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- PDB-6mcv: Crystal Structure of Holo Retinal-Bound Domain-Swapped Dimer of W... -

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Basic information

Entry
Database: PDB / ID: 6mcv
TitleCrystal Structure of Holo Retinal-Bound Domain-Swapped Dimer of Wild Type Human Cellular Retinol Binding Protein II
ComponentsRetinol-binding protein 2
KeywordsLIPID BINDING PROTEIN / iLBP / Protein Switch / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


vitamin A metabolic process / retinoid binding / retinal binding / molecular carrier activity / 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
RETINAL / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsGhanbarpour, A. / Geiger, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Engineering the hCRBPII Domain-Swapped Dimer into a New Class of Protein Switches.
Authors: Ghanbarpour, A. / Pinger, C. / Esmatpour Salmani, R. / Assar, Z. / Santos, E.M. / Nosrati, M. / Pawlowski, K. / Spence, D. / Vasileiou, C. / Jin, X. / Borhan, B. / Geiger, J.H.
History
DepositionSep 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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

Downloads & links

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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
E: Retinol-binding protein 2
F: Retinol-binding protein 2
G: Retinol-binding protein 2
H: Retinol-binding protein 2
I: Retinol-binding protein 2
J: Retinol-binding protein 2
K: Retinol-binding protein 2
L: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,73814
Polymers187,16912
Non-polymers5692
Water57632
1
A: Retinol-binding protein 2
K: 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
Buried area7340 Å2
ΔGint-36 kcal/mol
Surface area14160 Å2
MethodPISA
2
B: Retinol-binding protein 2
L: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4793
Polymers31,1952
Non-polymers2841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7840 Å2
ΔGint-36 kcal/mol
Surface area13900 Å2
MethodPISA
3
C: Retinol-binding protein 2
G: 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
Buried area7520 Å2
ΔGint-35 kcal/mol
Surface area14010 Å2
MethodPISA
4
D: Retinol-binding protein 2
H: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4793
Polymers31,1952
Non-polymers2841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7780 Å2
ΔGint-41 kcal/mol
Surface area13830 Å2
MethodPISA
5
E: Retinol-binding protein 2
I: Retinol-binding protein 2


Theoretical massNumber of molelcules
Total (without water)31,1952
Polymers31,1952
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7390 Å2
ΔGint-35 kcal/mol
Surface area14200 Å2
MethodPISA
6
F: Retinol-binding protein 2
J: 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
Buried area7350 Å2
ΔGint-38 kcal/mol
Surface area13920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.819, 74.362, 352.547
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: 15597.452 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P50120
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.3 Å3/Da / Density % sol: 46.63 %
Crystal growTemperature: 298 K / Method: evaporation / Details: 4000 PEG, Ammonium acetate, Sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3.3→14.993 Å / Num. obs: 24088 / % possible obs: 89.8 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.19 / Rrim(I) all: 0.2 / Net I/σ(I): 17.1
Reflection shellResolution: 3.3→3.36 Å / Num. unique obs: 2395 / CC1/2: 0.773 / Rpim(I) all: 0.303 / % possible all: 92.12

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RCT

2rct


Resolution: 3.3→14.993 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.12
RfactorNum. reflection% reflection
Rfree0.2658 770 3.2 %
Rwork0.2079 --
obs0.2098 24063 90.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→14.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13131 0 14 33 13178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00113371
X-RAY DIFFRACTIONf_angle_d0.34817989
X-RAY DIFFRACTIONf_dihedral_angle_d6.9387937
X-RAY DIFFRACTIONf_chiral_restr0.0391931
X-RAY DIFFRACTIONf_plane_restr0.0012319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.50430.34011280.25663850X-RAY DIFFRACTION91
3.5043-3.77090.30621270.22253851X-RAY DIFFRACTION91
3.7709-4.14310.29291270.22493835X-RAY DIFFRACTION89
4.1431-4.72610.2391260.17933784X-RAY DIFFRACTION89
4.7261-5.89360.26171250.20093806X-RAY DIFFRACTION88
5.8936-14.99270.23111370.20284167X-RAY DIFFRACTION92

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