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- PDB-3i9h: Crystal structure of a betagamma-crystallin domain from Clostridi... -

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Basic information

Entry
Database: PDB / ID: 3i9h
TitleCrystal structure of a betagamma-crystallin domain from Clostridium beijerinckii
ComponentsBeta and gamma crystallin
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 / Glycosyl hydrolases family 64 (GH64) domain profile. / Beta-1,3-glucanase, N-terminal / Glucan endo-1,3-beta-glucosidase / Beta-1,3-glucanase / : / CBM56 (carbohydrate binding type-56) domain profile. / Crystallins / Gamma-B Crystallin; domain 1 / Crystallins beta and gamma 'Greek key' motif profile. ...Beta-1,3-glucanase, N-terminal, subdomain 2 / Glycosyl hydrolases family 64 (GH64) domain profile. / Beta-1,3-glucanase, N-terminal / Glucan endo-1,3-beta-glucosidase / Beta-1,3-glucanase / : / 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 / molecular replacement / Resolution: 2 Å
AuthorsAravind, P. / Sankaranarayanan, R.
CitationJournal: Biochemistry / Year: 2009
Title: betagamma-Crystallin superfamily contains a universal motif for binding calcium.
Authors: Aravind, P. / Mishra, A. / Suman, S.K. / Jobby, M.K. / Sankaranarayanan, R. / Sharma, Y.
History
DepositionJul 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 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_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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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: Beta and gamma crystallin
B: Beta and gamma crystallin
C: Beta and gamma crystallin
D: Beta and gamma crystallin
E: Beta and gamma crystallin
F: Beta and gamma crystallin
G: Beta and gamma crystallin
H: Beta and gamma crystallin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,19124
Polymers78,5508
Non-polymers64116
Water14,880826
1
A: Beta and gamma crystallin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8993
Polymers9,8191
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta and gamma crystallin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8993
Polymers9,8191
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta and gamma crystallin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8993
Polymers9,8191
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta and gamma crystallin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8993
Polymers9,8191
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Beta and gamma crystallin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8993
Polymers9,8191
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Beta and gamma crystallin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8993
Polymers9,8191
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Beta and gamma crystallin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8993
Polymers9,8191
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Beta and gamma crystallin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8993
Polymers9,8191
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.500, 103.710, 105.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Beta and gamma crystallin


Mass: 9818.711 Da / Num. of mol.: 8 / Fragment: UNP residues 119-206
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium beijerinckii (bacteria) / Strain: NCIMB 8052 / Gene: 5294019 / 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.: 16 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 826 / 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: 2.34 Å3/Da / Density % sol: 47.52 % / Mosaicity: 0.79 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 26% PEG3350, 0.1M HEPES, 0.2M Li2SO4, pH7.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 49951 / % possible obs: 98.7 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.074 / Χ2: 0.773 / Net I/σ(I): 10.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.074.20.36547240.58795.4
2.07-2.154.50.27748440.60496.7
2.15-2.254.50.23548480.61996.9
2.25-2.374.70.19949180.65298.5
2.37-2.524.90.16750130.64999.8
2.52-2.715.10.13250250.684100
2.71-2.995.20.10150470.83100
2.99-3.425.20.06750710.845100
3.42-4.35.20.04751231.041100
4.3-2550.03753381.06199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NPS
Resolution: 2→25 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.262 2547 5 %
Rwork0.206 --
obs-49895 98.6 %
Solvent computationBsol: 48.117 Å2
Displacement parametersBiso max: 58.27 Å2 / Biso mean: 26.65 Å2 / Biso min: 11.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å20 Å2
2---0.086 Å20 Å2
3---0.916 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5495 0 16 826 6337
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.00541.5
X-RAY DIFFRACTIONc_angle_deg1.112
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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