[English] 日本語
Yorodumi
- PDB-6nsz: X-ray reduced Catalase 3 from N.Crassa (0.526 MGy) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nsz
TitleX-ray reduced Catalase 3 from N.Crassa (0.526 MGy)
ComponentsCatalase-3
KeywordsOXIDOREDUCTASE / X-ray reduced / Heme / 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 ...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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Catalase-3
B: Catalase-3
C: Catalase-3
D: Catalase-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)322,58342
Polymers317,2904
Non-polymers5,29338
Water36,2822014
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area62970 Å2
ΔGint-197 kcal/mol
Surface area71670 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

-
Components

-
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

-
Non-polymers , 9 types, 2052 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.: 6 / 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-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / 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.: 2014 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 277 K / Method: batch mode / pH: 6 / Details: Ammonium dibasic tatrate, PEG 3350

-
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→29.596 Å / Num. obs: 160372 / % possible obs: 96.83 % / Redundancy: 3.27 % / Biso Wilson estimate: 15.07 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.14 / Rrim(I) all: 0.166 / Net I/σ(I): 7.12
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 3.29 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 0.346 / Num. unique obs: 11717 / CC1/2: 0.797 / Rrim(I) all: 0.471 / % possible all: 96.36

-
Phasing

PhasingMethod: molecular replacement

-
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→29.596 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.65
RfactorNum. reflection% reflection
Rfree0.2041 8043 5.02 %
Rwork0.1567 --
obs0.159 160353 96.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 105.97 Å2 / Biso mean: 16.7029 Å2 / Biso min: 2.06 Å2
Refinement stepCycle: final / Resolution: 2.2→29.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21302 0 359 2014 23675
Biso mean--18.22 20.33 -
Num. residues----2713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00322519
X-RAY DIFFRACTIONf_angle_d0.57230568
X-RAY DIFFRACTIONf_chiral_restr0.0423195
X-RAY DIFFRACTIONf_plane_restr0.0034069
X-RAY DIFFRACTIONf_dihedral_angle_d16.36313176
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 (%)
2.2-2.2250.2682850.20785003528896
2.225-2.25120.27492670.20924995526296
2.2512-2.27860.27282500.2115019526997
2.2786-2.30740.25522750.19375005528096
2.3074-2.33780.26242800.18144980526097
2.3378-2.36980.26492570.18915023528097
2.3698-2.40370.23282480.17985052530097
2.4037-2.43950.24782400.1775093533397
2.4395-2.47760.242540.18015034528897
2.4776-2.51820.21952790.17545032531197
2.5182-2.56160.21872510.17215077532897
2.5616-2.60820.22542290.16875103533298
2.6082-2.65830.24722800.1725074535497
2.6583-2.71250.2252930.16295035532897
2.7125-2.77150.22782760.16315089536597
2.7715-2.83590.22392880.16125030531897
2.8359-2.90670.21332560.15665120537697
2.9067-2.98530.22842930.16115052534597
2.9853-3.0730.20842620.16035074533697
3.073-3.17210.20832480.16425088533697
3.1721-3.28530.19342490.15915129537897
3.2853-3.41670.2192360.1575111534797
3.4167-3.57190.18482990.15285095539497
3.5719-3.75990.19092920.14165073536597
3.7599-3.9950.1562910.12655061535297
3.995-4.30260.15982680.1225102537097
4.3026-4.7340.1452570.12165122537996
4.734-5.41530.14922300.12435172540296
5.4153-6.8090.17842750.14315208548397
6.809-29.59840.15853350.13845259559495

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more