2ZHI | pdb_00002zhi

Crystal Structure Analysis of the Sodium-Bound Annexin A4 at 1.58 A resolution

PDB DOI: https://doi.org/10.2210/pdb2ZHI/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Rattus norvegicus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-02-06 Released: 2009-02-10
Deposition Author(s): Butsushita, K., Ida, K., Fukuoka, S.-I., Arii, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free:
0.228 (Depositor), 0.960 (DCC)
R-Value Work:
0.185 (Depositor), 0.183 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Structural Analysis for the Sodium-Dependent Dissociation of Annexin A4: Crystal Structures of Soduim-Bound Annexin A4 at High Resolutions

Butsushita, K., Inoue, K., Ida, K., Fukuoka, S.-I., Arii, Y.

To be published.

Macromolecule Content

Total Structure Weight: 36.33 kDa
Atom Count: 2,864
Modeled Residue Count: 315
Deposited Residue Count: 322
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Annexin A4	A	322	Rattus norvegicus	Mutation(s): 0 Gene Names: Anxa4
UniProt
Find proteins for P55260 (Rattus norvegicus) Explore P55260 Go to UniProtKB: P55260
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P55260
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free: 0.228 (Depositor), 0.960 (DCC)
R-Value Work: 0.185 (Depositor), 0.183 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.287	α = 90
b = 40.244	β = 97.94
c = 65.447	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-02-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-02-10
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.