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- PDB-6nt1: Catalase 3 from N.Crassa in ferrous state (2.89 MGy) -

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Basic information

Entry
Database: PDB / ID: 6nt1
TitleCatalase 3 from N.Crassa in ferrous state (2.89 MGy)
ComponentsCatalase-3
KeywordsOXIDOREDUCTASE / X-ray reduced / Heme / ferrous 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 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 / ETHANOL / PROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Catalase-3
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsZarate-Romero, A. / Rudino-Pinera, E. / Stojanoff, V.
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
DepositionJan 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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)322,67142
Polymers317,2904
Non-polymers5,38138
Water36,1922009
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area63050 Å2
ΔGint-193 kcal/mol
Surface area71440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.100, 154.500, 160.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 79322.531 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (fungus)
Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987
Gene: cat-3, NCU00355 / Plasmid: pCold I / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9C169, catalase

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Non-polymers , 9 types, 2047 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O
#8: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#9: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2009 / 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: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 277 K / Method: batch mode / pH: 6.6 / Details: Ammonium tartrate dibasic, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9674 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 29, 2012
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9674 Å / Relative weight: 1
ReflectionResolution: 2.2→29.655 Å / Num. obs: 159994 / % possible obs: 96.6 % / Redundancy: 3.15 % / Biso Wilson estimate: 14.92 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.149 / Rrim(I) all: 0.177 / Net I/σ(I): 6.8
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 3.19 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 3.21 / Num. unique obs: 11710 / CC1/2: 0.806 / Rrim(I) all: 0.441 / % possible all: 80.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AJ9

4aj9


Resolution: 2.2→29.655 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.84
RfactorNum. reflection% reflection
Rfree0.1984 8033 5.02 %
Rwork0.1501 --
obs0.1525 159975 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 98.97 Å2 / Biso mean: 16.8862 Å2 / Biso min: 3 Å2
Refinement stepCycle: final / Resolution: 2.2→29.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21302 0 365 2009 23676
Biso mean--16.97 21.32 -
Num. residues----2713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722486
X-RAY DIFFRACTIONf_angle_d0.85730516
X-RAY DIFFRACTIONf_chiral_restr0.0523190
X-RAY DIFFRACTIONf_plane_restr0.0054059
X-RAY DIFFRACTIONf_dihedral_angle_d16.97913152
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.2250.27422830.19545016529997
2.225-2.25120.25932670.19264978524596
2.2512-2.27860.25542470.19365008525596
2.2786-2.30740.25582710.18394994526596
2.3074-2.33780.22472740.1684963523796
2.3378-2.36980.2462590.17515016527596
2.3698-2.40370.24482510.17335016526797
2.4037-2.43950.25152410.17095063530496
2.4395-2.47760.21862490.16855020526996
2.4776-2.51820.22272770.16384992526997
2.5182-2.56160.20232490.15925037528697
2.5616-2.60820.21722270.15695052527997
2.6082-2.65830.21512820.16015049533197
2.6583-2.71250.21182900.15395010530097
2.7125-2.77150.23572750.15745076535197
2.7715-2.83590.20632870.15795019530697
2.8359-2.90670.21842580.16045105536397
2.9067-2.98530.23322910.1615044533597
2.9853-3.0730.20582620.1595079534197
3.073-3.17210.19812550.15695096535197
3.1721-3.28530.20012500.15385106535697
3.2853-3.41670.20982360.15325117535397
3.4167-3.5720.17423080.14555071537997
3.572-3.75990.1692900.13065088537897
3.7599-3.9950.16272920.1245090538297
3.995-4.30260.15622730.11975127540097
4.3026-4.7340.14052570.11665147540497
4.734-5.41540.15132370.12025193543097
5.4154-6.80920.20272740.14225196547097
6.8092-29.65760.14953210.13235174549594

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