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- PDB-4zgu: Crystal structure of monomer Y60W hCRBPII -

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Basic information

Entry
Database: PDB / ID: 4zgu
TitleCrystal structure of monomer Y60W hCRBPII
ComponentsRetinol-binding protein 2
KeywordsTRANSPORT PROTEIN / 3D domain Swapping human CRBPII protein dimerization
Function / homology
Function and homology information


vitamin A metabolic process / retinoid binding / retinal binding / retinol binding / epidermis development / Retinoid metabolism and transport / fatty acid transport / fatty acid binding / nucleus / cytosol
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Lipocalin/cytosolic fatty-acid binding domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.49 Å
AuthorsNossoni, Z. / Geiger, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM101353 United States
Citation
Journal: Structure / Year: 2016
Title: Domain-Swapped Dimers of Intracellular Lipid-Binding Proteins: Evidence for Ordered Folding Intermediates.
Authors: Assar, Z. / Nossoni, Z. / Wang, W. / Santos, E.M. / Kramer, K. / McCornack, C. / Vasileiou, C. / Borhan, B. / Geiger, J.H.
#1: Journal: 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. / Nosrati, M. / Yapici, I. / Vasileiou, C. / Borhan, B. / Geiger, J.
History
DepositionApr 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,95412
Polymers62,4824
Non-polymers4728
Water7,044391
1
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7393
Polymers15,6201
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7984
Polymers15,6201
Non-polymers1773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7393
Polymers15,6201
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6802
Polymers15,6201
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.596, 54.335, 68.588
Angle α, β, γ (deg.)108.13, 97.03, 104.09
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: 15620.487 Da / Num. of mol.: 4 / Mutation: Y60W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2 / Plasmid: pET17 / Production host: Escherichia coli (E. coli) / References: UniProt: P50120
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.4 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% PEG 4000, 0.1M CH3COONa.3H2O pH4.6, 0.1M CH3COONH4
PH range: 4.2-4.6

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0781 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 77520 / % possible obs: 98.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 47.91
Reflection shellResolution: 1.49→1.51 Å / Rmerge(I) obs: 0.408 / % possible all: 89.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
DENZOdata reduction
HKL-2000data scaling
REFMACphasing
RefinementResolution: 1.49→30.01 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.859 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24558 3749 5.1 %RANDOM
Rwork0.19834 ---
obs0.20076 70382 95.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.618 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.49→30.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4314 0 32 391 4737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0224445
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3231.9196000
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9685536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14725.021239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5115786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.31528
X-RAY DIFFRACTIONr_chiral_restr0.1690.2646
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023416
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6911.52666
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.64724272
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.77531779
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.7844.51728
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.49→1.529 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 234 -
Rwork0.315 4814 -
obs--88.17 %

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