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- PDB-6c7z: Crystal structure of the Q108K:K40L:T51V:R58F mutant of human Cel... -

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Basic information

Entry
Database: PDB / ID: 6c7z
TitleCrystal structure of the Q108K:K40L:T51V:R58F mutant of human Cellular Retinol Binding Protein II in complex with synthetic Ligand Julolidine
ComponentsRetinol-binding protein 2
KeywordsTRANSPORT PROTEIN / Protein Engineering / Ratiometric pH probe / hCRBPII
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 / 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 / Chem-JLO / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsNosrati, M. / Geiger, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM101353 United States
CitationJournal: Chembiochem / Year: 2018
Title: A Genetically Encoded Ratiometric pH Probe: Wavelength Regulation-Inspired Design of pH Indicators.
Authors: Berbasova, T. / Tahmasebi Nick, S. / Nosrati, M. / Nossoni, Z. / Santos, E.M. / Vasileiou, C. / Geiger, J.H. / Borhan, B.
History
DepositionJan 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.4Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)31,7946
Polymers31,1412
Non-polymers6534
Water3,495194
1
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8973
Polymers15,5701
Non-polymers3262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8973
Polymers15,5701
Non-polymers3262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.787, 35.947, 64.089
Angle α, β, γ (deg.)90.51, 92.45, 113.31
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: 15570.489 Da / Num. of mol.: 2 / Mutation: Q108K,K40L,T51V,R58F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2 / Production host: Escherichia coli (E. coli) / References: UniProt: P50120
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-JLO / (2E,4E)-3-methyl-5-(2,3,6,7-tetrahydro-1H,5H-pyrido[3,2,1-ij]quinolin-9-yl)penta-2,4-dienal


Mass: 267.365 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H21NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.02 Å3/Da / Density % sol: 39.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 30% PEG 4000, 0.1M Ammonium Acetate, 0.1 M Sodium Acetate pH=4.5
PH range: 4.0-4.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.42→50 Å / Num. all: 43584 / Num. obs: 45939 / % possible obs: 94.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 42.2
Reflection shellResolution: 1.42→1.44 Å / Redundancy: 2 % / Rmerge(I) obs: 0.194 / Num. unique obs: 1812 / % possible all: 79.4

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Processing

Software
NameVersionClassification
PHENIX1.7.2_869refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RCT

2rct


Resolution: 1.42→29.003 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 0.14 / Phase error: 28.74
RfactorNum. reflection% reflection
Rfree0.2563 2014 4.74 %
Rwork0.2219 --
obs0.2235 42458 92.2 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Bsol: 42.607 Å2 / ksol: 0.393 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.2152 Å2-0.9994 Å2-0.7034 Å2
2--2.7238 Å2-0.3408 Å2
3----5.939 Å2
Refinement stepCycle: LAST / Resolution: 1.42→29.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2188 0 46 194 2428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072312
X-RAY DIFFRACTIONf_angle_d1.1443126
X-RAY DIFFRACTIONf_dihedral_angle_d16.326865
X-RAY DIFFRACTIONf_chiral_restr0.074331
X-RAY DIFFRACTIONf_plane_restr0.005406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4195-1.4550.32231080.27742193X-RAY DIFFRACTION71
1.455-1.49430.3041280.26822643X-RAY DIFFRACTION83
1.4943-1.53830.29011350.25392742X-RAY DIFFRACTION89
1.5383-1.5880.31661350.24792849X-RAY DIFFRACTION90
1.588-1.64470.27551430.24312918X-RAY DIFFRACTION92
1.6447-1.71060.28331500.24562885X-RAY DIFFRACTION93
1.7106-1.78840.27141440.24972911X-RAY DIFFRACTION93
1.7884-1.88270.30261510.24432983X-RAY DIFFRACTION95
1.8827-2.00060.25981500.22633035X-RAY DIFFRACTION96
2.0006-2.1550.24621540.22943009X-RAY DIFFRACTION97
2.155-2.37180.25841530.22033051X-RAY DIFFRACTION97
2.3718-2.71480.30181580.23693059X-RAY DIFFRACTION98
2.7148-3.41950.23761520.21313084X-RAY DIFFRACTION99
3.4195-29.00870.22181530.19643082X-RAY DIFFRACTION98

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