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- PDB-2jdf: Human gamma-B crystallin -

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Basic information

Entry
Database: PDB / ID: 2jdf
TitleHuman gamma-B crystallin
ComponentsGAMMA CRYSTALLIN B
KeywordsSTRUCTURAL PROTEIN / ARTIFICIAL BINDING PROTEIN / EYE LENS PROTEIN / GAMMA CRYSTALLIN / AFFILIN / OXIDATION / POLYMORPHISM / PHOSPHORYLATION
Function / homology
Function and homology information


lens fiber cell morphogenesis / structural constituent of eye lens / lens development in camera-type eye / visual perception / nucleus / cytoplasm
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 speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.7 Å
AuthorsEbersbach, H. / Fiedler, E. / Scheuermann, T. / Fiedler, M. / Stubbs, M.T. / Reimann, C. / Proetzel, G. / Rudolph, R. / Fiedler, U.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Affilin-Novel Binding Molecules Based on Human Gamma-B-Crystallin, an All Beta-Sheet Protein.
Authors: Ebersbach, H. / Fiedler, E. / Scheuermann, T. / Fiedler, M. / Stubbs, M.T. / Reimann, C. / Proetzel, G. / Rudolph, R. / Fiedler, U.
History
DepositionJan 8, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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)21,8741
Polymers21,8741
Non-polymers00
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)45.522, 45.522, 149.763
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein GAMMA CRYSTALLIN B / GAMMA-B CRYSTALLIN / GAMMA CRYSTALLIN 1-2


Mass: 21873.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P07316
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 1.88 Å3/Da / Density % sol: 39.9 % / Description: NONE

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.12714
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12714 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 20389 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.04

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Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.7→30 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2203 2004 9.7 %RANDOM
Rwork0.1957 ---
obs0.1957 20355 98.5 %-
Solvent computationBsol: 51.1888 Å2 / ksol: 0.384364 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.983 Å2-0.31 Å20 Å2
2---1.983 Å20 Å2
3---3.965 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1468 0 0 238 1706
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00513
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.24457
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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