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- PDB-3ej6: Neurospora Crassa Catalase-3 Crystal Structure -

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Basic information

Entry
Database: PDB / ID: 3ej6
TitleNeurospora Crassa Catalase-3 Crystal Structure
ComponentsCatalase-3
KeywordsOXIDOREDUCTASE / LARGE CATALASE STRUCTURE / NEUROSPORA CRASSA / HEME / HYDROGEN PEROXIDE / IRON / METAL-BINDING / 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 / Large catalase, C-terminal domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / 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 / Large catalase, C-terminal domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDiaz, A. / Valdes, V.-J. / Rudino-Pinera, E. / Horjales, E. / Hansberg, W.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structure-Function Relationships in Fungal Large-Subunit Catalases
Authors: Diaz, A. / Valdes, V.-J. / Rudino-Pinera, E. / Horjales, E. / Hansberg, W.
History
DepositionSep 17, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 1, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)308,97516
Polymers304,7394
Non-polymers4,23612
Water24,5901365
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area56510 Å2
ΔGint-262 kcal/mol
Surface area76440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.835, 154.507, 162.415
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: 76184.758 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: AERIAL MYCELIUM / Source: (natural) Neurospora crassa (fungus) / Strain: 74-ORS23-1A / References: UniProt: Q9C169, catalase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 1365 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS PROTEIN HAS SIGNALING SEQUENCE FOR PROCESSING AND SECRETION, MRVNALLPLSGLIGTALAACPFADPSALGRR ...THIS PROTEIN HAS SIGNALING SEQUENCE FOR PROCESSING AND SECRETION, MRVNALLPLSGLIGTALAACPFADPSALGRR AT THE N-TERMINAL.

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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: 2.71 Å3/Da / Density % sol: 54.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8
Details: 18% PEG 4000, 50MM TRIS, pH 8.00, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 12, 2002
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→34.68 Å / Num. obs: 152747 / % possible obs: 93.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.087 / Net I/σ(I): 7.2
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.333 / % possible all: 85.8

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SY7

1sy7


Resolution: 2.3→34.67 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.908 / SU B: 13.187 / SU ML: 0.171 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.551 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.242 -5 %RANDOM
Rwork0.193 ---
obs0.237 136823 92.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20 Å2
2--1.17 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21360 0 284 1365 23009
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.02221945
X-RAY DIFFRACTIONr_bond_other_d0.0070.0214656
X-RAY DIFFRACTIONr_angle_refined_deg0.7631.9629875
X-RAY DIFFRACTIONr_angle_other_deg0.752335332
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.61152720
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11424.0331086
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.499153285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8915140
X-RAY DIFFRACTIONr_chiral_restr0.0430.23172
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0225064
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024660
X-RAY DIFFRACTIONr_nbd_refined0.1450.24654
X-RAY DIFFRACTIONr_nbd_other0.1610.216840
X-RAY DIFFRACTIONr_nbtor_refined0.1650.210938
X-RAY DIFFRACTIONr_nbtor_other0.0820.211061
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0750.21621
X-RAY DIFFRACTIONr_metal_ion_refined0.0890.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.10.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.0970.213
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0570.29
X-RAY DIFFRACTIONr_mcbond_it0.0361.517285
X-RAY DIFFRACTIONr_mcbond_other0.0041.55548
X-RAY DIFFRACTIONr_mcangle_it0.034221591
X-RAY DIFFRACTIONr_scbond_it0.07939946
X-RAY DIFFRACTIONr_scangle_it0.114.58276
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 228 -
Rwork0.249 4325 -
obs--42.35 %
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)
10.3831-0.09080.04120.41630.04230.3250.00430.0116-0.1028-0.042-0.03010.25360.0512-0.18190.0258-0.0315-0.0316-0.0233-0.0269-0.00750.0204-22.913-10.82623.127
20.3898-0.1155-0.05020.55420.13030.44940.00360.1150.0167-0.1495-0.0069-0.1383-0.00410.10510.0033-0.0286-0.01310.0374-0.05870.0164-0.09527.518-6.2597.102
30.44470.00610.03130.4550.06780.4316-0.0256-0.069-0.02720.07270.0367-0.14030.04610.1465-0.0111-0.05510.0052-0.0202-0.0721-0.0007-0.090230.359-5.51839.257
40.4091-0.1311-0.09430.47560.08570.41610.00890.01950.0834-0.0361-0.00960.1519-0.0755-0.11890.0007-0.04760.0083-0.0077-0.08380.0079-0.0542-15.67519.54131.807
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 716
2X-RAY DIFFRACTION2B36 - 716
3X-RAY DIFFRACTION3C36 - 716
4X-RAY DIFFRACTION4D36 - 716

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