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- PDB-4bim: CATALASE 3 FROM NEUROSPORA CRASSA IN TETRAGONAL FORM EXPOSES A MO... -

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Basic information

Entry
Database: PDB / ID: 4bim
TitleCATALASE 3 FROM NEUROSPORA CRASSA IN TETRAGONAL FORM EXPOSES A MODIFIED TETRAMERIC ORGANIZATION
ComponentsCATALASE 3
KeywordsOXIDOREDUCTASE / PEROXIDASE / MODIFIED TETRAMER / LARGE SUBUNIT CATALASE
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 active site ...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 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 / 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
PROTOPORPHYRIN IX CONTAINING FE / Catalase-3
Similarity search - Component
Biological speciesNEUROSPORA CRASSA (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.95 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
DepositionApr 11, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Jul 17, 2013Group: Database references
Revision 1.3Dec 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 "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" 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 "BA" 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 SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)332,6758
Polymers330,2094
Non-polymers2,4664
Water5,441302
1
A: CATALASE 3
B: CATALASE 3
hetero molecules

A: CATALASE 3
B: CATALASE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,6758
Polymers330,2094
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area55430 Å2
ΔGint-277 kcal/mol
Surface area74350 Å2
MethodPISA
2
C: CATALASE 3
D: CATALASE 3
hetero molecules

C: CATALASE 3
D: CATALASE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,6758
Polymers330,2094
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area53200 Å2
ΔGint-248.5 kcal/mol
Surface area81500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.508, 207.508, 137.041
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
CATALASE 3


Mass: 82552.141 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-719
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEUROSPORA CRASSA (fungus) / Strain: 74-ORS23-1A / Plasmid: PCOLD1 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.37 Å3/Da / Density % sol: 48.07 % / Description: NONE
Crystal growpH: 5.5 / Details: MES 100 MM, PH 5.5, 50 % V/V MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV PLUS PLUS / Detector: IMAGE PLATE / Date: Aug 23, 2011 / Details: OSMIC BLUE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.95→30 Å / Num. obs: 62655 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 69.19 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.7
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.8 / % possible all: 98

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EJ6

3ej6


Resolution: 2.95→29.3 Å / Cor.coef. Fo:Fc: 0.8548 / Cor.coef. Fo:Fc free: 0.8017 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.555
RfactorNum. reflection% reflectionSelection details
Rfree0.3044 3166 5.07 %RANDOM
Rwork0.2553 ---
obs0.2678 62443 98.76 %-
Displacement parametersBiso mean: 76.5 Å2
Baniso -1Baniso -2Baniso -3
1--4.3768 Å20 Å20 Å2
2---4.3768 Å20 Å2
3---8.7535 Å2
Refine analyzeLuzzati coordinate error obs: 0.677 Å
Refinement stepCycle: LAST / Resolution: 2.95→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21335 0 172 302 21809
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00922067HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1129990HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7438SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes602HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3285HARMONIC5
X-RAY DIFFRACTIONt_it22067HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.36
X-RAY DIFFRACTIONt_other_torsion24.56
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2753SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact24455SEMIHARMONIC4
LS refinement shellResolution: 2.95→3.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 213 4.95 %
Rwork0.2673 4088 -
all0.2703 4301 -
obs--98.76 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.64590.1137-0.41951.4765-0.50090.1804-0.327-0.3263-0.60150.2410.12690.3936-0.0050.18670.2001-0.07010.18280.2125-0.14220.09960.125837.9508-70.681947.5215
21.29420.0213-0.21461.953-0.23580.1605-0.0810.2347-0.0926-0.25280.09651.02420.01860.0172-0.0155-0.24740.0729-0.1341-0.1927-0.03210.403117.2639-54.247628.8618
30.5125-0.7392-0.469700.23620.0611-0.1746-0.2062-0.04460.1427-0.09020.2580.0590.08340.2647-0.1251-0.24470.14390.0171-0.3040.236446.827-75.0812-15.6694
40.6352-0.0087-0.68810.306-0.27650.0365-0.0230.2378-0.00380.09490.03580.12930.0016-0.1152-0.0128-0.2334-0.1187-0.11320.1111-0.2810.16723.0136-61.4879-32.3227
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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