6VH5 | pdb_00006vh5

Crystal structure of prephenate dehydratase from brucella melitensis biovar abortus 2308 in complex with phenylalanine

PDB DOI: https://doi.org/10.2210/pdb6VH5/pdb

Classification: HYDROLASE
Organism(s): Brucella abortus 2308
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2020-01-09 Released: 2020-01-29
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.251 (Depositor), 0.252 (DCC)
R-Value Work:
0.207 (Depositor), 0.208 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Models: 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 prephenate dehydratase from Brucella melitensis biovar abortus 2308 in complex with phenylalanine

Abendroth, J., Dranow, D.M., Lorimer, D.D., Bullen, J.C., Sankaran, B., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 137.56 kDa
Atom Count: 8,683
Modeled Residue Count: 1,122
Deposited Residue Count: 1,232
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prephenate dehydratase:Amino acid-binding ACT	A, B, C, D	308	Brucella abortus 2308	Mutation(s): 0 Gene Names: pheA, BAB1_0034 EC: 4.2.1.51
UniProt
Find proteins for Q2YPM5 (Brucella abortus (strain 2308)) Explore Q2YPM5 Go to UniProtKB: Q2YPM5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2YPM5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PHE Query on PHE Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	E [auth A], G [auth B], J [auth C], L [auth D]	PHENYLALANINE C₉ H₁₁ N O₂ COLNVLDHVKWLRT-QMMMGPOBSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain N [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D]	F [auth A] H [auth B] I [auth B] K [auth C] M [auth D] F [auth A], H [auth B], I [auth B], K [auth C], M [auth D], N [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.251 (Depositor), 0.252 (DCC)
R-Value Work: 0.207 (Depositor), 0.208 (DCC)
R-Value Observed: 0.208 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 226.95	α = 90
b = 61.25	β = 112.95
c = 120.05	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
MR-Rosetta	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-01-29

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2020-01-29
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-04-03
Changes: Refinement description

6VH5 | pdb_00006vh5

Crystal structure of prephenate dehydratase from brucella melitensis biovar abortus 2308 in complex with phenylalanine

Literature

Crystal structure of prephenate dehydratase from Brucella melitensis biovar abortus 2308 in complex with phenylalanine

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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