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- PDB-2wj7: human alphaB crystallin -

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Basic information

Entry
Database: PDB / ID: 2wj7
Titlehuman alphaB crystallin
ComponentsALPHA-CRYSTALLIN B CHAINCRYAB
KeywordsCHAPERONE / DESMIN-RELATED MYOPATHY / PHOSPHOPROTEIN / DISEASE MUTATION / EYE LENS PROTEIN / METHYLATION / POLYMORPHISM / GLYCOPROTEIN / CATARACT / OXIDATION / ACETYLATION
Function / homology
Function and homology information


microtubule polymerization or depolymerization / negative regulation of intracellular transport / apoptotic process involved in morphogenesis / cardiac myofibril / regulation of programmed cell death / tubulin complex assembly / structural constituent of eye lens / negative regulation of amyloid fibril formation / M band / lens development in camera-type eye ...microtubule polymerization or depolymerization / negative regulation of intracellular transport / apoptotic process involved in morphogenesis / cardiac myofibril / regulation of programmed cell death / tubulin complex assembly / structural constituent of eye lens / negative regulation of amyloid fibril formation / M band / lens development in camera-type eye / muscle organ development / actin filament bundle / HSF1-dependent transactivation / negative regulation of reactive oxygen species metabolic process / negative regulation of protein-containing complex assembly / stress-activated MAPK cascade / muscle contraction / synaptic membrane / response to hydrogen peroxide / cellular response to gamma radiation / negative regulation of cell growth / Z disc / unfolded protein binding / protein folding / response to estradiol / amyloid-beta binding / response to heat / perikaryon / protein refolding / microtubule binding / dendritic spine / lysosome / response to hypoxia / protein stabilization / axon / negative regulation of gene expression / negative regulation of DNA-templated transcription / protein-containing complex binding / negative regulation of apoptotic process / structural molecule activity / cell surface / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Alpha-crystallin B chain, ACD domain / Alpha-crystallin, N-terminal / Alpha crystallin A chain, N terminal / Alpha crystallin/Small heat shock protein, animal type / Immunoglobulin-like - #790 / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / Immunoglobulin-like ...Alpha-crystallin B chain, ACD domain / Alpha-crystallin, N-terminal / Alpha crystallin A chain, N terminal / Alpha crystallin/Small heat shock protein, animal type / Immunoglobulin-like - #790 / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Alpha-crystallin B chain
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.631 Å
AuthorsNaylor, C.E. / Bagneris, C. / Bateman, O.A. / Cronin, N. / Keep, N.H. / Slingsby, C.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal Structures of Alpha-Crystallin Domain Dimers of Alphab-Crystallin and Hsp20.
Authors: Bagneris, C. / Bateman, O.A. / Naylor, C.E. / Cronin, N. / Boelens, W.C. / Keep, N.H. / Slingsby, C.
History
DepositionMay 22, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-CRYSTALLIN B CHAIN
B: ALPHA-CRYSTALLIN B CHAIN
C: ALPHA-CRYSTALLIN B CHAIN
D: ALPHA-CRYSTALLIN B CHAIN
E: ALPHA-CRYSTALLIN B CHAIN


Theoretical massNumber of molelcules
Total (without water)53,6465
Polymers53,6465
Non-polymers00
Water1,53185
1
A: ALPHA-CRYSTALLIN B CHAIN


Theoretical massNumber of molelcules
Total (without water)10,7291
Polymers10,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ALPHA-CRYSTALLIN B CHAIN


Theoretical massNumber of molelcules
Total (without water)10,7291
Polymers10,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: ALPHA-CRYSTALLIN B CHAIN


Theoretical massNumber of molelcules
Total (without water)10,7291
Polymers10,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: ALPHA-CRYSTALLIN B CHAIN


Theoretical massNumber of molelcules
Total (without water)10,7291
Polymers10,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: ALPHA-CRYSTALLIN B CHAIN


Theoretical massNumber of molelcules
Total (without water)10,7291
Polymers10,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)49.460, 66.070, 190.970
Angle α, β, γ (deg.)90.00, 92.68, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
12
22
13
23
33
14
24

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 12:32 OR RESSEQ 34:39 OR RESSEQ...
211CHAIN B AND (RESSEQ 12:32 OR RESSEQ 34:39 OR RESSEQ...
311CHAIN C AND (RESSEQ 12:32 OR RESSEQ 34:39 OR RESSEQ...
411CHAIN D AND (RESSEQ 14:32 OR RESSEQ 34:39 OR RESSEQ...
511CHAIN E AND (RESSEQ 12:32 OR RESSEQ 34:39 OR RESSEQ...
112CHAIN A AND (RESSEQ 3:11 )
212CHAIN C AND (RESSEQ 3:11 )
113CHAIN A AND (RESSEQ 61:77 )
213CHAIN C AND (RESSEQ 61:77 )
313CHAIN E AND (RESSEQ 61:77 )
114CHAIN B AND (RESSEQ 61:77 )
214CHAIN D AND (RESSEQ 61:77 )

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(-0.531, 0.834, 0.149), (0.836, 0.486, 0.257), (0.142, 0.261, -0.955)24.54846, -19.67877, 34.96871
2given(0.28427, 0.94882, 0.13759), (-0.95103, 0.29724, -0.08483), (-0.12139, -0.10674, 0.98685)4.76706, 23.9114, 40.89516
3given(0.67205, 0.71758, 0.18285), (0.72943, -0.68404, 0.00349), (0.12758, 0.13103, -0.98313)-2.80537, -7.61084, 74.04976
4given(-0.87669, 0.4795, 0.03864), (-0.47644, -0.8544, -0.20737), (-0.06641, -0.20021, 0.9775)35.02455, 21.46771, 78.21479

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Components

#1: Protein
ALPHA-CRYSTALLIN B CHAIN / CRYAB / ALPHA(B)-CRYSTALLIN / ROSENTHAL FIBER COMPONENT / HEAT SHOCK PROTEIN BETA-5 / HSPB5 / RENAL ...ALPHA(B)-CRYSTALLIN / ROSENTHAL FIBER COMPONENT / HEAT SHOCK PROTEIN BETA-5 / HSPB5 / RENAL CARCINOMA ANTIGEN NY-REN-27 / HUMAN ALPHAB


Mass: 10729.104 Da / Num. of mol.: 5 / Fragment: ALPHA-CRYSTALLIN DOMAIN, RESIDUES 67-157
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02511
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS RESIDUES 67-157 PRECEDED BY A GAM TAG

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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: 2.9 Å3/Da / Density % sol: 57.7 % / Description: NONE
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 4 DAYS AT 16 DEGREESC IN 100 MM BICINE PH 9.0, 55% 2-METHYL-2,4-PENTANDIOL, AT A PROTEIN CONCENTRATION OF 20 MG/ML USING 1 UL PROTEIN SOLUTION AND 2 UL RESERVOIR SOLUTION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0066
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 30, 2008
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0066 Å / Relative weight: 1
ReflectionResolution: 2.63→190 Å / Num. obs: 17862 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 68.8 Å2 / Rmerge(I) obs: 0.22 / Net I/σ(I): 9.6
Reflection shellResolution: 2.63→2.77 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.9 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WJ5

2wj5


Resolution: 2.631→39.034 Å / SU ML: 0.56 / σ(F): 1.34 / Phase error: 36.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.32 912 5.1 %
Rwork0.2516 --
obs0.2553 17813 96.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.9 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 61.2 Å2
Baniso -1Baniso -2Baniso -3
1-4.09 Å20 Å21.485 Å2
2--6.8857 Å2-0 Å2
3----10.9757 Å2
Refinement stepCycle: LAST / Resolution: 2.631→39.034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2953 0 0 85 3038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0223013
X-RAY DIFFRACTIONf_angle_d2.0714086
X-RAY DIFFRACTIONf_dihedral_angle_d18.9061076
X-RAY DIFFRACTIONf_chiral_restr0.119470
X-RAY DIFFRACTIONf_plane_restr0.008538
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A370X-RAY DIFFRACTIONPOSITIONAL
12B370X-RAY DIFFRACTIONPOSITIONAL0.146
13C373X-RAY DIFFRACTIONPOSITIONAL0.125
14D352X-RAY DIFFRACTIONPOSITIONAL0.14
15E376X-RAY DIFFRACTIONPOSITIONAL0.135
21A62X-RAY DIFFRACTIONPOSITIONAL
22C62X-RAY DIFFRACTIONPOSITIONAL0.134
31A114X-RAY DIFFRACTIONPOSITIONAL
32C114X-RAY DIFFRACTIONPOSITIONAL0.137
33E120X-RAY DIFFRACTIONPOSITIONAL0.148
41B117X-RAY DIFFRACTIONPOSITIONAL
42D117X-RAY DIFFRACTIONPOSITIONAL0.085
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6311-2.76980.36861180.26362192X-RAY DIFFRACTION87
2.7698-2.94320.38231160.27862391X-RAY DIFFRACTION96
2.9432-3.17040.42131190.29252451X-RAY DIFFRACTION98
3.1704-3.48930.30161370.23872456X-RAY DIFFRACTION99
3.4893-3.99370.31331230.20152452X-RAY DIFFRACTION99
3.9937-5.030.25861590.19482466X-RAY DIFFRACTION98
5.03-39.03830.31231400.28512493X-RAY DIFFRACTION98

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