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- PDB-1ytq: Structure of Native Human Beta B2 Crystallin -

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Basic information

Entry
Database: PDB / ID: 1ytq
TitleStructure of Native Human Beta B2 Crystallin
ComponentsBeta crystallin B2
KeywordsSTRUCTURAL PROTEIN / Crystallin / Domain Swapping / greek key
Function / homology
Function and homology information


structural constituent of eye lens / lens development in camera-type eye / visual perception / structural molecule activity / identical protein binding
Similarity search - Function
Crystallins / Gamma-B Crystallin; domain 1 / Beta/Gamma crystallin / : / Crystallins beta and gamma 'Greek key' motif profile. / Beta/gamma crystallins / Beta/gamma crystallin / Gamma-crystallin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSlingsby, C. / Smith, M.A. / Bateman, O.A.
CitationJournal: Protein Sci. / Year: 2007
Title: Mutation of interfaces in domain-swapped human betaB2-crystallin
Authors: Smith, M.A. / Bateman, O.A. / Jaenicke, R. / Slingsby, C.
History
DepositionFeb 10, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 26, 2013Group: Derived calculations
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Beta crystallin B2


Theoretical massNumber of molelcules
Total (without water)23,2811
Polymers23,2811
Non-polymers00
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Beta crystallin B2

A: Beta crystallin B2


Theoretical massNumber of molelcules
Total (without water)46,5612
Polymers46,5612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3880 Å2
ΔGint-14 kcal/mol
Surface area17120 Å2
MethodPISA
3
A: Beta crystallin B2

A: Beta crystallin B2

A: Beta crystallin B2

A: Beta crystallin B2


Theoretical massNumber of molelcules
Total (without water)93,1234
Polymers93,1234
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)76.892, 82.324, 108.104
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-207-

HOH

21A-307-

HOH

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Components

#1: Protein Beta crystallin B2 / BP / Beta B2 Crystallin


Mass: 23280.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRYBB2 / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P43320
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 3.67 Å3/Da / Density % sol: 66.5 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 8
Details: MPD, cacodylate, DTT, magnesium chloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 11, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.7→34.4 Å / Num. all: 36271 / Num. obs: 35758 / % possible obs: 95.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.7→34.4 Å / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→34.4 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.311 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19849 1814 5 %RANDOM
Rwork0.17971 ---
obs0.18067 34402 95.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.388 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→34.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1469 0 0 206 1675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221535
X-RAY DIFFRACTIONr_bond_other_d0.0010.021306
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9352078
X-RAY DIFFRACTIONr_angle_other_deg0.77633076
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7325180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59424.64384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35815264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.469159
X-RAY DIFFRACTIONr_chiral_restr0.0830.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021715
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02313
X-RAY DIFFRACTIONr_nbd_refined0.1940.2270
X-RAY DIFFRACTIONr_nbd_other0.1950.21375
X-RAY DIFFRACTIONr_nbtor_refined0.180.2725
X-RAY DIFFRACTIONr_nbtor_other0.0880.2839
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.2172
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3150.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.233
X-RAY DIFFRACTIONr_mcbond_it1.3251.51176
X-RAY DIFFRACTIONr_mcbond_other0.1981.5369
X-RAY DIFFRACTIONr_mcangle_it1.46421467
X-RAY DIFFRACTIONr_scbond_it2.4163758
X-RAY DIFFRACTIONr_scangle_it3.3794.5611
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 103 -
Rwork0.208 1930 -
obs--73.63 %

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