4QVT | pdb_00004qvt

Crystal structure of predicted N-acyltransferase (ypeA) in complex with acetyl-CoA from Escherichia coli

PDB DOI: https://doi.org/10.2210/pdb4QVT/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2014-07-15 Released: 2014-07-30
Deposition Author(s): Filippova, E.V., Minasov, G., Winsor, G., Dubrovska, I., Shuvalova, L., Wolfe, A.J., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.232 (Depositor), 0.232 (DCC)
R-Value Work:
0.188 (Depositor), 0.197 (DCC)
R-Value Observed:
0.190 (Depositor)

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

Crystal structure of predicted N-acyltransferase (ypeA) in complex with acetyl-CoA from Escherichia coli

Filippova, E.V., Minasov, G., Winsor, G., Dubrovska, I., Shuvalova, L., Wolfe, A.J., Anderson, W.F.

To be published.

Macromolecule Content

Total Structure Weight: 153.83 kDa
Atom Count: 9,904
Modeled Residue Count: 1,130
Deposited Residue Count: 1,264
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyltransferase YpeA	A, B, C, D, E A, B, C, D, E, F, G, H	158	Escherichia coli K-12	Mutation(s): 0 Gene Names: b2434, JW2427, ypeA EC: 2.3.1
UniProt
Find proteins for P76539 (Escherichia coli (strain K12)) Explore P76539 Go to UniProtKB: P76539
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P76539
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACO Query on ACO Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain R [auth E] SDF format, chain V [auth F] SDF format, chain W [auth G] SDF format, chain Z [auth H] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain R [auth E] MOL2 format, chain V [auth F] MOL2 format, chain W [auth G] MOL2 format, chain Z [auth H] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain R [auth E] mmCIF format, chain V [auth F] mmCIF format, chain W [auth G] mmCIF format, chain Z [auth H]	I [auth A] L [auth B] N [auth C] P [auth D] R [auth E] I [auth A], L [auth B], N [auth C], P [auth D], R [auth E], V [auth F], W [auth G], Z [auth H]	*ACETYL COENZYME A** C₂₃ H₃₈ N₇ O₁₇ P₃ S ZSLZBFCDCINBPY-ZSJPKINUSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain Z [auth H] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain Z [auth H]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain S [auth E] SDF format, chain T [auth E] SDF format, chain U [auth E] SDF format, chain X [auth G] SDF format, chain Y [auth G] SDF format, chain Q [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth E] MOL2 format, chain T [auth E] MOL2 format, chain U [auth E] MOL2 format, chain X [auth G] MOL2 format, chain Y [auth G] MOL2 format, chain Q [auth D] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain S [auth E] mmCIF format, chain T [auth E] mmCIF format, chain U [auth E] mmCIF format, chain X [auth G] mmCIF format, chain Y [auth G] mmCIF format, chain Q [auth D]	J [auth A] K [auth A] M [auth B] O [auth C] Q [auth D] J [auth A], K [auth A], M [auth B], O [auth C], Q [auth D], S [auth E], T [auth E], U [auth E], X [auth G], Y [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth E] Focus chain X [auth G] Focus chain Y [auth G] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth E] Focus chain X [auth G] Focus chain Y [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.232 (Depositor), 0.232 (DCC)
R-Value Work: 0.188 (Depositor), 0.197 (DCC)
R-Value Observed: 0.190 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.334	α = 90
b = 139.968	β = 112.11
c = 75.358	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-07-30

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2014-07-30
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description