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- PDB-4aj9: Catalase 3 from Neurospora crassa -

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Basic information

Entry
Database: PDB / ID: 4aj9
TitleCatalase 3 from Neurospora crassa
ComponentsCATALASE-3
KeywordsOXIDOREDUCTASE / PEROXIDASE
Function / homology
Function and homology information


catalase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / metal ion binding / cytosol
Similarity search - Function
Catalase, four-helical domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Large catalase, C-terminal domain / Catalase, mono-functional, haem-containing, clade 2, helical domain / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase / Catalase immune-responsive domain ...Catalase, four-helical domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Large catalase, C-terminal domain / Catalase, mono-functional, haem-containing, clade 2, helical domain / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / 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 / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Up-down Bundle / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / Catalase-3
Similarity search - Component
Biological speciesNEUROSPORA CRASSA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsZarate-Romero, A. / Rudino-Pinera, E.
CitationJournal: Arch.Biochem.Biophys. / Year: 2019
Title: X-ray driven reduction of Cpd I of Catalase-3 from N. crassa reveals differential sensitivity of active sites and formation of ferrous state.
Authors: Zarate-Romero, A. / Stojanoff, V. / Cohen, A.E. / Hansberg, W. / Rudino-Pinera, E.
History
DepositionFeb 16, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Other
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_database_status
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_database_status.recvd_author_approval
Revision 1.2Dec 20, 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 / struct_conn / struct_sheet / 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 / _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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CATALASE-3
B: CATALASE-3
C: CATALASE-3
D: CATALASE-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,22640
Polymers302,5694
Non-polymers8,65736
Water38,1022115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area61700 Å2
ΔGint-283.6 kcal/mol
Surface area71210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.750, 154.190, 160.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
CATALASE-3


Mass: 75642.211 Da / Num. of mol.: 4 / Fragment: RESIDUES 38-719
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEUROSPORA CRASSA (fungus) / Strain: 74-ORS23-1A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9C169, 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: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical...
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2115 / 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: 2.6 Å3/Da / Density % sol: 52.69 % / Description: NONE
Crystal growpH: 6.6
Details: 0.1 M MES PH 6.6, 20 % PEG 3350, 0.2 M AMMONIUM TARTRATE DIBASIC

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 8, 2011
Details: DOUBLE CRYSTAL CHANNEL CUT, SI(111), 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING.
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 269226 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 3.56 % / Biso Wilson estimate: 10.08 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.56
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 2.66 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.3 / % possible all: 87.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EJ6

3ej6


Resolution: 1.85→29.7 Å / SU ML: 0.47 / σ(F): 0.24 / Phase error: 20.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2176 13543 5 %
Rwork0.1775 --
obs0.1795 268553 97.81 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.441 Å2 / ksol: 0.388 e/Å3
Displacement parametersBiso mean: 11.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.0419 Å20 Å20 Å2
2---0.0166 Å20 Å2
3----0.0253 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21302 0 336 2115 23753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722515
X-RAY DIFFRACTIONf_angle_d1.07530577
X-RAY DIFFRACTIONf_dihedral_angle_d14.2338147
X-RAY DIFFRACTIONf_chiral_restr0.0753198
X-RAY DIFFRACTIONf_plane_restr0.0054075
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8502-1.87120.29313900.25087205X-RAY DIFFRACTION83
1.8712-1.89330.28133990.24597797X-RAY DIFFRACTION91
1.8933-1.91630.32874240.27067853X-RAY DIFFRACTION91
1.9163-1.94060.28774570.24858310X-RAY DIFFRACTION96
1.9406-1.96610.26514560.20878525X-RAY DIFFRACTION99
1.9661-1.9930.25324720.2038532X-RAY DIFFRACTION100
1.993-2.02150.26234610.20358629X-RAY DIFFRACTION99
2.0215-2.05170.26434470.20298582X-RAY DIFFRACTION99
2.0517-2.08370.27664840.2348397X-RAY DIFFRACTION98
2.0837-2.11790.2294910.17858551X-RAY DIFFRACTION99
2.1179-2.15440.23924790.1768532X-RAY DIFFRACTION99
2.1544-2.19360.2384500.17358565X-RAY DIFFRACTION99
2.1936-2.23570.23864590.1868578X-RAY DIFFRACTION99
2.2357-2.28140.28744430.23288392X-RAY DIFFRACTION97
2.2814-2.33090.21734220.16628581X-RAY DIFFRACTION99
2.3309-2.38510.20564010.1698632X-RAY DIFFRACTION99
2.3851-2.44480.22174680.17248585X-RAY DIFFRACTION99
2.4448-2.51080.22524790.16368599X-RAY DIFFRACTION99
2.5108-2.58470.18914210.15748648X-RAY DIFFRACTION99
2.5847-2.66810.21374460.16728610X-RAY DIFFRACTION99
2.6681-2.76330.21074670.16478610X-RAY DIFFRACTION99
2.7633-2.87390.19364490.16138647X-RAY DIFFRACTION99
2.8739-3.00460.21054520.17048669X-RAY DIFFRACTION99
3.0046-3.16280.19364750.16678631X-RAY DIFFRACTION99
3.1628-3.36070.19294810.16868626X-RAY DIFFRACTION99
3.3607-3.61980.19244430.16248650X-RAY DIFFRACTION99
3.6198-3.98330.17724540.14898595X-RAY DIFFRACTION98
3.9833-4.55790.14484330.12928721X-RAY DIFFRACTION99
4.5579-5.73570.16224750.14438778X-RAY DIFFRACTION99
5.7357-29.70420.23564650.28980X-RAY DIFFRACTION98

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