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- PDB-1gwe: Atomic resolution structure of Micrococcus Lysodeikticus catalase -

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Basic information

Entry
Database: PDB / ID: 1gwe
TitleAtomic resolution structure of Micrococcus Lysodeikticus catalase
ComponentsCatalase
KeywordsOXIDOREDUCTASE / CATALASE / HDYROGEN-PEROXIDE:HYDROGEN PEROXIDE OXIDOREDUCTASE
Function / homology
Function and homology information


catalase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / metal ion binding / cytoplasm
Similarity search - Function
Catalase, clade 3 / 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 active site / Catalase proximal active site signature. / Catalase immune-responsive domain ...Catalase, clade 3 / 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 active site / Catalase proximal active site signature. / Catalase immune-responsive domain / Catalase-related immune-responsive / 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 speciesMicrococcus luteus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 0.88 Å
AuthorsMurshudov, G.N. / Grebenko, A.I. / Brannigan, J.A. / Antson, A.A. / Barynin, V.V. / Dodson, G.G. / Dauter, Z. / Wilson, K.S. / Melik-Adamyan, W.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: The Structures of Micrococcus Lysodeikticus Catalase, its Ferryl Intermediate (Compound II) and Nadph Complex.
Authors: Murshudov, G.N. / Grebenko, A.I. / Brannigan, J.A. / Antson, A.A. / Barynin, V.V. / Dodson, G.G. / Dauter, Z. / Wilson, K.S. / Melik-Adamyan, W.R.
History
DepositionMar 15, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Jun 20, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / diffrn_source ...citation / diffrn_source / entity / entity_src_nat / pdbx_struct_special_symmetry / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.page_last / _diffrn_source.pdbx_synchrotron_site ..._citation.page_last / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _entity_src_nat.common_name / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _entity_src_nat.pdbx_organism_scientific / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.3Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8675
Polymers56,9631
Non-polymers9054
Water15,817878
1
A: Catalase
hetero molecules

A: Catalase
hetero molecules

A: Catalase
hetero molecules

A: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,46920
Polymers227,8504
Non-polymers3,61916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation7_555y,x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)105.785, 105.785, 105.001
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-2095-

HOH

21A-2226-

HOH

31A-2725-

HOH

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Components

#1: Protein Catalase /


Mass: 56962.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Micrococcus luteus (bacteria) / References: UniProt: P29422, catalase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 878 / 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: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growpH: 5.2 / Details: pH 5.20

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8906
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8906 Å / Relative weight: 1
ReflectionResolution: 0.882→74.536 Å / Num. obs: 457407 / % possible obs: 99.2 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 24.4
Reflection shellResolution: 0.88→0.89 Å / Redundancy: 3 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 3.44 / % possible all: 88.8

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Processing

Software
NameVersionClassification
REFMAC5.1.11refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 0.88→74.54 Å / Cor.coef. Fo:Fc: 0.989 / Cor.coef. Fo:Fc free: 0.988 / SU B: 0.067 / SU ML: 0.004 / Cross valid method: THROUGHOUT / ESU R: 0.009 / ESU R Free: 0.009 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.096 22913 5 %RANDOM
Rwork0.089 ---
obs0.089 433749 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 0.88→74.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3981 0 58 878 4917
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0214398
X-RAY DIFFRACTIONr_bond_other_d0.0020.023767
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.9521.9546007
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1.28638802
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr6.5865506
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024935
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02936
X-RAY DIFFRACTIONr_nbd_refined0.2320.2826
X-RAY DIFFRACTIONr_nbd_other0.2770.24257
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0810.22090
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2630.2462
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.241
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3380.2304
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4620.2131
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2341.52552
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.81624162
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.45631846
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5394.51843
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 0.88→0.91 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.192 1622
Rwork0.184 30226

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