[English] 日本語
Yorodumi
- PDB-6rjn: Crystal structure of a Fungal Catalase at 2.3 Angstroms -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rjn
TitleCrystal structure of a Fungal Catalase at 2.3 Angstroms
ComponentsCatalase
KeywordsOXIDOREDUCTASE / Pichia pastoris / Catalase / Heme / NADP
Function / homology
Function and homology information


catalase / catalase activity / hydrogen peroxide catabolic process / response to hydrogen peroxide / peroxisome / nucleotide binding / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase active site / Catalase proximal active site signature. ...Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / : / Chem-NDP / DI(HYDROXYETHYL)ETHER / Catalase
Similarity search - Component
Biological speciesKomagataella pastoris (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.295 Å
AuthorsGomez, S. / Navas-Yuste, S. / Payne, A.M. / Rivera, W. / Lopez-Estepa, M. / Brangbour, C. / Fulla, D. / Juanhuix, J. / Fernandez, F.J. / Vega, M.C.
Funding support Spain, 3items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessCTQ2015-66206-C2-2-R Spain
Spanish Ministry of Economy and CompetitivenessSAF2015-72961-EXP Spain
Spanish National Research CouncilPIE 20160E064 Spain
Citation
Journal: Free Radic. Biol. Med. / Year: 2019
Title: Peroxisomal catalases from the yeasts Pichia pastoris and Kluyveromyces lactis as models for oxidative damage in higher eukaryotes.
Authors: Gomez, S. / Navas-Yuste, S. / Payne, A.M. / Rivera, W. / Lopez-Estepa, M. / Brangbour, C. / Fulla, D. / Juanhuix, J. / Fernandez, F.J. / Vega, M.C.
#1: Journal: Front Microbiol / Year: 2017
Title: Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from the Gram-Positive Bacterial Pathogen
Authors: Querol-Garcia, J. / Fernandez, F.J. / Marin, A.V. / Gomez, S. / Fulla, D. / Melchor-Tafur, C. / Franco-Hidalgo, V. / Alberti, S. / Juanhuix, J. / Rodriguez de Cordoba, S. / Regueiro, J.R. / Vega, M.C.
History
DepositionApr 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / refine / struct_conn
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _refine.pdbx_diffrn_id / _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 / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)240,22349
Polymers232,2624
Non-polymers7,96145
Water22,1221228
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58320 Å2
ΔGint-448 kcal/mol
Surface area60030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.943, 173.690, 96.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Catalase


Mass: 58065.570 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella pastoris (fungus) / Gene: CTA1 / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta(DE3)pLysS / References: UniProt: C1PHG1, catalase

-
Non-polymers , 9 types, 1273 molecules

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


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
#8: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1228 / 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: 3 Å3/Da / Density % sol: 59.04 % / Description: Long thin needles
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium sulfate, 0.1 M Bis-Tris propane, pH 6.5, 20% (w/v) polyethylene glycol (PEG) 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2015
Details: CONVEX PREFOCUSSING MIRROR AND A KIRKPATRICK-BAEZ PAIR OF FOCUSSING MIRRORS
RadiationMonochromator: CRYOGENICALLY COOLED CHANNEL CUT SI[111] CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.29→57.9 Å / Num. obs: 124735 / % possible obs: 99.5 % / Redundancy: 6.7 % / CC1/2: 0.988 / Rmerge(I) obs: 0.253 / Rpim(I) all: 0.147 / Rrim(I) all: 0.279 / Net I/σ(I): 9
Reflection shellResolution: 2.29→2.42 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.477 / Num. unique obs: 17551 / CC1/2: 0.579 / Rpim(I) all: 0.619 / Rrim(I) all: 1.604 / % possible all: 97

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSMARCH 1, 2015data reduction
Aimless0.5.17data scaling
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: wwPDB 2XQ1

2xq1


Resolution: 2.295→54.665 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.53
RfactorNum. reflection% reflectionSelection details
Rfree0.1963 6078 4.9 %RANDOM SELECTION
Rwork0.1425 ---
obs0.1451 124065 99.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.295→54.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16148 0 506 1228 17882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01217302
X-RAY DIFFRACTIONf_angle_d1.16323506
X-RAY DIFFRACTIONf_dihedral_angle_d13.21510016
X-RAY DIFFRACTIONf_chiral_restr0.0552365
X-RAY DIFFRACTIONf_plane_restr0.0083084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2952-2.32130.29611600.26163094X-RAY DIFFRACTION80
2.3213-2.34860.28571940.23093944X-RAY DIFFRACTION100
2.3486-2.37730.28632030.23363907X-RAY DIFFRACTION100
2.3773-2.40740.28742120.22293924X-RAY DIFFRACTION100
2.4074-2.4390.28672030.21563856X-RAY DIFFRACTION100
2.439-2.47240.25952280.21083918X-RAY DIFFRACTION100
2.4724-2.50780.25782050.20523898X-RAY DIFFRACTION100
2.5078-2.54520.26471900.19963952X-RAY DIFFRACTION100
2.5452-2.5850.28521990.19943933X-RAY DIFFRACTION100
2.585-2.62730.25282230.18983894X-RAY DIFFRACTION100
2.6273-2.67260.24811970.1853948X-RAY DIFFRACTION100
2.6726-2.72120.2441820.19023946X-RAY DIFFRACTION100
2.7212-2.77360.251740.18963946X-RAY DIFFRACTION100
2.7736-2.83020.26322000.1783955X-RAY DIFFRACTION100
2.8302-2.89170.20821950.16123912X-RAY DIFFRACTION100
2.8917-2.9590.25762200.15923954X-RAY DIFFRACTION100
2.959-3.0330.21891760.15183959X-RAY DIFFRACTION100
3.033-3.1150.21342190.14313954X-RAY DIFFRACTION100
3.115-3.20660.20692320.14163916X-RAY DIFFRACTION100
3.2066-3.31010.20262100.13533934X-RAY DIFFRACTION100
3.3101-3.42840.17722040.13293963X-RAY DIFFRACTION100
3.4284-3.56570.18542110.11583938X-RAY DIFFRACTION100
3.5657-3.72790.15331900.10393983X-RAY DIFFRACTION100
3.7279-3.92440.13542250.09613961X-RAY DIFFRACTION100
3.9244-4.17020.1422090.09443996X-RAY DIFFRACTION100
4.1702-4.4920.12622140.08933974X-RAY DIFFRACTION100
4.492-4.94380.11711630.08934054X-RAY DIFFRACTION100
4.9438-5.65860.14451970.10624069X-RAY DIFFRACTION100
5.6586-7.12670.21192260.13634049X-RAY DIFFRACTION100
7.1267-54.68050.16582170.14954256X-RAY DIFFRACTION100

+
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