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- PDB-1qnn: Cambialistic superoxide dismutase from Porphyromonas gingivalis -

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Basic information

Entry
Database: PDB / ID: 1qnn
TitleCambialistic superoxide dismutase from Porphyromonas gingivalis
ComponentsSUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE
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 / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain
Similarity search - Domain/homology
: / Superoxide dismutase [Mn/Fe]
Similarity search - Component
Biological speciesPORPHYROMONAS GINGIVALIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSugio, S. / Hiraoka, B.Y. / Yamakura, F.
Citation
Journal: Eur.J.Biochem. / Year: 2000
Title: Crystal Structure of Cambialistic Superoxide Dismutase from Porphyromonas Gingivalis
Authors: Sugio, S. / Hiraoka, B.Y. / Yamakura, F.
#1: Journal: Eur.J.Biochem. / Year: 1998
Title: Inactivation and Destruction of Conserved Trp159 of Fe-Superoxide Dismutase from Porphyromonas Gingivalis by Hydrogen Peroxide
Authors: Yamakura, F. / Rardin, R.L. / Petsko, G.A. / Ringe, D. / Hiraoka, B.Y. / Nakayama, K. / Fujimura, T. / Taka, H. / Murayama, K.
#2: Journal: FEBS Lett. / Year: 1990
Title: The Primary Structure of Superoxide Dismutase Purified from Anaerobically Maintained Bacteroides Gingivalis
Authors: Amano, A. / Shizukuishi, S. / Tsunemitsu, A. / Maekawa, K. / Tsunemitsu, S.
#3: Journal: J.Bacteriol. / Year: 1990
Title: Characterization of Superoxide Dismutase Purified from Either Anaerobically Maintained or Aerated Bacteroides Gingivalis
Authors: Amano, A. / Shizukuishi, S. / Tamagawa, H. / Iwakura, K. / Tsunasawa, S. / Tsunemitsu, S.
History
DepositionOct 20, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Apr 10, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant
Revision 1.6May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.7Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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_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_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_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: SUPEROXIDE DISMUTASE
B: SUPEROXIDE DISMUTASE
C: SUPEROXIDE DISMUTASE
D: SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3368
Polymers86,1134
Non-polymers2234
Water7,855436
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-38 kcal/mol
Surface area38150 Å2
MethodPQS
Unit cell
Length a, b, c (Å)75.470, 102.660, 99.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.25611, -0.14686, -0.95543), (-0.14806, -0.98269, 0.11136), (-0.95524, 0.11294, -0.27342)89.17615, 112.99615, 100.2589
2given(-0.10262, -0.14021, 0.98479), (-0.13738, -0.97853, -0.15363), (0.98519, -0.15106, 0.08115)2.8558, 103.851, 18.22559
3given(-0.94388, 0.27076, 0.18916), (0.26912, 0.96248, -0.03482), (-0.19149, 0.01804, -0.98133)57.08716, 14.4361, 106.03601

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Components

#1: Protein
SUPEROXIDE DISMUTASE / FE/MN-SOD


Mass: 21528.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: EACH CHAIN CONTAINS ONE METAL ION (FE3+\:MN3+=3\:1).
Source: (gene. exp.) PORPHYROMONAS GINGIVALIS (bacteria) / Plasmid: PKD210 / Gene (production host): SOD / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): QC774 / References: UniProt: P19665, superoxide dismutase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: SOLUTION CONTAINING 6-9MG/ML PROTEIN AND 10MM TRIS/HCL (PH7.8) WERE USED FOR CRYSTALLIZATION. CRYSTALS WERE GROWN FROM HANGING DROPS SUSPENDED OVER A RESERVOIR SOLUTION CONTAINING 100MM ...Details: SOLUTION CONTAINING 6-9MG/ML PROTEIN AND 10MM TRIS/HCL (PH7.8) WERE USED FOR CRYSTALLIZATION. CRYSTALS WERE GROWN FROM HANGING DROPS SUSPENDED OVER A RESERVOIR SOLUTION CONTAINING 100MM POTASSIUM PHOSPHATE (PH5.8) AND 26-31% PEG4000 AT 293K WITHIN A FEW WEEKS., pH 5.80
Crystal grow
*PLUS
pH: 7.8 / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16-9 mg/mlprotein1drop
210 mMTris-HCl1drop
3100 mMpotassium phosphate1reservoir
426-31 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Aug 29, 1996 / Details: YALE MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.79→99.4 Å / Num. obs: 64134 / % possible obs: 88.2 % / Observed criterion σ(I): 0 / Redundancy: 5.64 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 11.6
Reflection shellResolution: 1.79→1.86 Å / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 2 / % possible all: 68.5
Reflection shell
*PLUS
% possible obs: 68.5 %

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
PROCESSdata reduction
PROCESSdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ISA

1isa


Resolution: 1.8→50 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: A RESOLUTION-DEPENDENT WEIGHTS AND BULK SOLVENT CORRECTION WERE APPLIED
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1927 3 %RANDOM
Rwork0.179 ---
obs0.179 63443 87.7 %-
Displacement parametersBiso mean: 31.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.18 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6096 0 4 436 6536
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.22
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.67
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.9991.5
X-RAY DIFFRACTIONx_mcangle_it1.5722
X-RAY DIFFRACTIONx_scbond_it1.5732
X-RAY DIFFRACTIONx_scangle_it2.3372.5
LS refinement shellResolution: 1.8→1.88 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.36 207 3.3 %
Rwork0.306 5976 -
obs--69.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2EXTRA.PAREXTRA.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.67

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