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- PDB-4zh6: Crystal Structure of the Domain-Swapped Dimer Y60L mutant of Huma... -

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Basic information

Entry
Database: PDB / ID: 4zh6
TitleCrystal Structure of the Domain-Swapped Dimer Y60L mutant of Human Cellular Retinol Binding Protein II
ComponentsRetinol-binding protein 2
KeywordsTRANSPORT PROTEIN / Domain-Swapped Dimer / Domain Swapping / Human Cellular Retinol Binding Protein II / Intracellular Lipid Binding Protein
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-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5497 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6663
Polymers15,5471
Non-polymers1182
Water2,738152
1
A: Retinol-binding protein 2
hetero molecules

A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3316
Polymers31,0952
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area8390 Å2
ΔGint-38 kcal/mol
Surface area13930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.776, 60.424, 63.603
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
DetailsDimer confirmed by gel filtration

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Components

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


Mass: 15547.437 Da / Num. of mol.: 1 / Mutation: Y60L
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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.27 Å3/Da / Density % sol: 45.88 %
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: 1.5497→50 Å / Num. obs: 21293 / % possible obs: 99.81 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 82.03
Reflection shellResolution: 1.5497→1.588 Å / Rmerge(I) obs: 0.695 / % 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: 1.5497→31.837 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 23.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2244 1990 9.38 %
Rwork0.1866 --
obs0.1902 21209 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5497→31.837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1091 0 8 152 1251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061115
X-RAY DIFFRACTIONf_angle_d0.9591498
X-RAY DIFFRACTIONf_dihedral_angle_d14.454413
X-RAY DIFFRACTIONf_chiral_restr0.041162
X-RAY DIFFRACTIONf_plane_restr0.004194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5497-1.58840.29121420.23541363X-RAY DIFFRACTION100
1.5884-1.63140.26041440.23351329X-RAY DIFFRACTION100
1.6314-1.67940.25521300.22261367X-RAY DIFFRACTION100
1.6794-1.73360.27331470.21691340X-RAY DIFFRACTION100
1.7336-1.79550.22251400.2121355X-RAY DIFFRACTION100
1.7955-1.86740.26461370.22051372X-RAY DIFFRACTION100
1.8674-1.95240.24681360.20291341X-RAY DIFFRACTION100
1.9524-2.05530.22191400.20161367X-RAY DIFFRACTION100
2.0553-2.18410.25221520.19811353X-RAY DIFFRACTION100
2.1841-2.35260.26221350.20221387X-RAY DIFFRACTION100
2.3526-2.58930.24751400.20451376X-RAY DIFFRACTION100
2.5893-2.96380.23891460.19411392X-RAY DIFFRACTION100
2.9638-3.73310.19591460.16891420X-RAY DIFFRACTION100
3.7331-31.84380.20361550.16771457X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 2.6871 Å / Origin y: 36.2798 Å / Origin z: -3.1689 Å
111213212223313233
T0.199 Å20.0059 Å2-0.0074 Å2-0.2959 Å20.0009 Å2--0.2291 Å2
L-0.3426 °20.0834 °20.0004 °2-2.7691 °2-0.1823 °2--0.5558 °2
S-0.025 Å °-0.0061 Å °-0.0228 Å °-0.0591 Å °-0.0262 Å °-0.0062 Å °-0.0766 Å °-0.024 Å °0.0476 Å °
Refinement TLS groupSelection details: all

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