth C] MOL2 format, chain S [auth C] mmCIF format, chain S [auth C]	S [auth C]	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE C₈ H₁₈ O₄ YFNKIDBQEZZDLK-UHFFFAOYSA-N		Interactions Focus chain S [auth C] Interactions & Density Focus chain S [auth C]
CYS Query on CYS Download:Ideal Coordinates CCD File SDF format, chain X [auth E] SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain R [auth B] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain NA [auth L] SDF format, chain MA [auth L] SDF format, chain IA [auth J] SDF format, chain EA [auth I] SDF format, chain DA [auth H] SDF format, chain AA [auth G] MOL2 format, chain X [auth E] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain R [auth B] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth L] MOL2 format, chain MA [auth L] MOL2 format, chain IA [auth J] MOL2 format, chain EA [auth I] MOL2 format, chain DA [auth H] MOL2 format, chain AA [auth G] mmCIF format, chain X [auth E] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain R [auth B] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth L] mmCIF format, chain MA [auth L] mmCIF format, chain IA [auth J] mmCIF format, chain EA [auth I] mmCIF format, chain DA [auth H] mmCIF format, chain AA [auth G]	AA [auth G] DA [auth H] EA [auth I] IA [auth J] MA [auth L] AA [auth G], DA [auth H], EA [auth I], IA [auth J], MA [auth L], NA [auth L], O [auth A], P [auth A], R [auth B], U [auth D], V [auth D], X [auth E]	CYSTEINE C₃ H₇ N O₂ S XUJNEKJLAYXESH-REOHCLBHSA-N		Interactions Focus chain AA [auth G] Focus chain DA [auth H] Focus chain EA [auth I] Focus chain IA [auth J] Focus chain MA [auth L] Focus chain NA [auth L] Focus chain O [auth A] Focus chain P [auth A] Focus chain R [auth B] Focus chain U [auth D] Focus chain V [auth D] Focus chain X [auth E] Interactions & Density Focus chain AA [auth G] Focus chain DA [auth H] Focus chain EA [auth I] Focus chain IA [auth J] Focus chain MA [auth L] Focus chain NA [auth L] Focus chain O [auth A] Focus chain P [auth A] Focus chain R [auth B] Focus chain U [auth D] Focus chain V [auth D] Focus chain X [auth E]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain LA [auth L] MOL2 format, chain LA [auth L] mmCIF format, chain LA [auth L]	LA [auth L]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain LA [auth L] Interactions & Density Focus chain LA [auth L]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Y [auth F] SDF format, chain M [auth A] SDF format, chain KA [auth L] SDF format, chain JA [auth K] SDF format, chain BA [auth H] MOL2 format, chain Y [auth F] MOL2 format, chain M [auth A] MOL2 format, chain KA [auth L] MOL2 format, chain JA [auth K] MOL2 format, chain BA [auth H] mmCIF format, chain Y [auth F] mmCIF format, chain M [auth A] mmCIF format, chain KA [auth L] mmCIF format, chain JA [auth K] mmCIF format, chain BA [auth H]	BA [auth H], JA [auth K], KA [auth L], M [auth A], Y [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth H] Focus chain JA [auth K] Focus chain KA [auth L] Focus chain M [auth A] Focus chain Y [auth F] Interactions & Density Focus chain BA [auth H] Focus chain JA [auth K] Focus chain KA [auth L] Focus chain M [auth A] Focus chain Y [auth F]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain W [auth E] SDF format, chain Q [auth B] SDF format, chain FA [auth J] SDF format, chain CA [auth H] MOL2 format, chain Z [auth F] MOL2 format, chain W [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain FA [auth J] MOL2 format, chain CA [auth H] mmCIF format, chain Z [auth F] mmCIF format, chain W [auth E] mmCIF format, chain Q [auth B] mmCIF format, chain FA [auth J] mmCIF format, chain CA [auth H]	CA [auth H], FA [auth J], Q [auth B], W [auth E], Z [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth H] Focus chain FA [auth J] Focus chain Q [auth B] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain CA [auth H] Focus chain FA [auth J] Focus chain Q [auth B] Focus chain W [auth E] Focus chain Z [auth F]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain N [auth A] SDF format, chain HA [auth J] SDF format, chain GA [auth J] MOL2 format, chain T [auth C] MOL2 format, chain N [auth A] MOL2 format, chain HA [auth J] MOL2 format, chain GA [auth J] mmCIF format, chain T [auth C] mmCIF format, chain N [auth A] mmCIF format, chain HA [auth J] mmCIF format, chain GA [auth J]	GA [auth J], HA [auth J], N [auth A], T [auth C]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain GA [auth J] Focus chain HA [auth J] Focus chain N [auth A] Focus chain T [auth C] Interactions & Density Focus chain GA [auth J] Focus chain HA [auth J] Focus chain N [auth A] Focus chain T [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.265 (Depositor), 0.256 (DCC)
R-Value Work: 0.199 (Depositor), 0.191 (DCC)
R-Value Observed: 0.202 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.472	α = 97.07
b = 81.228	β = 95.32
c = 139.406	γ = 94.72

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
MOLREP	phasing
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-05-12

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2009-05-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description