4ERR | pdb_00004err

1.55 Angstrom Crystal Structure of the Four Helical Bundle Membrane Localization Domain (4HBM) of the Vibrio vulnificus MARTX Effector Domain DUF5

PDB DOI: https://doi.org/10.2210/pdb4ERR/pdb

Classification: PROTEIN BINDING
Organism(s): Vibrio vulnificus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-04-20 Released: 2012-05-02
Deposition Author(s): Minasov, G., Wawrzak, Z., Geissler, B., Shuvalova, L., Dubrovska, I., Winsor, J., Satchell, K.J., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.215 (Depositor), 0.210 (DCC)
R-Value Work:
0.167 (Depositor), 0.171 (DCC)
R-Value Observed:
0.170 (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

1.55 Angstrom Crystal Structure of the Four Helical Bundle Membrane Localization Domain (4HBM) of the Vibrio vulnificus MARTX Effector Domain DUF5.

Minasov, G., Wawrzak, Z., Geissler, B., Shuvalova, L., Dubrovska, I., Winsor, J., Satchell, K.J., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 20.53 kDa
Atom Count: 1,763
Modeled Residue Count: 165
Deposited Residue Count: 180
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Autotransporter adhesin	A, B	90	Vibrio vulnificus	Mutation(s): 0 Gene Names: VV2_0479

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BR Query on BR Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.215 (Depositor), 0.210 (DCC)
R-Value Work: 0.167 (Depositor), 0.171 (DCC)
R-Value Observed: 0.170 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.896	α = 90
b = 49.874	β = 90
c = 72.102	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-05-02

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2012-05-02
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description