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

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Basic information

Entry
Database: PDB / ID: 4qzu
TitleCrystal Structure of wild type Human Cellular Retinol Binding Protein II (hCRBPII) bound to retinol at 11 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 / molecular carrier activity / 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: 1.5 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)63,69614
Polymers62,3904
Non-polymers1,30610
Water7,116395
1
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0354
Polymers15,5971
Non-polymers4383
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)16,0024
Polymers15,5971
Non-polymers4053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7163
Polymers15,5971
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.476, 54.139, 68.298
Angle α, β, γ (deg.)107.64, 96.94, 103.71
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.: 3 / Source method: obtained synthetically / Formula: C20H30O
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 1.496→34.66 Å / Num. obs: 76284 / % possible obs: 95.2 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 26.45
Reflection shellResolution: 1.5→1.51 Å / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 2.41 / % possible all: 88

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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: 1.5→34.66 Å / SU ML: 0.18 / σ(F): 1.97 / Phase error: 23.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.218 3675 5.05 %
Rwork0.162 --
obs0.165 72755 95.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→34.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4379 0 93 395 4867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074553
X-RAY DIFFRACTIONf_angle_d1.0666118
X-RAY DIFFRACTIONf_dihedral_angle_d15.5731712
X-RAY DIFFRACTIONf_chiral_restr0.043645
X-RAY DIFFRACTIONf_plane_restr0.004793
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.496-1.51560.29441180.21512491X-RAY DIFFRACTION88
1.5156-1.53640.28921220.19782590X-RAY DIFFRACTION92
1.5364-1.55830.29211390.18172586X-RAY DIFFRACTION93
1.5583-1.58160.27851400.17412600X-RAY DIFFRACTION93
1.5816-1.60630.26141460.16722591X-RAY DIFFRACTION94
1.6063-1.63270.2591460.17912601X-RAY DIFFRACTION93
1.6327-1.66080.28121370.17642636X-RAY DIFFRACTION94
1.6608-1.6910.27851470.17372565X-RAY DIFFRACTION94
1.691-1.72350.2761150.16772664X-RAY DIFFRACTION94
1.7235-1.75870.25251260.15342677X-RAY DIFFRACTION94
1.7587-1.7970.23111540.14982663X-RAY DIFFRACTION95
1.797-1.83880.23211300.14952612X-RAY DIFFRACTION95
1.8388-1.88470.25971420.15662649X-RAY DIFFRACTION95
1.8847-1.93570.23091450.15832682X-RAY DIFFRACTION95
1.9357-1.99260.21561290.15882667X-RAY DIFFRACTION96
1.9926-2.05690.22141550.15562662X-RAY DIFFRACTION96
2.0569-2.13050.23071550.16062675X-RAY DIFFRACTION96
2.1305-2.21570.23761390.16172683X-RAY DIFFRACTION96
2.2157-2.31660.24931480.16722684X-RAY DIFFRACTION97
2.3166-2.43870.22071540.17172720X-RAY DIFFRACTION97
2.4387-2.59140.20681500.17482706X-RAY DIFFRACTION97
2.5914-2.79140.22161540.17282711X-RAY DIFFRACTION98
2.7914-3.07220.22351180.17542747X-RAY DIFFRACTION98
3.0722-3.51640.18671310.15672744X-RAY DIFFRACTION98
3.5164-4.42880.17611810.13842735X-RAY DIFFRACTION99
4.4288-34.66990.19781540.15552739X-RAY DIFFRACTION98

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