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- PDB-6on5: Crystal Structure of the Zn-bound Domain-Swapped Dimer Q108K:T51D... -

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Basic information

Entry
Database: PDB / ID: 6on5
TitleCrystal Structure of the Zn-bound Domain-Swapped Dimer Q108K:T51D:A28C:L36C:F57H Mutant of Human Cellular Retinol Binding Protein II
ComponentsRetinol-binding protein 2
KeywordsLIPID BINDING PROTEIN / Retinol / iLBP / Protein Switch / CYTOSOLIC PROTEIN
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 domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.638 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
DepositionApr 20, 2019Deposition 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3163
Polymers31,2512
Non-polymers651
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-73 kcal/mol
Surface area13800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.416, 61.759, 72.638
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: 15625.511 Da / Num. of mol.: 2 / Mutation: Q108K,T51D,A28C,L36C,F57H
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.17 Å3/Da / Density % sol: 43.27 % / Description: Cubic
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Bis-Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97623 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.638→37.122 Å / Num. obs: 32802 / % possible obs: 96.19 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.063 / Net I/σ(I): 22.03
Reflection shellResolution: 1.638→1.697 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.35 / Num. unique obs: 3193 / Rpim(I) all: 0.347 / % possible all: 95.68

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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: 1.638→37.122 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2547 1991 6.07 %
Rwork0.2044 --
obs0.2075 32787 96.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.638→37.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2188 0 1 199 2388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072343
X-RAY DIFFRACTIONf_angle_d0.9023181
X-RAY DIFFRACTIONf_dihedral_angle_d6.4431945
X-RAY DIFFRACTIONf_chiral_restr0.056341
X-RAY DIFFRACTIONf_plane_restr0.005415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6381-1.67910.33691340.28122111X-RAY DIFFRACTION94
1.6791-1.72450.32291450.26262239X-RAY DIFFRACTION99
1.7245-1.77520.26741440.23722194X-RAY DIFFRACTION99
1.7752-1.83250.2711410.22872234X-RAY DIFFRACTION98
1.8325-1.8980.25921450.22232180X-RAY DIFFRACTION97
1.898-1.9740.31681320.2292162X-RAY DIFFRACTION95
1.974-2.06380.25671480.21682187X-RAY DIFFRACTION97
2.0638-2.17260.28621420.21862234X-RAY DIFFRACTION98
2.1726-2.30870.26661460.20492199X-RAY DIFFRACTION97
2.3087-2.48690.29321460.21192221X-RAY DIFFRACTION97
2.4869-2.73710.26311480.21132213X-RAY DIFFRACTION96
2.7371-3.1330.25691400.21382223X-RAY DIFFRACTION96
3.133-3.94660.23031340.17472130X-RAY DIFFRACTION91
3.9466-37.13140.21181460.18242269X-RAY DIFFRACTION92

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