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- PDB-1ues: Crystal structure of Porphyromonas gingivalis SOD -

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Basic information

Entry
Database: PDB / ID: 1ues
TitleCrystal structure of Porphyromonas gingivalis SOD
Componentssuperoxide dismutase
KeywordsOXIDOREDUCTASE / metal-specific / cambialistic / superoxide dismutase / SOD
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding
Similarity search - Function
Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Manganese/iron superoxide dismutase, N-terminal domain superfamily
Similarity search - Domain/homology
: / Superoxide dismutase [Mn/Fe]
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYamakura, F. / Sugio, S. / Hiraoka, B.Y. / Yokota, T. / Ohmori, D.
Citation
Journal: Biochemistry / Year: 2003
Title: Pronounced conversion of the metal-specific activity of superoxide dismutase from Porphyromonas gingivalis by the mutation of a single amino acid (Gly155Thr) located apart from the active site
Authors: Yamakura, F. / Sugio, S. / Hiraoka, B.Y. / Ohmori, D. / Yokota, T.
#1: Journal: EUR.J.BIOCHEM. / Year: 2000
Title: Crystal structure of cambialistic superoxide dismutase from Porphyromonas gingivalis
Authors: Sugio, S. / Hiraoka, B.Y. / Yamakura, F.
History
DepositionMay 20, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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.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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: superoxide dismutase
B: superoxide dismutase
C: superoxide dismutase
D: superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5088
Polymers86,2894
Non-polymers2204
Water6,341352
1
A: superoxide dismutase
B: superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2544
Polymers43,1442
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-20 kcal/mol
Surface area15610 Å2
MethodPISA
2
C: superoxide dismutase
D: superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2544
Polymers43,1442
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-13 kcal/mol
Surface area16280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.68, 95.12, 98.75
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
superoxide dismutase / / SOD


Mass: 21572.186 Da / Num. of mol.: 4 / Mutation: G155T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P19665, superoxide dismutase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 1.95 Å3/Da / Density % sol: 36.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: PEG4000, potassium phosphate , pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.836 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Sep 28, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.836 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 568538 / Num. obs: 84510 / % possible obs: 76 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.055

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
X-PLORmodel building
X-PLOR98.1refinement
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rfree0.25 -
Rwork0.221 -
all-74648
obs-74648
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6116 0 4 352 6472

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