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- PDB-5dpq: Crystal Structure of E72A mutant of domain swapped dimer Human Ce... -

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Basic information

Entry
Database: PDB / ID: 5dpq
TitleCrystal Structure of E72A mutant of domain swapped dimer Human Cellular Retinol Binding Protein
ComponentsRetinol-binding protein 2
KeywordsRetinol Binding Protein / domain swapped dimer / iLBP
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 protein family / Lipocalin/cytosolic fatty-acid binding 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: 1.775 Å
AuthorsAssar, Z. / Nossoni, Z. / Wang, W. / Geiger, J.H. / Borhan, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM101353 United States
CitationJournal: 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.
History
DepositionSep 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 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 / _citation_author.name / _pdbx_audit_support.funding_organization / _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: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3156
Polymers31,0792
Non-polymers2364
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-39 kcal/mol
Surface area13660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.238, 72.901, 60.487
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 2 / Cellular retinol-binding protein II / CRBP-II


Mass: 15539.415 Da / Num. of mol.: 2 / Mutation: E72A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: DH5a / Gene: RBP2, CRBP2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P50120
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.21 Å3/Da / Density % sol: 44.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 30% PEG 4000, 0.1 M sodium acetate, 0.1 M ammonium acetate, pH 4.6, EVAPORATION, temperature 298K
PH range: 4.0-4.8

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 27242 / % possible obs: 100 % / Redundancy: 1.19 % / Rmerge(I) obs: 0.05 / Net I/av σ(I): 1.9 / Net I/σ(I): 75.13
Reflection shellResolution: 1.77→1.8 Å / Mean I/σ(I) obs: 2.76 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data scaling
MOLREPphasing
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.775→31.453 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 21.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2198 1994 7.34 %
Rwork0.1745 --
obs0.1778 27152 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.775→31.453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 16 285 2483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062240
X-RAY DIFFRACTIONf_angle_d1.0123013
X-RAY DIFFRACTIONf_dihedral_angle_d14.661825
X-RAY DIFFRACTIONf_chiral_restr0.04324
X-RAY DIFFRACTIONf_plane_restr0.004390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7751-1.81950.25571300.20671719X-RAY DIFFRACTION98
1.8195-1.86870.24211430.19381757X-RAY DIFFRACTION100
1.8687-1.92370.22831420.19241779X-RAY DIFFRACTION100
1.9237-1.98580.24271320.18731776X-RAY DIFFRACTION100
1.9858-2.05680.24081450.17681781X-RAY DIFFRACTION100
2.0568-2.13910.25031390.18231797X-RAY DIFFRACTION100
2.1391-2.23640.23371470.17571778X-RAY DIFFRACTION100
2.2364-2.35430.23421410.18051781X-RAY DIFFRACTION100
2.3543-2.50170.25581400.18651794X-RAY DIFFRACTION100
2.5017-2.69480.24131490.19251801X-RAY DIFFRACTION100
2.6948-2.96580.21661420.17791804X-RAY DIFFRACTION100
2.9658-3.39450.22551440.16761817X-RAY DIFFRACTION100
3.3945-4.2750.16591480.14511851X-RAY DIFFRACTION100
4.275-31.45820.2271520.18311923X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 61.8451 Å / Origin y: 3.2379 Å / Origin z: 16.002 Å
111213212223313233
T0.1675 Å20.0003 Å2-0.01 Å2-0.206 Å20.0051 Å2--0.2805 Å2
L0.1332 °2-0.0236 °2-0.3311 °2-0.0418 °20.1311 °2--1.8591 °2
S0.0164 Å °-0.0005 Å °-0.0787 Å °-0.0096 Å °-0.0063 Å °-0.009 Å °0.012 Å °0.0201 Å °-0.0187 Å °
Refinement TLS groupSelection details: all

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