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- PDB-1xca: APO-CELLULAR RETINOIC ACID BINDING PROTEIN II -

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Basic information

Entry
Database: PDB / ID: 1xca
TitleAPO-CELLULAR RETINOIC ACID BINDING PROTEIN II
ComponentsCELLULAR RETINOIC ACID BINDING PROTEIN TYPE II
KeywordsRETINOIC ACID TRANSPORT / CRABPII / RETINOIC ACID / LIGAND ENTRY / VITAMIN A
Function / homology
Function and homology information


positive regulation of collateral sprouting / retinoid binding / retinoic acid binding / retinal binding / embryonic forelimb morphogenesis / retinoic acid metabolic process / retinol binding / Signaling by Retinoic Acid / epidermis development / fatty acid transport ...positive regulation of collateral sprouting / retinoid binding / retinoic acid binding / retinal binding / embryonic forelimb morphogenesis / retinoic acid metabolic process / retinol binding / Signaling by Retinoic Acid / epidermis development / fatty acid transport / cyclin binding / fatty acid binding / regulation of DNA-templated transcription / endoplasmic reticulum / signal transduction / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Cellular retinoic acid-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChen, X. / Ji, X.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Crystal structure of apo-cellular retinoic acid-binding protein type II (R111M) suggests a mechanism of ligand entry.
Authors: Chen, X. / Tordova, M. / Gilliland, G.L. / Wang, L. / Li, Y. / Yan, H. / Ji, X.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Crystal Structure of Cellular Retinoic Acid Binding Protein I Shows Increased Access to the Binding Cavity due to Formation of an Intermolecular Beta-Sheet
Authors: Thompson, J.R. / Bratt, J.M. / Banaszak, L.J.
#2: Journal: Structure / Year: 1994
Title: Crystal Structures of Cellular Retinoic Acid Binding Proteins I and II in Complex with All-Trans-Retinoic Acid and a Synthetic Retinoid
Authors: Kleywegt, G.J. / Bergfors, T. / Senn, H. / Le Motte, P. / Gsell, B. / Shudo, K. / Jones, T.A.
History
DepositionDec 31, 1996Processing site: BNL
Revision 1.0Jul 1, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 11, 2019Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_distant_solvent_atoms ...pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_database_status.process_site
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.6Aug 30, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CELLULAR RETINOIC ACID BINDING PROTEIN TYPE II
B: CELLULAR RETINOIC ACID BINDING PROTEIN TYPE II


Theoretical massNumber of molelcules
Total (without water)31,1122
Polymers31,1122
Non-polymers00
Water5,170287
1
A: CELLULAR RETINOIC ACID BINDING PROTEIN TYPE II


Theoretical massNumber of molelcules
Total (without water)15,5561
Polymers15,5561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CELLULAR RETINOIC ACID BINDING PROTEIN TYPE II


Theoretical massNumber of molelcules
Total (without water)15,5561
Polymers15,5561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.580, 62.270, 35.120
Angle α, β, γ (deg.)106.41, 90.69, 110.64
Int Tables number1
Space group name H-MP1

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Components

#1: Protein CELLULAR RETINOIC ACID BINDING PROTEIN TYPE II


Mass: 15555.804 Da / Num. of mol.: 2 / Mutation: R111M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Cellular location: CYTOPLASM / Plasmid: BL21 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P29373
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 48.6 %
Crystal growpH: 8
Details: PROTEIN CONC, 30MG/ML BUFFER 0.1M TRIS, PH 8.0 SALT 0.2M SODIUM ACETATE PRECIPITANT 30% PEG 8000
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
2100 mMTris-HCl1drop
3100 mMsodium acetate1drop
415 %PEG80001drop
5100 mMTris-HCl1reservoir
6200 mMsodium acetate1reservoir
730 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Apr 15, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 13213 / % possible obs: 81.9 % / Observed criterion σ(I): 0 / Redundancy: 2.75 % / Biso Wilson estimate: 57.5 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.059 / Net I/σ(I): 10.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.64 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.279 / % possible all: 55.9
Reflection
*PLUS
Num. measured all: 32588

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
XENGENdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CBS WITH LIGAND AND SOLVENT MOLECULES REMOVED

1cbs


Resolution: 2.3→8 Å / Rfactor Rfree error: 0.0086 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: UNRESTRAINED / Cross valid method: THROUGHOUT UNTIL LAST FEW CYCLES / σ(F): 2
Details: RESIDUES 24 - 37 OF CHAIN A WERE NOT OBSERVED AND NOT INCLUDED IN THE REFINEMENT; RESTRAINTS BETWEEN THE TWO COPIES OF MOLECULES WERE APPLIED DURING THE INITIAL STAGE OF THE REFINEMENT THE ...Details: RESIDUES 24 - 37 OF CHAIN A WERE NOT OBSERVED AND NOT INCLUDED IN THE REFINEMENT; RESTRAINTS BETWEEN THE TWO COPIES OF MOLECULES WERE APPLIED DURING THE INITIAL STAGE OF THE REFINEMENT THE DISORDERED REGION (RESIDUES 24 - 37 OF CHAIN A) WAS MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1084 10 %RANDOM
Rwork0.18 ---
obs0.18 10509 85.4 %-
Displacement parametersBiso mean: 37.6 Å2
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2176 0 0 287 2463
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.24
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.06
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.391 99 6.42 %
Rwork0.336 799 -
obs--58.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.H2OTOPOL.H2O
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.18 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.06

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