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- PDB-5dg4: Crystal structure of monomer human cellular retinol binding prote... -

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Basic information

Entry
Database: PDB / ID: 5dg4
TitleCrystal structure of monomer human cellular retinol binding protein II-Y60L
ComponentsRetinol-binding protein 2
KeywordsTRANSPORT PROTEIN / DOMAIN SWAPPING
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 / 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 / Resolution: 1.5 Å
AuthorsAssar, Z. / Nossoni, Z. / Wang, W. / Gieger, 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
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. D Biol. Crystallogr. / 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.
History
DepositionAug 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 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_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
C: Retinol-binding protein 2
D: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3677
Polymers62,1904
Non-polymers1773
Water6,756375
1
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6663
Polymers15,5471
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Retinol-binding protein 2


Theoretical massNumber of molelcules
Total (without water)15,5471
Polymers15,5471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Retinol-binding protein 2


Theoretical massNumber of molelcules
Total (without water)15,5471
Polymers15,5471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6062
Polymers15,5471
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.526, 36.224, 129.086
Angle α, β, γ (deg.)84.34, 80.26, 67.47
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: 15547.437 Da / Num. of mol.: 4 / 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) / Strain (production host): BL21-DE3 / References: UniProt: P50120
#2: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.02 Å3/Da / Density % sol: 39.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% PEG 4000, 0.1 M sodium acetate, 0.1 M ammonium acetate, pH 4.6
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 300 mm CCD / Detector: CCD / Date: Nov 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 268817 / Num. obs: 77790 / % possible obs: 94.7 % / Redundancy: 3.3 % / Net I/σ(I): 43.37
Reflection shellResolution: 1.5→1.53 Å / % possible all: 94.6

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data scaling
PHENIX1.8.4_1496phasing
PHENIX1.8.4_1496model building
RefinementResolution: 1.5→30.055 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 46.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2434 2006 2.71 %
Rwork0.224 --
obs0.2246 74068 95.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→30.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4358 0 12 375 4745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074439
X-RAY DIFFRACTIONf_angle_d1.0735970
X-RAY DIFFRACTIONf_dihedral_angle_d15.4261647
X-RAY DIFFRACTIONf_chiral_restr0.04648
X-RAY DIFFRACTIONf_plane_restr0.004770
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5003-1.53780.43371470.39524971X-RAY DIFFRACTION91
1.5378-1.57940.39031360.36345051X-RAY DIFFRACTION94
1.5794-1.62580.35291260.33455112X-RAY DIFFRACTION94
1.6258-1.67830.33181610.31475109X-RAY DIFFRACTION95
1.6783-1.73830.31341370.29095237X-RAY DIFFRACTION95
1.7383-1.80790.29131400.27525115X-RAY DIFFRACTION95
1.8079-1.89010.23521480.24235177X-RAY DIFFRACTION96
1.8901-1.98980.22991330.23045190X-RAY DIFFRACTION96
1.9898-2.11440.211450.21355238X-RAY DIFFRACTION96
2.1144-2.27760.27721370.2145222X-RAY DIFFRACTION96
2.2776-2.50670.23861520.21235164X-RAY DIFFRACTION96
2.5067-2.86920.25621530.20585225X-RAY DIFFRACTION97
2.8692-3.61390.20171480.19165280X-RAY DIFFRACTION97
3.6139-30.06130.21991430.19824971X-RAY DIFFRACTION92
Refinement TLS params.Method: refined / Origin x: -3.007 Å / Origin y: 16.9858 Å / Origin z: 7.9355 Å
111213212223313233
T0.1456 Å20.0026 Å2-0.0038 Å2-0.1258 Å20.0028 Å2--0.1893 Å2
L0.0628 °2-0.0058 °2-0.1557 °2-0.0085 °20.2075 °2--4.5474 °2
S-0.0253 Å °0.0091 Å °0.0139 Å °-0.0363 Å °-0.0304 Å °0.0135 Å °0.0373 Å °-0.1107 Å °0.0562 Å °
Refinement TLS groupSelection details: all

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