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- PDB-3zj5: NEUROSPORA CRASSA CATALASE-3 EXPRESSED IN E. COLI, ORTHORHOMBIC FORM. -

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Basic information

Entry
Database: PDB / ID: 3zj5
TitleNEUROSPORA CRASSA CATALASE-3 EXPRESSED IN E. COLI, ORTHORHOMBIC FORM.
ComponentsCATALASE-3
KeywordsOXIDOREDUCTASE / HYDROGEN PEROXIDE / 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
2-(2-ETHOXYETHOXY)ETHANOL / PROTOPORPHYRIN IX CONTAINING FE / D(-)-TARTARIC ACID / Catalase-3
Similarity search - Component
Biological speciesNEUROSPORA CRASSA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsZarate-Romero, A. / Rudino-Pinera, E.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Conformational Stability and Crystal Packing: Polymorphism in Neurospora Crassa Cat-3
Authors: Zarate-Romero, A. / Stojanoff, V. / Rojas-Trejo, S.P. / Hansberg, W. / Rudino-Pinera, E.
History
DepositionJan 17, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
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 "BB" 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 "CB" 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)336,24135
Polymers330,2094
Non-polymers6,03231
Water39,4352189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area59040 Å2
ΔGint-232.9 kcal/mol
Surface area72590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.520, 154.800, 160.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
CATALASE-3


Mass: 82552.141 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: BEFORE RESIDUE 1 A HIS TAG SIGNATURE IS PRESENT / Source: (gene. exp.) NEUROSPORA CRASSA (fungus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9C169, catalase

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Non-polymers , 6 types, 2220 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-AE3 / 2-(2-ETHOXYETHOXY)ETHANOL


Mass: 134.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O3
#5: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2189 / 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: 2.63 Å3/Da / Density % sol: 53.18 % / Description: NONE
Crystal growpH: 6.6
Details: 200 MM AMMONIUM DIBASIC TARTRATE, 20 % PEG 3350, pH 6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9794
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 11, 2012
Details: SI(111) CHANNEL CUT MONOCHROMATOR, TOROIDAL FOCUSING MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.95→42.5 Å / Num. obs: 270245 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 7
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.6 / % possible all: 87.8

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Processing

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

3ej6


Resolution: 1.95→42.525 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 17.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1971 11249 5 %
Rwork0.1568 --
obs0.1588 225166 94.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.9 Å2
Refinement stepCycle: LAST / Resolution: 1.95→42.525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21284 0 326 2189 23799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722422
X-RAY DIFFRACTIONf_angle_d1.12130443
X-RAY DIFFRACTIONf_dihedral_angle_d14.6528105
X-RAY DIFFRACTIONf_chiral_restr0.0783188
X-RAY DIFFRACTIONf_plane_restr0.0054047
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.97220.26253250.21276495X-RAY DIFFRACTION87
1.9722-1.99540.28393430.21766485X-RAY DIFFRACTION87
1.9954-2.01970.25323410.21546491X-RAY DIFFRACTION87
2.0197-2.04530.26513310.21016551X-RAY DIFFRACTION88
2.0453-2.07220.24983320.20086632X-RAY DIFFRACTION88
2.0722-2.10060.24923230.18916663X-RAY DIFFRACTION89
2.1006-2.13060.23463450.18336690X-RAY DIFFRACTION90
2.1306-2.16240.23923520.17356795X-RAY DIFFRACTION90
2.1624-2.19620.21173580.17076850X-RAY DIFFRACTION92
2.1962-2.23220.21263570.17236909X-RAY DIFFRACTION92
2.2322-2.27070.21613800.16856892X-RAY DIFFRACTION93
2.2707-2.31190.21413600.16897010X-RAY DIFFRACTION93
2.3119-2.35640.23213520.15777017X-RAY DIFFRACTION94
2.3564-2.40450.21233780.16057074X-RAY DIFFRACTION95
2.4045-2.45680.20873770.15987152X-RAY DIFFRACTION95
2.4568-2.51390.22834000.15057212X-RAY DIFFRACTION96
2.5139-2.57680.19333870.14697227X-RAY DIFFRACTION97
2.5768-2.64640.21233930.14927356X-RAY DIFFRACTION98
2.6464-2.72430.18354010.15217413X-RAY DIFFRACTION99
2.7243-2.81220.20374150.15827435X-RAY DIFFRACTION99
2.8122-2.91270.19373750.15427493X-RAY DIFFRACTION99
2.9127-3.02930.19794200.16067476X-RAY DIFFRACTION100
3.0293-3.16710.20434120.15877493X-RAY DIFFRACTION100
3.1671-3.3340.19114330.15937486X-RAY DIFFRACTION100
3.334-3.54280.20863960.15577560X-RAY DIFFRACTION100
3.5428-3.81620.16053890.13797551X-RAY DIFFRACTION99
3.8162-4.20.1433900.12097571X-RAY DIFFRACTION99
4.2-4.8070.13884040.11497561X-RAY DIFFRACTION99
4.807-6.05350.14354130.12987609X-RAY DIFFRACTION99
6.0535-42.5350.15543670.15037768X-RAY DIFFRACTION97

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