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- PDB-1m7s: Crystal Structure Analysis of Catalase CatF of Pseudomonas syringae -

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Basic information

Entry
Database: PDB / ID: 1m7s
TitleCrystal Structure Analysis of Catalase CatF of Pseudomonas syringae
ComponentsCatalase
KeywordsOXIDOREDUCTASE / BETA BARREL / ALPHA HELICAL DOMAIN
Function / homology
Function and homology information


catalase / catalase activity / hydrogen peroxide catabolic process / response to hydrogen peroxide / periplasmic space / heme binding / metal ion binding / cytoplasm
Similarity search - Function
Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase active site / Catalase proximal active site signature. ...Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase active site / Catalase proximal active site signature. / Catalase core domain / Catalase, mono-functional, haem-containing / Catalase / catalase family profile. / Catalase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Catalase
Similarity search - Component
Biological speciesPseudomonas syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCarpena, X. / Soriano, M. / Klotz, M.G. / Duckworth, H.W. / Donald, L.J. / Melik-Adamyan, W. / Fita, I. / Loewen, P.C.
CitationJournal: Proteins / Year: 2003
Title: Structure of the Clade 1 catalase, CatF of Pseudomonas syringae, at 1.8 A resolution
Authors: Carpena, X. / Soriano, M. / Klotz, M.G. / Duckworth, H.W. / Donald, L.J. / Melik-Adamyan, W. / Fita, I. / Loewen, P.C.
History
DepositionJul 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Remark 999SEQUENCE ACCORDING TO THE AUTHOR, THERE WERE ERRORS IN THE ORIGINAL DNA SEQUENCE. THE SEQUENCE ...SEQUENCE ACCORDING TO THE AUTHOR, THERE WERE ERRORS IN THE ORIGINAL DNA SEQUENCE. THE SEQUENCE PRESENTED IN THE ENTRY IS CORRECT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catalase
B: Catalase
C: Catalase
D: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,6358
Polymers216,1694
Non-polymers2,4664
Water38,3542129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area46030 Å2
ΔGint-203 kcal/mol
Surface area57850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.630, 153.870, 109.190
Angle α, β, γ (deg.)90.00, 102.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Catalase


Mass: 54042.305 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae (bacteria) / Gene: CATF / Plasmid: pEC3E56 / Production host: Escherichia coli (E. coli) / Strain (production host): UM255 / References: UniProt: P46206, catalase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2129 / 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: 46.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 4000, sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16 mg/mlprotein1drop
212 %PEG40001reservoir
30.1 Msodium cacodylate1reservoirpH6.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 21, 1999
RadiationMonochromator: DIAMOND CRYSTALS [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 175279 / Num. obs: 175279 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.6 Å2 / Rsym value: 0.084
Reflection shellResolution: 1.8→1.87 Å / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.9 / Num. unique all: 17810 / Rsym value: 0.21 / % possible all: 95.1
Reflection
*PLUS
Lowest resolution: 21.9 Å / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
% possible obs: 95.1 % / Num. unique obs: 17810 / Rmerge(I) obs: 0.21

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→21.9 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.24 8773 Random
Rwork0.187 --
all0.183 175279 -
obs0.183 166506 -
Refinement stepCycle: LAST / Resolution: 1.8→21.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15260 0 172 2129 17561
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.241
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.011
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg2.1
LS refinement shell
*PLUS
Rfactor Rfree: 0.294 / Num. reflection Rfree: 900 / Rfactor Rwork: 0.234 / Num. reflection Rwork: 16910

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