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- PDB-6mkv: Crystal structure of Retinal-bound holo Q108K:K40L:T51W domain-sw... -

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Basic information

Entry
Database: PDB / ID: 6mkv
TitleCrystal structure of Retinal-bound holo Q108K:K40L:T51W domain-swapped dimer of human cellular retinol binding protein 2
ComponentsRetinol-binding protein 2
KeywordsLIPID BINDING PROTEIN / iLBP / Protein Switch / CYTOSOLIC 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 / RETINAL / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.107 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 26, 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)64,12116
Polymers62,6704
Non-polymers1,45112
Water2,774154
1
A: Retinol-binding protein 2
C: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6794
Polymers31,3352
Non-polymers3432
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-41 kcal/mol
Surface area13720 Å2
MethodPISA
2
B: Retinol-binding protein 2
D: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,44212
Polymers31,3352
Non-polymers1,10710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11460 Å2
ΔGint-47 kcal/mol
Surface area13010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.332, 63.137, 118.218
Angle α, β, γ (deg.)90.00, 96.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 15667.587 Da / Num. of mol.: 4 / Mutation: Q108K,K40L,T51W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2
Production host: Bacterial expression vector pBEN1-SGC (others)
References: UniProt: P50120
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, Sodium acetate, Ammonium acetate / PH range: 4-4.8

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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: Mar 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.107→39.17 Å / Num. obs: 29781 / % possible obs: 96.5 % / Redundancy: 3 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.06 / Rrim(I) all: 0.109 / Net I/σ(I): 14.4
Reflection shellResolution: 2.107→2.14 Å / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2740 / Rrim(I) all: 0.66 / % possible all: 91.4

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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: 2RCQ

2rcq


Resolution: 2.107→39.167 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.78
RfactorNum. reflection% reflection
Rfree0.2728 1995 6.7 %
Rwork0.1996 --
obs0.2045 29770 96.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.107→39.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4363 0 100 154 4617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074568
X-RAY DIFFRACTIONf_angle_d0.9266157
X-RAY DIFFRACTIONf_dihedral_angle_d7.8543454
X-RAY DIFFRACTIONf_chiral_restr0.055648
X-RAY DIFFRACTIONf_plane_restr0.004795
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1066-2.15930.35851340.2521773X-RAY DIFFRACTION87
2.1593-2.21770.32961380.24821930X-RAY DIFFRACTION94
2.2177-2.28290.29821470.22921980X-RAY DIFFRACTION96
2.2829-2.35660.31321360.21881975X-RAY DIFFRACTION97
2.3566-2.44080.32621480.20911989X-RAY DIFFRACTION97
2.4408-2.53850.2831450.20591954X-RAY DIFFRACTION97
2.5385-2.6540.27521420.20161986X-RAY DIFFRACTION97
2.654-2.79390.31241470.20182020X-RAY DIFFRACTION97
2.7939-2.96890.28581370.20671967X-RAY DIFFRACTION97
2.9689-3.19810.27631520.2062019X-RAY DIFFRACTION98
3.1981-3.51970.26131470.19372035X-RAY DIFFRACTION98
3.5197-4.02860.26181380.17692050X-RAY DIFFRACTION98
4.0286-5.07380.21551400.16712057X-RAY DIFFRACTION99
5.0738-39.17370.2741440.2222040X-RAY DIFFRACTION96

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