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- PDB-1a7h: GAMMA S CRYSTALLIN C-TERMINAL DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1a7h
TitleGAMMA S CRYSTALLIN C-TERMINAL DOMAIN
ComponentsGAMMAS CRYSTALLIN
KeywordsEYE-LENS PROTEIN / GAMMA CRYSTALLIN S / EYE LENS PROTEIN / MULTIGENE FAMILY
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: 2.56 Å
AuthorsBasak, A.K. / Slingsby, C.
CitationJournal: Protein Eng. / Year: 1998
Title: The C-terminal domains of gammaS-crystallin pair about a distorted twofold axis.
Authors: Basak, A.K. / Kroone, R.C. / Lubsen, N.H. / Naylor, C.E. / Jaenicke, R. / Slingsby, C.
History
DepositionMar 13, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Refinement description / Category: database_2 / software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GAMMAS CRYSTALLIN
B: GAMMAS CRYSTALLIN


Theoretical massNumber of molelcules
Total (without water)20,6402
Polymers20,6402
Non-polymers00
Water90150
1
A: GAMMAS CRYSTALLIN


Theoretical massNumber of molelcules
Total (without water)10,3201
Polymers10,3201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GAMMAS CRYSTALLIN


Theoretical massNumber of molelcules
Total (without water)10,3201
Polymers10,3201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.250, 62.250, 170.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.35584, -0.08497, -0.93068), (-0.60532, -0.73777, 0.2988), (-0.71202, 0.66968, 0.21109)
Vector: 103.14307, 54.72361, 51.32024)
DetailsTHE PROTEIN IN THE CRYSTAL LATTICE IS A DIMER. IN DILUTE SOLUTION IT IS A MONOMER. THERE IS NO NATURALLY OCCURRING BIOLOGICAL EQUIVALENT.

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Components

#1: Protein GAMMAS CRYSTALLIN


Mass: 10319.770 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN / Mutation: Q87M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Cell line: BL21 / Gene: CRYGS / Organ: EYE / Organelle: EYE-LENS / Plasmid: BL21 / Gene (production host): CRYGS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P06504
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.33 Å3/Da / Density % sol: 43 % / Description: TAKEN FROM WHOLE STRUCTURE.
Crystal growpH: 5
Details: PROTEIN CONCENTRATION 5MGS/ML. 0.1M NA-CITRATE, PH 5.0, 20-22%(W/V) PEG8K, 2% 1,4-DIOXANE, AT ROOM-TEMPERATURE.
Temp details: room temp
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
225 mMMes/NaOH1drop
311 %(w/v)PEG80001reservoir
4Na-citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1996 / Details: PLATINUM VERTICAL MIRROR
RadiationMonochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.56→45.64 Å / Num. obs: 6716 / % possible obs: 98.6 % / Redundancy: 5 % / Biso Wilson estimate: 17.84 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 14.7
Reflection shellResolution: 2.56→2.65 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.058 / Mean I/σ(I) obs: 11.5 / % possible all: 97.9
Reflection
*PLUS
Num. measured all: 33311
Reflection shell
*PLUS
% possible obs: 97.9 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLORrefinement
DENZOdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: GAMMA B C-TERMINAL

Resolution: 2.56→30 Å / Isotropic thermal model: RESTRAINED INDIVIDUAL / Cross valid method: THROUGHOUT REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.295 434 6 %RANDOM
Rwork0.208 ---
obs0.208 6709 98.7 %-
Displacement parametersBiso mean: 25.48 Å2
Refine analyzeLuzzati d res low obs: 30 Å / Luzzati sigma a obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.56→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1444 0 0 50 1494
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.68
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.13
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.46
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.571.5
X-RAY DIFFRACTIONx_mcangle_it2.63
X-RAY DIFFRACTIONx_scbond_it4.572.5
X-RAY DIFFRACTIONx_scangle_it2.65
Refine LS restraints NCSNCS model details: RESTRAINED / Rms dev position: 0.406 Å / Weight position: 300
LS refinement shellResolution: 2.56→2.68 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.358 56 7 %
Rwork0.276 738 -
obs--97.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.13
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.46
LS refinement shell
*PLUS
Rfactor obs: 0.276

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