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- PDB-4w9a: Crystal structure of Gamma-B Crystallin expressed in E. coli base... -

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Basic information

Entry
Database: PDB / ID: 4w9a
TitleCrystal structure of Gamma-B Crystallin expressed in E. coli based on mRNA variant 2
ComponentsGamma-crystallin B
KeywordsSTRUCTURAL PROTEIN / Eye lens protein
Function / homology
Function and homology information


structural constituent of eye lens / lens development in camera-type eye / visual perception
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 speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsKudlinzki, D. / Buhr, F. / Linhard, V.L. / Jha, S. / Komar, A.A. / Schwalbe, H.
CitationJournal: To Be Published
Title: Two synonymous gene variants encode proteins with identical sequence, but different folding conformations.
Authors: Buhr, F. / Jha, S. / Thommen, M. / Rodnina, M. / Kutz, F. / Kudlinzki, D. / Linhard, V.L. / Komar, A.A. / Schwalbe, H.
History
DepositionAug 27, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Gamma-crystallin B


Theoretical massNumber of molelcules
Total (without water)21,9531
Polymers21,9531
Non-polymers00
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.644, 123.644, 56.568
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-296-

HOH

21A-316-

HOH

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Components

#1: Protein Gamma-crystallin B / Gamma-B-crystallin / Gamma-crystallin II


Mass: 21952.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: CRYGB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02526
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1% Trypton, 20% PEG 3350, 50mM HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.38→38.89 Å / Num. obs: 33993 / % possible obs: 99.9 % / Redundancy: 5.93 % / Rsym value: 0.065 / Net I/σ(I): 19.93
Reflection shellResolution: 1.38→1.46 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.16 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSXDSappdata reduction
Cootmodel building
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GCR

4gcr


Resolution: 1.38→26.295 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1844 1699 5 %
Rwork0.1634 --
obs0.1644 33989 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.38→26.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1450 0 0 207 1657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051528
X-RAY DIFFRACTIONf_angle_d1.0182067
X-RAY DIFFRACTIONf_dihedral_angle_d12.44589
X-RAY DIFFRACTIONf_chiral_restr0.045193
X-RAY DIFFRACTIONf_plane_restr0.006277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3799-1.42050.34721400.31582664X-RAY DIFFRACTION99
1.4205-1.46640.26741400.25052662X-RAY DIFFRACTION100
1.4664-1.51880.22011410.22232668X-RAY DIFFRACTION100
1.5188-1.57960.24821410.20522688X-RAY DIFFRACTION100
1.5796-1.65150.23351400.18172665X-RAY DIFFRACTION100
1.6515-1.73850.17621410.16912677X-RAY DIFFRACTION100
1.7385-1.84740.19231420.16232693X-RAY DIFFRACTION100
1.8474-1.990.18541410.15642672X-RAY DIFFRACTION100
1.99-2.19020.17491420.14872709X-RAY DIFFRACTION100
2.1902-2.50690.19571420.16092688X-RAY DIFFRACTION100
2.5069-3.15760.18891430.16242724X-RAY DIFFRACTION100
3.1576-26.29960.14181460.13492780X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.86220.30270.00243.67760.20510.91560.0999-0.10150.10360.3643-0.0544-0.0813-0.27240.0476-0.01910.2367-0.02190.01150.0981-0.0120.1323-20.04252.361-9.725
21.71180.7992-0.75164.3607-0.4433.29690.06670.04360.1052-0.12070.03750.0428-0.2098-0.012-0.06760.15240.0120.00590.0583-0.010.102-23.4916-1.5891-17.5552
34.7779-5.4114-2.20467.1153.55042.9743-0.166-0.14160.04440.63480.1017-0.1370.13550.21920.00460.1432-0.0135-0.01650.10640.02450.1191-17.695-15.8315-10.2988
45.60960.69880.79654.59740.21714.86610.1039-0.0728-0.0737-0.0738-0.11810.10450.2998-0.337-0.03270.0997-0.00180.00540.0777-0.01690.0755-29.0204-28.2155-21.8954
56.10113.10480.09564.2344-0.40082.44990.0402-0.045-0.1462-0.1323-0.0922-0.03960.161-0.0209-0.02720.07520.02760.00980.0674-0.0290.0808-22.0256-26.9725-25.2086
61.5180.1660.06831.65870.04341.6650.01320.13450.0173-0.1277-0.08020.0106-0.0996-0.05980.06380.07840.0283-0.00360.0753-0.00570.0733-23.4574-19.2276-26.1275
73.40873.2078-1.03154.2319-3.13154.6161-0.0026-0.01330.1635-0.02-0.0140.1727-0.1113-0.1357-0.03430.06220.01480.00480.0792-0.01780.0602-27.1553-17.7957-15.7126
83.4522-0.46010.15461.8761-0.3823.3965-0.1146-0.01120.0297-0.04010.02630.0729-0.1147-0.210.02490.0760.0211-0.00520.0516-0.02920.0941-27.3589-17.2863-21.5872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 77 )
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 89 )
4X-RAY DIFFRACTION4chain 'A' and (resid 90 through 99 )
5X-RAY DIFFRACTION5chain 'A' and (resid 100 through 112 )
6X-RAY DIFFRACTION6chain 'A' and (resid 113 through 143 )
7X-RAY DIFFRACTION7chain 'A' and (resid 144 through 152 )
8X-RAY DIFFRACTION8chain 'A' and (resid 153 through 173 )

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