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- PDB-4zr2: Crystal Structure of the Domain-Swapped Dimer K40L:Q108K:Y60W mut... -

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Basic information

Entry
Database: PDB / ID: 4zr2
TitleCrystal Structure of the Domain-Swapped Dimer K40L:Q108K:Y60W mutant of Human Cellular Retinol Binding Protein II
ComponentsRetinol-binding protein 2
KeywordsLIPID BINDING PROTEIN / Domain Swapped Dimer / Domain Swapping / Protein folding / Human Cellular Retinol Binding Protein II / Intracellular Lipid Binding Protein / Retinal
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 / RETINAL / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8024 Å
AuthorsAssar, Z. / Nossoni, Z. / 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
Citation
Journal: Structure / Year: 2016
Title: Domain-Swapped Dimers of Intracellular Lipid-Binding Proteins: Evidence for Ordered Folding Intermediates.
Authors: Assar, Z. / Nossoni, Z. / Wang, W. / Santos, E.M. / Kramer, K. / McCornack, C. / Vasileiou, C. / Borhan, B. / Geiger, J.H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structures of holo wild-type human cellular retinol-binding protein II (hCRBPII) bound to retinol and retinal.
Authors: Nossoni, Z. / Assar, Z. / Yapici, I. / Nosrati, M. / Wang, W. / Berbasova, T. / Vasileiou, C. / Borhan, B. / Geiger, J.
#2: Journal: Science / Year: 2012
Title: Tuning the electronic absorption of protein-embedded all-trans-retinal.
Authors: Wang, W. / Nossoni, Z. / Berbasova, T. / Watson, C.T. / Yapici, I. / Lee, K.S. / Vasileiou, C. / Geiger, J.H. / Borhan, B.
History
DepositionMay 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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

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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)31,7918
Polymers31,2112
Non-polymers5806
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-42 kcal/mol
Surface area14060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.768, 109.225, 36.389
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-384-

HOH

DetailsDimer confirmed by gel filtration

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Components

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


Mass: 15605.519 Da / Num. of mol.: 2 / Mutation: Q108K, K40L, Y60W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / References: UniProt: P50120
#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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 Å3/Da / Density % sol: 38.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 25% PEG 4000 (40%), 0.1M Sodium Acetate pH 4.5, Ammonium Acetate 0.1M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.802→50 Å / Num. all: 23873 / Num. obs: 23839 / % possible obs: 99.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 6.23
Reflection shellResolution: 1.802→1.94 Å / Rmerge(I) obs: 0.465 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data collection
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RCT

2rct


Resolution: 1.8024→41.201 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 21.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2184 2000 8.39 %
Rwork0.1764 --
obs0.18 23835 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8024→41.201 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 25 178 2385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082248
X-RAY DIFFRACTIONf_angle_d1.1053026
X-RAY DIFFRACTIONf_dihedral_angle_d14.102819
X-RAY DIFFRACTIONf_chiral_restr0.051325
X-RAY DIFFRACTIONf_plane_restr0.004392
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8024-1.84750.27641380.2194150998
1.8475-1.89740.25891380.18841513100
1.8974-1.95320.25311420.18911538100
1.9532-2.01630.2311420.18131557100
2.0163-2.08830.21881390.17751518100
2.0883-2.1720.23261410.17591545100
2.172-2.27080.21431430.1791554100
2.2708-2.39050.2421400.19461527100
2.3905-2.54030.27591420.18491551100
2.5403-2.73640.24381450.18681577100
2.7364-3.01170.24871430.18281567100
3.0117-3.44730.20571440.17031573100
3.4473-4.34240.16291470.14951603100
4.34240.21581560.1811703100
Refinement TLS params.Method: refined / Origin x: -8.9351 Å / Origin y: 10.2512 Å / Origin z: -14.9282 Å
111213212223313233
T0.1904 Å20.0082 Å20.0122 Å2-0.2203 Å20.0031 Å2--0.2081 Å2
L0.1654 °20.2072 °20.1089 °2-1.0601 °2-0.0774 °2--0.0106 °2
S0.0252 Å °-0.0427 Å °-0.0527 Å °0.0408 Å °0.0032 Å °0.0989 Å °0.0164 Å °-0.0159 Å °-0.0319 Å °
Refinement TLS groupSelection details: all

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