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- PDB-4qzt: Crystal Structure of wild type Human Cellular Retinol Binding Pro... -

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Basic information

Entry
Database: PDB / ID: 4qzt
TitleCrystal Structure of wild type Human Cellular Retinol Binding Protein II (hCRBPII) bound to retinol at 7 KeV beam energy
ComponentsRetinol-binding protein 2
KeywordsPROTEIN BINDING / Retinol / Human Cellular Retinol Binding Protein II / intracellular lipid binding protein / X-ray flux / X-ray damage / Retinal / Retinoid Chaperones
Function / homology
Function and homology information


vitamin A metabolic process / retinoid binding / retinal binding / retinol binding / epidermis development / fatty acid transport / Retinoid metabolism and transport / fatty acid binding / nucleus / cytosol
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
ACETATE ION / RETINOL / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAssar, Z. / Geiger, J.H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structures of holo wild-type human cellular retinol-binding protein II (hCRBPII) bound to retinol and retinal.
Authors: Nossoni, Z. / Assar, Z. / Yapici, I. / Nosrati, M. / Wang, W. / Berbasova, T. / Vasileiou, C. / Borhan, B. / Geiger, J.
History
DepositionJul 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Dec 31, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retinol-binding protein 2
C: Retinol-binding protein 2
B: Retinol-binding protein 2
D: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1409
Polymers62,3904
Non-polymers7505
Water5,260292
1
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9433
Polymers15,5971
Non-polymers3452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9433
Polymers15,5971
Non-polymers3452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6562
Polymers15,5971
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Retinol-binding protein 2


Theoretical massNumber of molelcules
Total (without water)15,5971
Polymers15,5971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.406, 54.179, 68.444
Angle α, β, γ (deg.)107.72, 97.19, 103.59
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Retinol-binding protein 2 / Cellular retinol-binding protein II / CRBP-II


Mass: 15597.452 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2 / Plasmid: Pet17b / Production host: Escherichia coli (E. coli) / References: UniProt: P50120
#2: Chemical ChemComp-RTL / RETINOL


Mass: 286.452 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H30O
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 1.96 Å3/Da / Density % sol: 37.17 %
Crystal growTemperature: 298 K / pH: 4.5
Details: 25% PEG 4000 (40%), 0.1M Sodium Acetate pH 4.5, Ammonium Acetate 0.1M, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.89→29.79 Å / Num. obs: 76284 / % possible obs: 92.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.95
Reflection shellResolution: 1.89→1.94 Å / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 6.23 / % possible all: 86

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RCT

2rct


Resolution: 1.9→29.79 Å / SU ML: 0.24 / σ(F): 2.03 / Phase error: 27.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 2000 5.77 %
Rwork0.18 --
obs0.183 34646 92.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4380 0 54 292 4726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084550
X-RAY DIFFRACTIONf_angle_d1.0796129
X-RAY DIFFRACTIONf_dihedral_angle_d17.3071712
X-RAY DIFFRACTIONf_chiral_restr0.043650
X-RAY DIFFRACTIONf_plane_restr0.004797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8962-1.94360.32821270.2232190X-RAY DIFFRACTION86
1.9436-1.99620.24571420.20112244X-RAY DIFFRACTION89
1.9962-2.05490.27541370.18952252X-RAY DIFFRACTION90
2.0549-2.12120.2751370.19622285X-RAY DIFFRACTION90
2.1212-2.1970.27931360.19182283X-RAY DIFFRACTION91
2.197-2.28490.2841500.19182323X-RAY DIFFRACTION91
2.2849-2.38890.28961370.19822300X-RAY DIFFRACTION92
2.3889-2.51470.27381490.20772358X-RAY DIFFRACTION93
2.5147-2.67220.29311410.20572363X-RAY DIFFRACTION94
2.6722-2.87840.29451460.20622386X-RAY DIFFRACTION94
2.8784-3.16770.26781470.19792394X-RAY DIFFRACTION95
3.1677-3.62540.211540.16022449X-RAY DIFFRACTION96
3.6254-4.5650.18331500.14232427X-RAY DIFFRACTION97
4.565-29.79160.23291470.17462392X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 21.6411 Å / Origin y: 5.0451 Å / Origin z: 22.763 Å
111213212223313233
T0.1162 Å20.001 Å20.0086 Å2-0.1598 Å2-0.0033 Å2--0.1546 Å2
L-0.0876 °2-0.0223 °20.1039 °2-0.1935 °2-0.0221 °2--0.2935 °2
S-0.0139 Å °0.0315 Å °-0.0112 Å °0.0163 Å °0.0423 Å °-0.029 Å °-0.0129 Å °0.0237 Å °-0 Å °
Refinement TLS groupSelection details: all

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