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- PDB-2v2u: Structure of Mouse gammaC-crystallin -

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Basic information

Entry
Database: PDB / ID: 2v2u
TitleStructure of Mouse gammaC-crystallin
ComponentsGAMMA CRYSTALLIN C
KeywordsSTRUCTURAL PROTEIN / EYE LENS PROTEIN
Function / homology
Function and homology information


structural constituent of eye lens / eye development / camera-type eye development
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 speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPurkiss, A.G. / Bateman, O.A. / Wyatt, K. / David, L.L. / Wistow, G.J. / Slingsby, C.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Evolutionary Adaptation of Human and Mouse Eye Lens Gammac-Crystallins for Solubility and Stability: Fine-Tuning of Molecular Dipoles.
Authors: Purkiss, A.G. / Bateman, O.A. / Wyatt, K. / David, L.L. / Wistow, G.J. / Slingsby, C.
History
DepositionJun 7, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 4, 2013Group: Derived calculations / Source and taxonomy / Structure summary
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GAMMA CRYSTALLIN C
B: GAMMA CRYSTALLIN C


Theoretical massNumber of molelcules
Total (without water)41,6292
Polymers41,6292
Non-polymers00
Water2,450136
1
A: GAMMA CRYSTALLIN C


Theoretical massNumber of molelcules
Total (without water)20,8141
Polymers20,8141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GAMMA CRYSTALLIN C


Theoretical massNumber of molelcules
Total (without water)20,8141
Polymers20,8141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.911, 46.317, 53.317
Angle α, β, γ (deg.)108.53, 94.08, 99.37
Int Tables number1
Space group name H-MP1

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Components

#1: Protein GAMMA CRYSTALLIN C / GAMMAC-CRYSTALLIN


Mass: 20814.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Tissue: LENS / Cell: FIBER / Organ: EYE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYS / References: UniProt: Q61597
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.91 Å3/Da / Density % sol: 35.68 % / Description: NONE
Crystal growpH: 6.5
Details: 0.2 M SODIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5 AND 30% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 17, 2006 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.9→43.1 Å / Num. obs: 28779 / % possible obs: 93.5 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 4.2
Reflection shellResolution: 1.93→2.12 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 0.8 / % possible all: 89.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HK0

1hk0


Resolution: 1.9→43.07 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.917 / SU B: 11.793 / SU ML: 0.177 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1149 5.1 %RANDOM
Rwork0.205 ---
obs0.209 21170 91.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.26 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20.01 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2909 0 0 136 3045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213062
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.9364125
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5995358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.81822.135178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.315528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.1121540
X-RAY DIFFRACTIONr_chiral_restr0.1280.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022448
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.21340
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21977
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2154
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2610.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6431.51827
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.99922835
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.68731450
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5644.51288
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.396 74
Rwork0.291 1050
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)
13.919-1.8757-0.32136.79280.92233.23450.0264-0.29650.3180.16530.0283-0.0188-0.1017-0.0891-0.0547-0.157-0.0258-0.0158-0.0614-0.0068-0.06994.7652-1.703-0.6916
22.0233-1.0487-0.30613.16850.07963.37250.0755-0.0057-0.009-0.25230.0395-0.0510.09540.0283-0.115-0.05960.0017-0.0209-0.08170.032-0.079817.7646-17.3692-13.5413
37.9333-2.2825-1.24667.19594.58498.00970.0861-0.1201-0.2140.12730.2749-0.54330.54230.0298-0.361-0.1343-0.08590.0025-0.15950.0086-0.0640.849-9.2502-34.9508
43.1645-0.62-1.09863.90821.82154.8584-0.09110.11450.2055-0.06390.15-0.1423-0.2062-0.1393-0.0589-0.09040.00040.0081-0.04630.0346-0.0603-9.59978.9372-22.9717
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 80
2X-RAY DIFFRACTION1A200
3X-RAY DIFFRACTION2A87 - 171
4X-RAY DIFFRACTION3B1 - 80
5X-RAY DIFFRACTION4B87 - 171

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