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- PDB-4w9b: Crystal structure of Gamma-B Crystallin expressed in E. coli base... -

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Basic information

Entry
Database: PDB / ID: 4w9b
TitleCrystal structure of Gamma-B Crystallin expressed in E. coli based on mRNA variant 1
ComponentsGamma-crystallin BCRYGB
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 / Beta/Gamma crystallin / Gamma-B Crystallin; domain 1 / 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 (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.279 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 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _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: Gamma-crystallin B


Theoretical massNumber of molelcules
Total (without water)21,9531
Polymers21,9531
Non-polymers00
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.641, 123.641, 56.548
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-299-

HOH

21A-305-

HOH

31A-316-

HOH

41A-324-

HOH

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Components

#1: Protein Gamma-crystallin B / CRYGB / 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 (cattle) / Gene: CRYGB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02526
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 1.89 Å3/Da / Density % sol: 35.08 %
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: 1.279→38.88 Å / Num. obs: 42474 / % possible obs: 99.7 % / Redundancy: 11.14 % / Rsym value: 0.15 / Net I/σ(I): 19
Reflection shellResolution: 1.279→1.36 Å / Redundancy: 11 % / Mean I/σ(I) obs: 2.27 / % possible all: 99.3

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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: 1.279→26.292 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1876 2123 5 %
Rwork0.1697 --
obs0.1706 42460 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.279→26.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1450 0 0 218 1668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051531
X-RAY DIFFRACTIONf_angle_d1.0282070
X-RAY DIFFRACTIONf_dihedral_angle_d12.937585
X-RAY DIFFRACTIONf_chiral_restr0.044192
X-RAY DIFFRACTIONf_plane_restr0.006279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2792-1.3090.4091390.33142628X-RAY DIFFRACTION98
1.309-1.34170.26871410.27952675X-RAY DIFFRACTION100
1.3417-1.3780.26651400.2562662X-RAY DIFFRACTION100
1.378-1.41860.25741420.24552706X-RAY DIFFRACTION100
1.4186-1.46430.28061400.22242655X-RAY DIFFRACTION100
1.4643-1.51670.22411420.21282692X-RAY DIFFRACTION100
1.5167-1.57740.22931410.19652684X-RAY DIFFRACTION100
1.5774-1.64920.1791410.17242682X-RAY DIFFRACTION100
1.6492-1.73610.18931410.16152680X-RAY DIFFRACTION100
1.7361-1.84480.18071420.15742696X-RAY DIFFRACTION99
1.8448-1.98720.18461400.15542658X-RAY DIFFRACTION99
1.9872-2.18710.1641420.14672701X-RAY DIFFRACTION99
2.1871-2.50340.16761420.15672696X-RAY DIFFRACTION100
2.5034-3.15320.17861430.15712729X-RAY DIFFRACTION100
3.1532-26.29780.14521470.1372793X-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)
11.12290.4566-0.17063.94390.18921.02310.1228-0.0780.08360.3774-0.0725-0.1265-0.23980.0591-0.03940.2041-0.02250.00210.0894-0.01060.1034-19.28794.0117-8.7816
20.9766-0.26750.25823.441-0.2511.35510.0511-0.11270.07630.2998-0.029-0.0431-0.2465-0.0438-0.00570.1929-0.01820.01690.0671-0.01820.111-21.35354.0503-10.2435
34.111-0.2828-1.46975.13290.53123.03250.06070.0181-0.01270.1829-0.05780.2685-0.0658-0.1798-0.01540.1049-0.00770.01440.0305-0.00740.0522-26.2794-5.8636-11.8151
42.33441.1943-0.65953.9726-0.44752.62810.03090.05810.0475-0.16620.0165-0.1718-0.09850.1599-0.0560.11620.00490.01410.0447-0.01290.0722-19.5788-1.8163-18.9526
50.2264-0.5549-0.40013.7450.51061.2964-0.0062-0.03720.01070.2593-0.0039-0.0331-0.09320.07670.03130.0753-0.0164-0.00560.06840.00090.0913-21.6745-8.8838-13.7013
65.41330.1840.54843.4860.05964.0270.0613-0.0015-0.0468-0.0692-0.08220.05790.1996-0.1874-0.00780.07180.00560.00860.0356-0.00970.0614-28.8061-28.1711-21.8684
74.7022.02010.08323.1425-0.2521.66480.0783-0.1007-0.1128-0.0826-0.1144-0.02250.1371-0.00490.00990.06040.02770.00390.0512-0.02180.0646-21.9851-26.9851-25.1234
81.19170.1593-0.1261.4881-0.06261.13980.02080.09610.0016-0.1078-0.0667-0.0019-0.0936-0.03390.03550.06130.0237-0.00470.0558-0.00330.0584-23.4322-19.1361-26.1917
92.78822.2672-0.82853.1307-2.62653.67450.0351-0.06310.07650.0488-0.07250.1117-0.0953-0.0941-0.01750.05170.01030.0050.0717-0.0150.0476-27.1653-17.7767-15.736
102.4882-0.53750.05381.7716-0.33382.7461-0.06410.01750.0134-0.02280.0160.1003-0.0473-0.1735-0.02040.06130.01920.00010.029-0.02590.0766-27.3585-17.2609-21.5811
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 40 )
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 51 )
4X-RAY DIFFRACTION4chain 'A' and (resid 52 through 69 )
5X-RAY DIFFRACTION5chain 'A' and (resid 70 through 89 )
6X-RAY DIFFRACTION6chain 'A' and (resid 90 through 99 )
7X-RAY DIFFRACTION7chain 'A' and (resid 100 through 112 )
8X-RAY DIFFRACTION8chain 'A' and (resid 113 through 143 )
9X-RAY DIFFRACTION9chain 'A' and (resid 144 through 152 )
10X-RAY DIFFRACTION10chain 'A' and (resid 153 through 173 )

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