[English] 日本語
Yorodumi
- PDB-7ld8: Crystal Structure of Putative non-heme bromoperoxidase BpoC from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ld8
TitleCrystal Structure of Putative non-heme bromoperoxidase BpoC from Mycobacterium tuberculosis H37Rv
ComponentsPutative non-heme bromoperoxidase BpoC
KeywordsOXIDOREDUCTASE / SSGCID / Putative non-heme bromoperoxidase / BpoC / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologybromide peroxidase activity / : / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / membrane / Putative non-heme bromoperoxidase BpoC
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Putative non-heme bromoperoxidase BpoC from Mycobacterium tuberculosis H37Rv
Authors: DeBouver, N.D. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJan 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Oct 18, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative non-heme bromoperoxidase BpoC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5343
Polymers29,4491
Non-polymers852
Water6,305350
1
A: Putative non-heme bromoperoxidase BpoC
hetero molecules

A: Putative non-heme bromoperoxidase BpoC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0676
Polymers58,8972
Non-polymers1704
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4000 Å2
ΔGint-38 kcal/mol
Surface area21420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.550, 113.500, 43.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-666-

HOH

-
Components

#1: Protein Putative non-heme bromoperoxidase BpoC


Mass: 29448.588 Da / Num. of mol.: 1 / Fragment: MytuD.00095.b.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: bpoC, Rv0554 / Plasmid: MytuD.00095.b.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WNH1, bromide peroxidase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.37 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: MytuD.00095.b.B1.PW38899[Barcode: 318836d7, PuckID: neu1-3, Cryo: 20% EG, Concentration: 18 mg/mL] 100 mM Sodium Citrate/Citric Acid pH 5.5, 20% (w/v) PEG 3000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 10, 2020 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 38202 / % possible obs: 97.3 % / Redundancy: 7.164 % / Biso Wilson estimate: 22.769 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.042 / Χ2: 0.967 / Net I/σ(I): 28.16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.546.1790.3235.3725160.9470.35288
1.54-1.587.0560.2717.1526770.9720.29296.6
1.58-1.637.4370.2278.7526390.9830.24496.7
1.63-1.687.4330.1810.9725780.9880.19397.3
1.68-1.737.4310.14613.3924610.9910.15797.3
1.73-1.797.4230.1215.9524230.9940.12997.5
1.79-1.867.4090.09519.5223330.9960.10297.7
1.86-1.947.3720.07723.7222580.9970.08298.1
1.94-2.027.3710.06228.8621710.9980.06698
2.02-2.127.3020.05134.0120820.9990.05598.3
2.12-2.247.3170.04637.4419980.9990.0598.4
2.24-2.377.2190.04140.9418980.9990.04498.8
2.37-2.547.2360.03844.6218000.9990.04198.7
2.54-2.747.1080.03547.3416650.9990.03799.1
2.74-37.0540.03151.2415510.9990.03499.2
3-3.356.9520.02855.5814290.9990.0399.5
3.35-3.876.8980.02657.83126310.02899.7
3.87-4.746.8590.02259.49108910.02499.8
4.74-6.716.6930.02258.6486010.024100
6.71-506.0020.02456.255110.9990.02697.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19rc4-4035refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HSS

3hss


Resolution: 1.5→43.37 Å / SU ML: 0.1153 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.1257
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1778 2068 5.41 %
Rwork0.1339 36133 -
obs0.1362 38201 97.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.03 Å2
Refinement stepCycle: LAST / Resolution: 1.5→43.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 5 350 2397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532172
X-RAY DIFFRACTIONf_angle_d0.75952976
X-RAY DIFFRACTIONf_chiral_restr0.0539332
X-RAY DIFFRACTIONf_plane_restr0.0078397
X-RAY DIFFRACTIONf_dihedral_angle_d11.107797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.23241140.13922100X-RAY DIFFRACTION86.79
1.53-1.570.19491450.1282358X-RAY DIFFRACTION96.72
1.57-1.620.171300.11782365X-RAY DIFFRACTION96.89
1.62-1.660.19841290.12292380X-RAY DIFFRACTION97.02
1.66-1.720.20571500.12342361X-RAY DIFFRACTION97.29
1.72-1.780.17051320.12812355X-RAY DIFFRACTION97.41
1.78-1.850.17521330.13022404X-RAY DIFFRACTION97.73
1.85-1.930.18361440.1232409X-RAY DIFFRACTION98
1.93-2.040.20911440.13052408X-RAY DIFFRACTION98.08
2.04-2.160.17721660.13152413X-RAY DIFFRACTION98.4
2.16-2.330.1781260.13032440X-RAY DIFFRACTION98.58
2.33-2.560.19271400.14292467X-RAY DIFFRACTION98.79
2.57-2.940.19091230.14672484X-RAY DIFFRACTION99.16
2.94-3.70.16981440.13492531X-RAY DIFFRACTION99.48
3.7-43.370.15021480.13472658X-RAY DIFFRACTION99.47

+
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