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- PDB-6mlb: Crystal structure of the holo retinal-bound domain-swapped dimer ... -

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Basic information

Entry
Database: PDB / ID: 6mlb
TitleCrystal structure of the holo retinal-bound domain-swapped dimer Q108K:K40L:T51F mutant of human cellular retinol binding protein II
ComponentsRetinol-binding protein 2
KeywordsLIPID BINDING PROTEIN / iLBP / Protein Switch
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 / RETINAL / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 27, 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 13, 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)63,74715
Polymers62,5144
Non-polymers1,23211
Water2,324129
1
A: Retinol-binding protein 2
C: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7526
Polymers31,2572
Non-polymers4954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9460 Å2
ΔGint-44 kcal/mol
Surface area13110 Å2
MethodPISA
2
B: Retinol-binding protein 2
D: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9959
Polymers31,2572
Non-polymers7387
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9460 Å2
ΔGint-44 kcal/mol
Surface area13660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.476, 63.282, 117.782
Angle α, β, γ (deg.)90.00, 95.94, 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: 15628.552 Da / Num. of mol.: 4 / Fragment: Q108K, K40L, T51F
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-RET / RETINAL


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


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.16 Å3/Da / Density % sol: 43.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, ammonium acetate, sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.15→33.685 Å / Num. obs: 28616 / % possible obs: 97.98 % / Redundancy: 7.2 % / Biso Wilson estimate: 42.12 Å2 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.112 / Net I/σ(I): 32.2
Reflection shellResolution: 2.15→2.227 Å / Rmerge(I) obs: 0.84 / Num. unique obs: 2760 / Rpim(I) all: 0.348 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RCT

2rct


Resolution: 2.15→33.685 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.18
RfactorNum. reflection% reflection
Rfree0.3024 1307 4.57 %
Rwork0.2283 --
obs0.2316 28584 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.15→33.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4358 0 84 132 4574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024585
X-RAY DIFFRACTIONf_angle_d0.5466180
X-RAY DIFFRACTIONf_dihedral_angle_d8.6913735
X-RAY DIFFRACTIONf_chiral_restr0.044659
X-RAY DIFFRACTIONf_plane_restr0.002799
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.23610.39251380.28442919X-RAY DIFFRACTION97
2.2361-2.33780.31271440.26843005X-RAY DIFFRACTION97
2.3378-2.4610.36851450.27123014X-RAY DIFFRACTION98
2.461-2.61520.38731450.27533049X-RAY DIFFRACTION98
2.6152-2.8170.36021450.26143022X-RAY DIFFRACTION98
2.817-3.10030.3231410.25813020X-RAY DIFFRACTION98
3.1003-3.54850.28851490.2143048X-RAY DIFFRACTION98
3.5485-4.46910.28951450.18943078X-RAY DIFFRACTION99
4.4691-33.68890.26681550.22373122X-RAY DIFFRACTION98

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