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- PDB-1bd7: CIRCULARLY PERMUTED BB2-CRYSTALLIN -

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Basic information

Entry
Database: PDB / ID: 1bd7
TitleCIRCULARLY PERMUTED BB2-CRYSTALLIN
ComponentsCIRCULARLY PERMUTED BB2-CRYSTALLIN
KeywordsEYE-LENS PROTEIN / BETA-CRYSTALLIN B / MULTIGENE FAMILY
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
Beta-crystallin B2 / 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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsWright, G. / Basak, A.K. / Mayr, E.-M. / Glockshuber, R. / Slingsby, C.
CitationJournal: Protein Sci. / Year: 1998
Title: Circular permutation of betaB2-crystallin changes the hierarchy of domain assembly.
Authors: Wright, G. / Basak, A.K. / Wieligmann, K. / Mayr, E.M. / Slingsby, C.
History
DepositionMay 12, 1998Processing site: BNL
Revision 1.0Oct 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: 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 / software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CIRCULARLY PERMUTED BB2-CRYSTALLIN
B: CIRCULARLY PERMUTED BB2-CRYSTALLIN


Theoretical massNumber of molelcules
Total (without water)40,3072
Polymers40,3072
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.000, 48.500, 54.500
Angle α, β, γ (deg.)66.70, 74.90, 77.50
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99112, 0.07111, -0.11239), (0.07292, -0.99726, 0.01213), (-0.11122, -0.02021, -0.99359)
Vector: 1.31497, 3.17762, 25.53048)

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Components

#1: Protein CIRCULARLY PERMUTED BB2-CRYSTALLIN


Mass: 20153.424 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PROTEIN IN THE CRYSTAL LATTICE IS A DIMER / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Tissue: EYE-LENS / Cell line: BL21 / Plasmid: PETCPBB2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P62697
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 43 % / Description: TAKEN FROM WHOLE STRUCTURE
Crystal growpH: 6.1
Details: PROTEIN CONCENTRATION 6 MGS/ML. 0.10 ML OF 0.5M MES-NAOH, PH 6.1, 0.51 ML OF 40% (W/V) PEG 8K, 0.10 ML OF 2M AMMONIUM ACETATE, 0.29 ML OF WATER, AT ROOM-TEMPERATURE.
Temp details: room temp
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16 mg/mlprotein1drop0.002ml
240 %PEG80001reservoir0.51ml
32 Mammonium acetate1reservoir0.1ml
40.5 MMES1reservoir0.1ml, pH6.1
5water1reservoir0.29ml

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1996 / Details: MIRRORS
RadiationMonochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.78→26.88 Å / Num. obs: 7225 / % possible obs: 81.8 % / Redundancy: 1.9 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 6.6
Reflection shellResolution: 2.78→2.88 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.081 / Mean I/σ(I) obs: 7.7 / % possible all: 81.9

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BB2 (C-TERMINAL DOMAIN)

Resolution: 2.78→26.88 Å / Isotropic thermal model: RESTRAINT INDIVIDUALS / Cross valid method: THROUGHOUT
Details: CIRCULAR PERMUTATION OF THE TWO DOMAIN DIMER OF BB2-CRYSTALLIN CONVERTS INTERMOLECULAR DOMAIN PAIRING INTO INTRAMOLECULAR PAIRING, PROMOTING A HIGHER LEVEL QUATERNARY ORGANISATION. PHE 173 ...Details: CIRCULAR PERMUTATION OF THE TWO DOMAIN DIMER OF BB2-CRYSTALLIN CONVERTS INTERMOLECULAR DOMAIN PAIRING INTO INTRAMOLECULAR PAIRING, PROMOTING A HIGHER LEVEL QUATERNARY ORGANISATION. PHE 173 COULD NOT BE MODELED IN THE ELECTRON DENSITY AND HAS BEEN EXCLUDED FROM BOTH SUBUNITS.
RfactorNum. reflection% reflectionSelection details
Rfree0.278 394 5.45 %RANDOM
Rwork0.19 ---
obs0.19 7224 81.1 %-
Displacement parametersBiso mean: 29 Å2
Refine analyzeLuzzati d res low obs: 26.8 Å
Refinement stepCycle: LAST / Resolution: 2.78→26.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2797 0 0 22 2819
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.534
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.83
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.485
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev position: 0.136 Å / Weight position: 300
LS refinement shellResolution: 2.78→2.91 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.409 44 5.45 %
Rwork0.251 861 -
obs--81.9 %
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
Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.831
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.485

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