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- PDB-6nsw: X-ray reduced Catalase 3 From N.Crassa in Cpd I state (0.135 MGy) -

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Basic information

Entry
Database: PDB / ID: 6nsw
TitleX-ray reduced Catalase 3 From N.Crassa in Cpd I state (0.135 MGy)
ComponentsCatalase-3
KeywordsOXIDOREDUCTASE / X-ray reduced / Heme / compound I
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 / OXYGEN ATOM / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Catalase-3
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 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 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

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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)322,45144
Polymers317,2904
Non-polymers5,16140
Water35,4361967
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area62530 Å2
ΔGint-196 kcal/mol
Surface area71700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.100, 154.400, 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 , 10 types, 2007 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.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C2H6O
#9: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#10: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 1967 / 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: 54.29 %
Crystal growTemperature: 277 K / Method: batch mode / Details: PEG 3350, Ammonium dibasic phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9764 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 2.099→29.596 Å / Num. obs: 153203 / % possible obs: 80.52 % / Observed criterion σ(I): -3 / Redundancy: 2.02 % / Biso Wilson estimate: 16.54 Å2 / CC1/2: 0.964 / Rmerge(I) obs: 0.157 / Rrim(I) all: 0.198 / Net I/σ(I): 4.39
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 1.92 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 11159 / CC1/2: 0.739 / Rrim(I) all: 0.48 / % possible all: 79.94
Serial crystallography sample deliveryMethod: fixed target

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Processing

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

4aj9


Resolution: 2.099→29.596 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.3
RfactorNum. reflection% reflection
Rfree0.2195 7671 5.01 %
Rwork0.17 --
obs0.1725 153183 80.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.94 Å2 / Biso mean: 18.4103 Å2 / Biso min: 2.43 Å2
Refinement stepCycle: final / Resolution: 2.099→29.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21294 0 350 1967 23611
Biso mean--17.62 21.18 -
Num. residues----2711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00322481
X-RAY DIFFRACTIONf_angle_d0.63630519
X-RAY DIFFRACTIONf_chiral_restr0.0443192
X-RAY DIFFRACTIONf_plane_restr0.0044062
X-RAY DIFFRACTIONf_dihedral_angle_d17.37813151
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 (%)
2.0988-2.12270.3122110.23564449466074
2.1227-2.14770.25022450.2164918516383
2.1477-2.17380.29662850.21484916520183
2.1738-2.20130.25632570.19814959521683
2.2013-2.23030.26082700.19944953522383
2.2303-2.26080.27752670.21454925519282
2.2608-2.29310.26472680.20224959522783
2.2931-2.32730.26292510.18865008525984
2.3273-2.36370.25542640.18444949521383
2.3637-2.40240.24232740.18135024529884
2.4024-2.44380.27322850.18434980526584
2.4438-2.48830.2382770.18044942521983
2.4883-2.53610.25372570.17894980523783
2.5361-2.58780.2232500.1714970522083
2.5878-2.64410.23722480.17664894514282
2.6441-2.70550.26322310.17424917514881
2.7055-2.77310.22652740.1734819509381
2.7731-2.84810.25182320.17124825505780
2.8481-2.93180.21282470.17154760500779
2.9318-3.02630.23662760.17464734501079
3.0263-3.13440.22492780.17954738501679
3.1344-3.25970.20972500.17354732498279
3.2597-3.40790.19152550.16584823507880
3.4079-3.58730.20072450.16324825507080
3.5873-3.81160.19582540.15334805505980
3.8116-4.10520.16462720.14024792506479
4.1052-4.5170.19092230.13264750497378
4.517-5.16760.15292460.13074709495577
5.1676-6.49930.18072390.15644729496876
6.4993-29.59870.17242400.15164728496874

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