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- PDB-2rcq: Crystal structure of human apo Cellular Retinol Binding Protein I... -

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Basic information

Entry
Database: PDB / ID: 2rcq
TitleCrystal structure of human apo Cellular Retinol Binding Protein II (CRBP-II)
ComponentsRetinol-binding protein II, cellular
KeywordsRETINOL-BINDING PROTEIN / cellular retinol binding protein II / CRBP-II / retinol / lipid-binding protein / Retinol-binding / Transport / Vitamin A
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
L(+)-TARTARIC ACID / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.2 Å
AuthorsMonaco, H.L. / Capaldi, S. / Perduca, M.
CitationJournal: Proteins / Year: 2007
Title: Crystal structure of human cellular retinol-binding protein II to 1.2 A resolution.
Authors: Tarter, M. / Capaldi, S. / Carrizo, M.E. / Ambrosi, E. / Perduca, M. / Monaco, H.L.
History
DepositionSep 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 14, 2016Group: Structure summary
Revision 1.3Aug 30, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Retinol-binding protein II, cellular
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8394
Polymers16,4971
Non-polymers3423
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.518, 49.834, 74.398
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Retinol-binding protein II, cellular / CRBP-II


Mass: 16496.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2 / Plasmid: pQE50 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: P50120
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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 Å3/Da / Density % sol: 38.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium citrate, 0.2 M sodium/potassium tartrate, 1.4 M ammonium sulphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 12, 2006
Details: DOUBLE CRYSTAL (SI111, SI220) THREE-SEGMENT PT-COATED TOROIDAL MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→27 Å / Num. obs: 40046 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 18.9
Reflection shellResolution: 1.2→1.23 Å / Redundancy: 4 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 8 / Num. unique all: 5747 / Rsym value: 0.187 / % possible all: 95.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementStarting model: PDB ENTRY 1OPA

1opa


Resolution: 1.2→25 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.932 / SU B: 0.569 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 2028 5.1 %RANDOM
Rwork0.196 ---
all0.197 37993 --
obs0.197 40021 95.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.582 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2---0.12 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1158 0 20 156 1334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221211
X-RAY DIFFRACTIONr_angle_refined_deg1.0441.951633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6835142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.98324.53164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6915225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.854159
X-RAY DIFFRACTIONr_chiral_restr0.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02916
X-RAY DIFFRACTIONr_nbd_refined0.1920.2493
X-RAY DIFFRACTIONr_nbtor_refined0.3090.2814
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0770.2127
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0950.212
X-RAY DIFFRACTIONr_mcbond_it1.1763721
X-RAY DIFFRACTIONr_mcangle_it1.69731140
X-RAY DIFFRACTIONr_scbond_it1.2382558
X-RAY DIFFRACTIONr_scangle_it1.8753493
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.193 147 -
Rwork0.191 2754 -
all-2901 -
obs--94.68 %

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