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- PDB-3so0: Crystal structure of a mutant T41S of a betagamma-crystallin doma... -

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Basic information

Entry
Database: PDB / ID: 3so0
TitleCrystal structure of a mutant T41S of a betagamma-crystallin domain from Clostridium beijerinckii
ComponentsClostrillin
KeywordsMETAL BINDING PROTEIN / calcium-bound betagamma-crystallin
Function / homology
Function and homology information


carbohydrate binding / metal ion binding
Similarity search - Function
Beta-1,3-glucanase, N-terminal, subdomain 2 / Beta-1,3-glucanase, N-terminal / Glucan endo-1,3-beta-glucosidase / Beta-1,3-glucanase / Glycosyl hydrolases family 64 (GH64) domain profile. / : / Carbohydrate binding module family 56 / CBM56 (carbohydrate binding type-56) domain profile. / Crystallins / Gamma-B Crystallin; domain 1 ...Beta-1,3-glucanase, N-terminal, subdomain 2 / Beta-1,3-glucanase, N-terminal / Glucan endo-1,3-beta-glucosidase / Beta-1,3-glucanase / Glycosyl hydrolases family 64 (GH64) domain profile. / : / Carbohydrate binding module family 56 / CBM56 (carbohydrate binding type-56) domain profile. / Crystallins / Gamma-B Crystallin; domain 1 / Crystallins beta and gamma 'Greek key' motif profile. / Beta/gamma crystallins / Beta/gamma crystallin / Gamma-crystallin-like / Osmotin/thaumatin-like superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Beta and gamma crystallin
Similarity search - Component
Biological speciesClostridium beijerinckii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsSrivastava, S.S. / Sankaranarayanan, R.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Decoding the molecular design principles underlying Ca(2+) binding to beta gamma-crystallin motifs
Authors: Mishra, A. / Suman, S.K. / Srivastava, S.S. / Sankaranarayanan, R. / Sharma, Y.
History
DepositionJun 29, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
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_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: Clostrillin
B: Clostrillin
C: Clostrillin
D: Clostrillin
E: Clostrillin
F: Clostrillin
G: Clostrillin
H: Clostrillin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,95821
Polymers85,4378
Non-polymers52113
Water6,864381
1
A: Clostrillin
C: Clostrillin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5206
Polymers21,3592
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Clostrillin
D: Clostrillin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5206
Polymers21,3592
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Clostrillin
H: Clostrillin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4394
Polymers21,3592
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: Clostrillin
G: Clostrillin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4795
Polymers21,3592
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.579, 89.509, 101.567
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Clostrillin / Beta and gamma crystallin


Mass: 10679.602 Da / Num. of mol.: 8 / Fragment: betagamma-crystallin domain, UNP residues 118-213 / Mutation: T41S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium beijerinckii (bacteria) / Strain: NCIMB 8052 / Gene: Cbei_2825 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6LX94
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 1.717916 Å3/Da / Density % sol: 28.401621 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 25-30% PEG 3350, 0.1M HEPES, 0.1-0.2M lithium sulphate, pH 7.0-7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 13, 2010 / Details: VariMax optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 44875 / Redundancy: 4.2 % / Rsym value: 0.099 / Net I/σ(I): 14.2
Reflection shellResolution: 1.93→2 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.459

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
BALBESphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I9H

3i9h


Resolution: 1.93→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.038 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23804 2261 5 %RANDOM
Rwork0.19782 ---
obs0.19987 42558 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.262 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.93→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5310 0 13 381 5704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225459
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9871.9177478
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2425664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.59726.049243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59915814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0640.2820
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214184
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4281.53344
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.80825445
X-RAY DIFFRACTIONr_scbond_it1.04932115
X-RAY DIFFRACTIONr_scangle_it1.714.52033
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.931→1.981 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 167 -
Rwork0.256 3061 -
obs--98.53 %

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