4I6K | pdb_00004i6k

Crystal structure of probable 2-PYRONE-4,6-DICARBOXYLIC ACID HYDROLASE ABAYE1769 (TARGET EFI-505029) from Acinetobacter baumannii with citric acid bound

PDB DOI: https://doi.org/10.2210/pdb4I6K/pdb

Classification: HYDROLASE
Organism(s): Acinetobacter baumannii AB0057
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-11-29 Released: 2012-12-12
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Al Obaidi, N.F., Stead, M., Love, J., Gerlt, J.A., Raushel, F.M., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free:
0.280 (Depositor), 0.281 (DCC)
R-Value Work:
0.213 (Depositor), 0.202 (DCC)
R-Value Observed:
0.215 (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 PROBABLE 2-PYRONE-4,6-DICARBOXYLIC ACID HYDROLASE (TARGET EFI-505029) FROM Acinetobacter baumannii

Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Al Obaidi, N.F., Stead, M., Love, J., Gerlt, J.A., Raushel, F.M., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 34.07 kDa
Atom Count: 2,253
Modeled Residue Count: 267
Deposited Residue Count: 294
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amidohydrolase family protein	A	294	Acinetobacter baumannii AB0057	Mutation(s): 0 Gene Names: AB57_2135
UniProt
Find proteins for A0A7U3Y778 (Acinetobacter baumannii (strain AB0057)) Explore A0A7U3Y778 Go to UniProtKB: A0A7U3Y778
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A7U3Y778
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.280 (Depositor), 0.281 (DCC)
R-Value Work: 0.213 (Depositor), 0.202 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.168	α = 90
b = 75.168	β = 90
c = 88.966	γ = 120

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-12-12

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2012-12-12
Type: Initial release
Version 1.1: 2018-01-24
Changes: Structure summary
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description