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- PDB-3lwk: Crystal structure of human Beta-crystallin A4 (CRYBA4) -

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Basic information

Entry
Database: PDB / ID: 3lwk
TitleCrystal structure of human Beta-crystallin A4 (CRYBA4)
ComponentsBeta-crystallin A4
KeywordsSTRUCTURAL PROTEIN / Beta-crystallin / Structural Genomics Consortium / SGC / Cataract / Disease mutation / Eye lens protein / Microphthalmia / Oxidation / Phosphoprotein
Function / homology
Function and homology information


structural constituent of eye lens / camera-type eye development / lens development in camera-type eye / visual perception / identical protein binding
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
PHOSPHATE ION / Beta-crystallin A4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsChaikuad, A. / Shafqat, N. / Krojer, T. / Yue, W.W. / Cocking, R. / Vollmar, M. / Muniz, J.R.C. / Pike, A.C.W. / Arrowsmith, C.H. / Weigelt, J. ...Chaikuad, A. / Shafqat, N. / Krojer, T. / Yue, W.W. / Cocking, R. / Vollmar, M. / Muniz, J.R.C. / Pike, A.C.W. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / Bountra, C. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human Beta-crystallin A4 (CRYBA4)
Authors: Chaikuad, A. / Shafqat, N. / Krojer, T. / Yue, W.W. / Cocking, R. / Vollmar, M. / Muniz, J.R.C. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / Bountra, C. / Oppermann, U.
History
DepositionFeb 24, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-crystallin A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3677
Polymers21,8121
Non-polymers5556
Water3,423190
1
A: Beta-crystallin A4
hetero molecules

A: Beta-crystallin A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,73514
Polymers43,6242
Non-polymers1,11112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area2450 Å2
ΔGint-9 kcal/mol
Surface area16300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.790, 94.790, 90.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-1-

PO4

21A-3-

GOL

31A-258-

HOH

41A-270-

HOH

51A-286-

HOH

61A-315-

HOH

71A-331-

HOH

DetailsAUTHOR STATES THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN.

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Components

#1: Protein Beta-crystallin A4 / Beta-A4 crystallin


Mass: 21812.057 Da / Num. of mol.: 1 / Fragment: residues 8-196
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRYBA4 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: P53673
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 1.5M Ammonium Phosphate, 5% Glycerol, 0.1M Tris, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 25, 2009 / Details: Kirkpatrick Baez bimorph mirror pair
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.7→67.03 Å / Num. all: 22916 / Num. obs: 22910 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 13.6
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 8 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.8 / Num. unique all: 3284 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1oki

1oki


Resolution: 1.7→37.42 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.585 / SU ML: 0.054 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18823 1173 5.1 %RANDOM
Rwork0.16085 ---
all0.16085 22910 --
obs0.1622 21737 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.119 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.24 Å2
Refine analyzeLuzzati coordinate error obs: 0.187 Å
Refinement stepCycle: LAST / Resolution: 1.7→37.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1460 0 35 190 1685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211619
X-RAY DIFFRACTIONr_bond_other_d0.0020.021139
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.9222188
X-RAY DIFFRACTIONr_angle_other_deg0.9132728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4045199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.40523.22290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66615246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6831513
X-RAY DIFFRACTIONr_chiral_restr0.1020.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021845
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02381
X-RAY DIFFRACTIONr_mcbond_it1.6831.5933
X-RAY DIFFRACTIONr_mcbond_other0.5781.5392
X-RAY DIFFRACTIONr_mcangle_it2.80521485
X-RAY DIFFRACTIONr_scbond_it4.3293686
X-RAY DIFFRACTIONr_scangle_it6.594.5695
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 101 -
Rwork0.281 1565 -
obs--100 %
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)
10.88450.1311-0.20811.19280.36780.95550.0232-0.0152-0.05270.0587-0.0097-0.1190.05590.0073-0.01340.0441-0.0048-0.02510.00730.00130.046419.69898.650410.9077
20.43590.35580.35470.99230.57491.56070.0845-0.1737-0.01390.0936-0.0549-0.01810.112-0.232-0.02960.0223-0.0333-0.0160.09360.0050.046114.02218.541430.4692
32.07470.52531.05560.81150.79394.44750.1348-0.2557-0.14810.0673-0.0849-0.08250.4508-0.2087-0.04990.0471-0.0244-0.00750.03920.01190.033317.87919.562828.3531
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 82
2X-RAY DIFFRACTION2A88 - 179
3X-RAY DIFFRACTION3A184 - 196

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