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- PDB-1a4e: CATALASE A FROM SACCHAROMYCES CEREVISIAE -

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Basic information

Entry
Database: PDB / ID: 1a4e
TitleCATALASE A FROM SACCHAROMYCES CEREVISIAE
ComponentsCATALASE A
KeywordsOXIDOREDUCTASE / CATALASE / PEROXIDASE
Function / homology
Function and homology information


: / catalase / catalase activity / peroxisomal matrix / response to reactive oxygen species / hydrogen peroxide catabolic process / response to hydrogen peroxide / peroxisome / mitochondrial matrix / heme binding ...: / catalase / catalase activity / peroxisomal matrix / response to reactive oxygen species / hydrogen peroxide catabolic process / response to hydrogen peroxide / peroxisome / mitochondrial matrix / heme binding / mitochondrion / 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 active site / Catalase proximal active site signature. / Catalase immune-responsive domain ...: / 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
AZIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Peroxisomal catalase A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMate, M.J.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Structure of catalase-A from Saccharomyces cerevisiae.
Authors: Mate, M.J. / Zamocky, M. / Nykyri, L.M. / Herzog, C. / Alzari, P.M. / Betzel, C. / Koller, F. / Fita, I.
History
DepositionJan 29, 1998Processing site: BNL
Revision 1.0Aug 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)225,32214
Polymers222,4964
Non-polymers2,82610
Water17,240957
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area47440 Å2
ΔGint-332 kcal/mol
Surface area56840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.172, 184.172, 304.977
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.4302, -0.3362, -0.8378), (-0.3438, -0.7971, 0.4964), (-0.8347, 0.5015, 0.2273)206.6273, 63.0117, 115.1995
2given(-0.9998, 0.02, -0.0081), (0.0201, 0.7208, -0.6929), (-0.008, -0.6929, -0.721)238.117, 27.6432, 75.6976
3given(0.429, 0.3223, 0.8438), (0.3212, -0.9275, 0.191), (0.8443, 0.1891, -0.5015)31.9415, -2.8987, -52.8178

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Components

#1: Protein
CATALASE A


Mass: 55623.930 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: PEROXISOMES / References: UniProt: P15202, catalase
#2: Chemical
ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: N3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 957 / 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: 3.35 Å3/Da / Density % sol: 60 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5 Mammonium sulfate1drop
20.2 MTris1drop
328 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Type: EMBL/DESY, HAMBURG / Wavelength: 0.928
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 123230 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 33.6 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 25.12
Reflection shellResolution: 2.35→2.39 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 5.69 / Rsym value: 0.33 / % possible all: 94.5
Reflection
*PLUS
Num. measured all: 1276062
Reflection shell
*PLUS
% possible obs: 95 %

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 7CAT

7cat


Resolution: 2.4→20 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.198 11084 10 %RANDOM
Rwork0.154 ---
obs0.154 110950 93.9 %-
Displacement parametersBiso mean: 33.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15724 0 188 960 16872
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
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_deg2.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.85
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.641.5
X-RAY DIFFRACTIONx_mcangle_it2.552
X-RAY DIFFRACTIONx_scbond_it3.142
X-RAY DIFFRACTIONx_scangle_it4.612.5
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.265 1106 10 %
Rwork0.239 9968 -
obs--95 %
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_deg24.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.85

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