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- PDB-4zh9: Crystal Structure of the Domain-Swapped Dimer Wild-Type of Human ... -

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Basic information

Entry
Database: PDB / ID: 4zh9
TitleCrystal Structure of the Domain-Swapped Dimer Wild-Type of Human Cellular Retinol Binding Protein II
ComponentsRetinol-binding protein 2
KeywordsTRANSPORT PROTEIN / Domain Swapped Dimer / Domain Swapping / Protein folding / Human Cellular Retinol Binding Protein II / Intra Cellular Retinol Binding Protein II
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 / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsAssar, Z. / Nossoni, Z. / Geiger, J.H.
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. / Yapici, I. / Nosrati, M. / Wang, W. / Berbasova, T. / Vasileiou, C. / Borhan, B. / Geiger, J.
#2: Journal: Science / Year: 2012
Title: Tuning the electronic absorption of protein-embedded all-trans-retinal.
Authors: Wang, W. / Nossoni, Z. / Berbasova, T. / Watson, C.T. / Yapici, I. / Lee, K.S. / Vasileiou, C. / Geiger, J.H. / Borhan, B.
History
DepositionApr 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_audit_support / pdbx_struct_oper_list
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 1.2Nov 1, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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


Theoretical massNumber of molelcules
Total (without water)15,5971
Polymers15,5971
Non-polymers00
Water61334
1
A: Retinol-binding protein 2

A: Retinol-binding protein 2


Theoretical massNumber of molelcules
Total (without water)31,1952
Polymers31,1952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area7140 Å2
ΔGint-36 kcal/mol
Surface area13850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.851, 60.544, 64.021
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-227-

HOH

21A-228-

HOH

DetailsDimer confirmed by gel filtration

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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.: 1
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 25% PEG 4000 (40%), 0.1M Sodium Acetate pH 4.5, Ammonium Acetate 0.1M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.66→50 Å / Num. obs: 4455 / % possible obs: 99.7 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 2.41
Reflection shellResolution: 2.66→3.04 Å / Rmerge(I) obs: 0.731 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data collection
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RCT

2rct


Resolution: 2.66→43.989 Å / SU ML: 0.29 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 25.06 / Stereochemistry target values: LS_WUNIT_K1
RfactorNum. reflection% reflection
Rfree0.2736 450 10.19 %
Rwork0.2 --
obs0.2075 4417 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.66→43.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1075 0 0 34 1109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021095
X-RAY DIFFRACTIONf_angle_d0.4721477
X-RAY DIFFRACTIONf_dihedral_angle_d11.281396
X-RAY DIFFRACTIONf_chiral_restr0.016161
X-RAY DIFFRACTIONf_plane_restr0.002192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6597-3.04450.34241440.29611288X-RAY DIFFRACTION100
3.0445-3.83530.26811490.19941310X-RAY DIFFRACTION100
3.8353-43.9890.25121570.16721369X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 2.7298 Å / Origin y: 36.4241 Å / Origin z: -2.9222 Å
111213212223313233
T0.2493 Å2-0.0035 Å2-0.0253 Å2-0.4037 Å20.0004 Å2--0.2147 Å2
L-0.2588 °2-0.2521 °2-0.1678 °2-2.9345 °2-0.4903 °2--0.0975 °2
S0.0335 Å °0.023 Å °-0.0111 Å °-0.0163 Å °-0.1083 Å °0.0432 Å °0.0013 Å °0.0417 Å °0.0827 Å °
Refinement TLS groupSelection details: all

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