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- PDB-5ht7: Crystal structure of a transition-metal-ion-binding betagamma-cry... -

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Basic information

Entry
Database: PDB / ID: 5ht7
TitleCrystal structure of a transition-metal-ion-binding betagamma-crystallin from Methanosaeta thermophila
ComponentsUncharacterized protein
KeywordsMETAL BINDING PROTEIN / Novel transition-metal-binding protein / betagamma-crystallin
Function / homologyBeta/Gamma crystallin / Beta/gamma crystallin / Gamma-crystallin-like / metal ion binding / : / Beta/gamma crystallin 'Greek key' domain-containing protein
Function and homology information
Biological speciesMethanosaeta thermophila PT (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.862 Å
AuthorsSrivastava, S.S. / Sankaranarayanan, R.
CitationJournal: Biochemistry / Year: 2017
Title: A Transition Metal-Binding, Trimeric beta gamma-Crystallin from Methane-Producing Thermophilic Archaea, Methanosaeta thermophila
Authors: Srivastava, S.S. / Jamkhindikar, A.A. / Raman, R. / Jobby, M.K. / Chadalawada, S. / Sankaranarayanan, R. / Sharma, Y.
History
DepositionJan 26, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5734
Polymers27,5173
Non-polymers561
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-36 kcal/mol
Surface area11340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.732, 52.821, 51.718
Angle α, β, γ (deg.)90.00, 100.48, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-241-

HOH

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Components

#1: Protein Uncharacterized protein / Methallin


Mass: 9172.340 Da / Num. of mol.: 3 / Fragment: UNP residues 57-138
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosaeta thermophila PT (archaea) / Strain: NBRC 101360 / PT / Gene: Mthe_0038 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0B567
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 15-20% PEG, 0.1 M Tris-Cl, 0.01 M NiCl2 / PH range: 8.0-9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54178 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.86→25 Å / Num. obs: 20985 / % possible obs: 98.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 26.15 Å2 / Rmerge(I) obs: 0.045 / Χ2: 0.849 / Net I/av σ(I): 29.474 / Net I/σ(I): 16.8 / Num. measured all: 89114
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.86-1.933.70.3063.1191.2
1.93-24.20.218198.7
2-2.094.20.161199.1
2.09-2.214.30.115199.5
2.21-2.344.30.097199.7
2.34-2.524.30.084199.9
2.52-2.784.30.0611100
2.78-3.184.40.0441100
3.18-44.40.0331100
4-254.30.0281100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
HKL-2000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.862→24.25 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2198 1009 4.81 %
Rwork0.1824 --
obs0.1842 20983 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.862→24.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1914 0 1 136 2051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071965
X-RAY DIFFRACTIONf_angle_d0.9612667
X-RAY DIFFRACTIONf_dihedral_angle_d11.926702
X-RAY DIFFRACTIONf_chiral_restr0.04279
X-RAY DIFFRACTIONf_plane_restr0.004354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8623-1.96040.2741320.20552736X-RAY DIFFRACTION95
1.9604-2.08320.25171420.17072829X-RAY DIFFRACTION99
2.0832-2.24390.23571610.1732827X-RAY DIFFRACTION99
2.2439-2.46950.25841350.18052881X-RAY DIFFRACTION100
2.4695-2.82640.19841530.18282852X-RAY DIFFRACTION100
2.8264-3.55920.19831460.16982888X-RAY DIFFRACTION100
3.5592-24.25220.21571400.19162961X-RAY DIFFRACTION100

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