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- PDB-3hz2: Crystal structure of a betagamma-crystallin from an Archaea -

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Basic information

Entry
Database: PDB / ID: 3hz2
TitleCrystal structure of a betagamma-crystallin from an Archaea
ComponentsBeta/gama crystallin family protein
KeywordsMETAL BINDING PROTEIN / calcium-bound betagamma-crystallin
Function / homology
Function and homology information


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
Beta/gama crystallin family protein
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 Å
AuthorsAravind, P. / Sankaranarayanan, R.
CitationJournal: Biochemistry / Year: 2009
Title: The 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
DepositionJun 23, 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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

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Assembly

Deposited unit
A: Beta/gama crystallin family protein
B: Beta/gama crystallin family protein
C: Beta/gama crystallin family protein
D: Beta/gama crystallin family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,33312
Polymers37,0124
Non-polymers3218
Water8,107450
1
A: Beta/gama crystallin family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3333
Polymers9,2531
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta/gama crystallin family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3333
Polymers9,2531
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta/gama crystallin family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3333
Polymers9,2531
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta/gama crystallin family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3333
Polymers9,2531
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.300, 54.202, 54.179
Angle α, β, γ (deg.)85.810, 74.310, 74.320
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Beta/gama crystallin family protein / M-Crystallin


Mass: 9252.976 Da / Num. of mol.: 4 / Fragment: UNP residues 37-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans (archaea) / Strain: C2A / Gene: 1474415 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8TMX3
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 2.15 Å3/Da / Density % sol: 42.92 % / Mosaicity: 0.594 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12% PEG 20000, 0.1M NaMES, pH6.5, temperature 298K, VAPOR DIFFUSION, SITTING DROP

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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: Jan 29, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.86→25 Å / Num. obs: 24461 / % possible obs: 94.1 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.037 / Χ2: 1.176 / Net I/σ(I): 28.857
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.86-1.932.40.1058.0722590.82786.4
1.93-22.60.07724150.80792.1
2-2.092.60.0624280.87492.5
2.09-2.212.60.05523540.92493.3
2.21-2.342.60.0524560.9493.9
2.34-2.522.60.04724241.02894.8
2.52-2.782.60.04224891.26295.4
2.78-3.182.60.03525411.30796.4
3.18-42.60.02925031.78297.4
4-252.60.02525921.85998.7

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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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BV2

2bv2


Resolution: 1.86→25 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1214 4.7 %RANDOM
Rwork0.172 ---
obs-24457 94.3 %-
Solvent computationBsol: 42.207 Å2
Displacement parametersBiso max: 55.4 Å2 / Biso mean: 15.638 Å2 / Biso min: 5.04 Å2
Baniso -1Baniso -2Baniso -3
1-3.506 Å20.387 Å21.049 Å2
2---1.282 Å20 Å2
3----2.224 Å2
Refinement stepCycle: LAST / Resolution: 1.86→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2624 0 8 450 3082
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.00511.5
X-RAY DIFFRACTIONc_angle_deg1.092
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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