[English] 日本語
Yorodumi
- PDB-6v59: Crystal structure of the diheme peroxidase BthA Y463M variant fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6v59
TitleCrystal structure of the diheme peroxidase BthA Y463M variant from Burkholderia thailandensis E264
ComponentsDi-haem cytochrome c peroxidase family protein
KeywordsOXIDOREDUCTASE / Heme / peroxidase / diheme / BthA
Function / homology
Function and homology information


peroxidase activity / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Di-haem cytochrome c peroxidase / Di-haem cytochrome c peroxidase / : / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
HEME C / Di-haem cytochrome c peroxidase family protein
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.593 Å
AuthorsCohen, S.E. / Drennan, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)126982 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)008334 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: A Stable Ferryl Porphyrin at the Active Site of Y463M BthA.
Authors: Rizzolo, K. / Weitz, A.C. / Cohen, S.E. / Drennan, C.L. / Hendrich, M.P. / Elliott, S.J.
History
DepositionDec 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.2Oct 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Di-haem cytochrome c peroxidase family protein
B: Di-haem cytochrome c peroxidase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,26122
Polymers102,6072
Non-polymers3,65320
Water15,763875
1
A: Di-haem cytochrome c peroxidase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,00410
Polymers51,3041
Non-polymers1,7019
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Di-haem cytochrome c peroxidase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,25612
Polymers51,3041
Non-polymers1,95311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.970, 87.605, 184.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Di-haem cytochrome c peroxidase family protein


Mass: 51303.688 Da / Num. of mol.: 2 / Mutation: Y463M
Source method: isolated from a genetically manipulated source
Details: The first 66 residues of the protein are a periplasmic localization sequence and were not included in the heterologous construct. However, all residues are still named according to NCBI ...Details: The first 66 residues of the protein are a periplasmic localization sequence and were not included in the heterologous construct. However, all residues are still named according to NCBI convention. Therefore, what would be M397 is actually M463 in the pdb file. In addition, the first fifty-nine residues of the construct are not resolved in the crystal structure.
Source: (gene. exp.) Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264) (bacteria)
Strain: ATCC 700388 / DSM 13276 / CIP 106301 / E264 / Gene: BTH_II1092 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2T6B0

-
Non-polymers , 5 types, 895 molecules

#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 875 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.38 % / Description: Red rod-like crystals
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris, pH 8.5, 160 mM magnesium chloride, 18% PEG 4000, 20% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.593→50 Å / Num. obs: 107369 / % possible obs: 98.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.038 / Rrim(I) all: 0.102 / Χ2: 0.962 / Net I/σ(I): 6.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.593-1.665.60.482100700.8840.1990.5240.93394
1.66-1.7260.4105710.9230.1650.4340.95398.2
1.72-1.86.10.326105970.9470.1370.3550.98298.7
1.8-1.96.60.265106710.9670.1080.2870.97699.3
1.9-2.0270.209107590.9810.0830.2261.00799.5
2.02-2.176.60.166107630.9840.0680.180.99199.7
2.17-2.396.90.132108170.990.0530.1430.93699.6
2.39-2.746.90.106108850.9920.0420.1140.96599.9
2.74-3.457.30.081109190.9960.0310.0870.99799.5
3.45-48.2370.06113170.9960.0240.0640.87899.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.59 Å48.23 Å
Translation6.59 Å48.23 Å

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data scaling
PHASER2.7.16phasing
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NX0

6nx0


Resolution: 1.593→48.23 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.38
RfactorNum. reflection% reflection
Rfree0.1774 5364 5 %
Rwork0.151 --
obs0.1523 107267 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.67 Å2 / Biso mean: 23.6069 Å2 / Biso min: 10.28 Å2
Refinement stepCycle: final / Resolution: 1.593→48.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6345 0 458 875 7678
Biso mean--22.95 30.85 -
Num. residues----838
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5933-1.61140.26671510.239285883
1.6114-1.63040.25041690.2198320595
1.6304-1.65020.25051700.2133325296
1.6502-1.67110.24851740.1975330396
1.6711-1.69310.24511750.1929334799
1.6931-1.71630.22181800.1834340899
1.7163-1.74080.21461750.1744332699
1.7408-1.76680.23411800.17243414100
1.7668-1.79440.19861760.1642335398
1.7944-1.82390.18411780.1632337799
1.8239-1.85530.22961790.1585339299
1.8553-1.8890.19021780.1553389100
1.889-1.92540.19081790.1507341199
1.9254-1.96470.18931790.15313395100
1.9647-2.00740.17571810.1485343099
2.0074-2.05410.18561790.1513404100
2.0541-2.10550.17891800.14373420100
2.1055-2.16240.18311800.14123431100
2.1624-2.2260.17181790.1442338899
2.226-2.29790.18151820.14343461100
2.2979-2.380.15761820.13963447100
2.38-2.47530.20551800.13923428100
2.4753-2.58790.17161820.14353460100
2.5879-2.72440.17831820.14453463100
2.7244-2.8950.18331810.1476341899
2.895-3.11850.17611830.15053492100
3.1185-3.43230.16061840.14843484100
3.4323-3.92870.14741850.1323526100
3.9287-4.9490.13811850.1283352399
4.949-48.230.18141960.1779369899

+
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