3D97 | pdb_00003d97

Crystal Structure of the R132K:R111L:L121E Mutant of Apo-Cellular Retinoic Acid Binding Protein Type II At 1.50 Angstroms Resolution

PDB DOI: https://doi.org/10.2210/pdb3D97/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2008-05-26 Released: 2008-07-22
Deposition Author(s): Vaezeslami, S., Geiger, J.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.227 (Depositor), 0.229 (DCC)
R-Value Work:
0.154 (Depositor), 0.157 (DCC)
R-Value Observed:
0.161 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3D97

This is version 1.5 of the entry. See complete history.

Literature

Determining Crystal Structures of Proteins and Protein Complexes by X-Ray Crystallography: X-Ray Crystallographic Studies of the Mutants of Cellular Retinoic Acid Binding Protein Type II Toward Designing a Mimic of Rhodopsin.

Vaezeslami, S., Jia, X., Vasileiou, C., Borhan, B., Geiger, J.H.

(null) Thesis

Macromolecule Content

Total Structure Weight: 31.38 kDa
Atom Count: 2,536
Modeled Residue Count: 274
Deposited Residue Count: 274
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellular retinoic acid-binding protein 2	A, B	137	Homo sapiens	Mutation(s): 3 Gene Names: CRABP2
UniProt & NIH Common Fund Data Resources
Find proteins for P29373 (Homo sapiens) Explore P29373 Go to UniProtKB: P29373
PHAROS: P29373 GTEx: ENSG00000143320
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29373
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B3P Query on B3P 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]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₁₁ H₂₆ N₂ O₆ HHKZCCWKTZRCCL-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain D [auth B] mmCIF format, chain E [auth B] mmCIF format, chain D [auth B]	D [auth B], E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain E [auth B] Interactions & Density Focus chain D [auth B] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.227 (Depositor), 0.229 (DCC)
R-Value Work: 0.154 (Depositor), 0.157 (DCC)
R-Value Observed: 0.161 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.553	α = 73.4
b = 37.22	β = 73.7
c = 61.058	γ = 89.73

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
AUTOMAR	data reduction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-07-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-07-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Advisory, Refinement description
Version 1.3: 2018-10-10
Changes: Data collection, Database references, Structure summary
Version 1.4: 2021-10-20
Changes: Advisory, Database references, Derived calculations, Structure summary
Version 1.5: 2023-08-30
Changes: Data collection, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.