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- PDB-1coj: FE-SOD FROM AQUIFEX PYROPHILUS, A HYPERTHERMOPHILIC BACTERIUM -

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Basic information

Entry
Database: PDB / ID: 1coj
TitleFE-SOD FROM AQUIFEX PYROPHILUS, A HYPERTHERMOPHILIC BACTERIUM
ComponentsPROTEIN (SUPEROXIDE DISMUTASE)
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding
Similarity search - Function
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 [Fe]
Similarity search - Component
Biological speciesAquifex pyrophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLim, J.H. / Yu, Y.G. / Kim, S.-H. / Cho, S.-J. / Ahn, B.Y. / Han, Y.S. / Cho, Y.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: The crystal structure of an Fe-superoxide dismutase from the hyperthermophile Aquifex pyrophilus at 1.9 A resolution: structural basis for thermostability.
Authors: Lim, J.H. / Yu, Y.G. / Han, Y.S. / Cho, S. / Ahn, B.Y. / Kim, S.H. / Cho, Y.
History
DepositionMay 28, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 14, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (SUPEROXIDE DISMUTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4322
Polymers24,3771
Non-polymers561
Water1,838102
1
A: PROTEIN (SUPEROXIDE DISMUTASE)
hetero molecules

A: PROTEIN (SUPEROXIDE DISMUTASE)
hetero molecules

A: PROTEIN (SUPEROXIDE DISMUTASE)
hetero molecules

A: PROTEIN (SUPEROXIDE DISMUTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7308
Polymers97,5064
Non-polymers2234
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area16310 Å2
ΔGint-55 kcal/mol
Surface area27870 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.700, 75.630, 87.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein PROTEIN (SUPEROXIDE DISMUTASE)


Mass: 24376.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex pyrophilus (bacteria) / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9X6W9
#2: Chemical ChemComp-FE / FE (III) 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.: 102 / 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: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of enzyme and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlenzyme1drop
220 mMphosphate1drop
330-35 %(v/v)methyl pentanediol1reservoir
4100 mMsodium acetate1reservoir
520 mMcalcium chloride1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 18506 / % possible obs: 98.4 % / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.146 / Rsym value: 0.161 / % possible all: 96.8
Reflection
*PLUS
Num. measured all: 100516
Reflection shell
*PLUS
% possible obs: 96.8 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→8 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Details: OCCUPANCY OF FE ION WAS REFINED AT THE LATER STAGE
RfactorNum. reflection% reflectionSelection details
Rfree0.2 -10 %RANDOM
Rwork0.17 ---
obs0.17 17793 95.7 %-
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1716 0 1 102 1819
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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