[English] 日本語
Yorodumi
- PDB-8i55: Wild-type CfbA at 1.99 angstrom resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8i55
TitleWild-type CfbA at 1.99 angstrom resolution
ComponentsSirohydrochlorin cobaltochelatase
KeywordsBIOSYNTHETIC PROTEIN / Chelatase / Nickel
Function / homology
Function and homology information


sirohydrochlorin nickelchelatase / sirohydrochlorin cobaltochelatase / anaerobic cobalamin biosynthetic process / sirohydrochlorin cobaltochelatase activity / methanogenesis / cobalt ion binding / nickel cation binding
Similarity search - Function
Sirohydrochlorin cobaltochelatase / Sirohydrochlorin cobaltochelatase CbiX-like / CbiX
Similarity search - Domain/homology
Sirohydrochlorin cobaltochelatase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsOgawa, S. / Fujishiro, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H04639 Japan
CitationJournal: To be published
Title: Substrate selectivity of CfbA
Authors: Ogawa, S. / Hikita, M. / Fujishiro, T.
History
DepositionJan 24, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sirohydrochlorin cobaltochelatase
B: Sirohydrochlorin cobaltochelatase


Theoretical massNumber of molelcules
Total (without water)33,1082
Polymers33,1082
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-28 kcal/mol
Surface area11680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.720, 67.720, 82.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein Sirohydrochlorin cobaltochelatase / / CbiXS / Sirohydrochlorin nickelchelatase


Mass: 16554.045 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Gene: cbiX, cfbA, MJ0970 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: Q58380, sirohydrochlorin cobaltochelatase, sirohydrochlorin nickelchelatase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.86 Å3/Da / Density % sol: 56.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.3M Na-malonate, 0.1M Tris-HCl, 8% (w/v) Gamma-PGA

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 1, 2021
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 25589 / % possible obs: 100 % / Redundancy: 9.44 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.086 / Net I/σ(I): 14.87
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.99-2.090.99934880.7561.0641
2.09-2.190.56128590.9060.5961
2.19-2.30.36626190.9570.3861
2.3-2.50.22336550.9840.2351
2.5-30.11554250.9960.1211
3-3.50.07327690.9970.0771
3.5-40.06415730.9960.0681
4-50.06415430.9970.0681
5-60.0646970.9970.0681
6-100.0737460.9960.0771
10-500.082150.9910.0851

-
Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→47.89 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2023 1279 5 %
Rwork0.1803 --
obs0.1814 25575 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1887 0 0 79 1966
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091935
X-RAY DIFFRACTIONf_angle_d1.4882618
X-RAY DIFFRACTIONf_dihedral_angle_d33.548262
X-RAY DIFFRACTIONf_chiral_restr0.086309
X-RAY DIFFRACTIONf_plane_restr0.01336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.070.30731420.26362692X-RAY DIFFRACTION100
2.07-2.160.27281410.21822686X-RAY DIFFRACTION100
2.16-2.280.22911410.19462673X-RAY DIFFRACTION100
2.28-2.420.2431420.18582700X-RAY DIFFRACTION100
2.42-2.610.20071420.19322705X-RAY DIFFRACTION100
2.61-2.870.27221420.20882689X-RAY DIFFRACTION100
2.87-3.280.17261420.18412697X-RAY DIFFRACTION100
3.29-4.140.1931430.15812708X-RAY DIFFRACTION100
4.14-47.890.18291440.17312746X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.7215-1.5223-2.3877.26471.93286.8991-0.0104-0.2965-0.32560.7349-0.07950.39370.33140.16360.0780.4741-0.0085-0.07120.30780.07170.3042-20.476415.676214.228
25.34380.45811.18742.552-0.49217.89480.342-0.31020.09690.4921-0.07470.3418-0.4773-1.5553-0.15040.4260.04080.030.4560.04570.4043-31.787620.65110.4053
38.8973-2.0038-4.5224.74921.75429.20980.20920.33450.732-0.0470.0739-0.3753-0.89830.3676-0.32710.3647-0.097-0.0610.33680.04490.4016-15.193621.5515-1.222
47.5268-1.1352-1.63265.2252.56286.0246-0.09490.6356-0.2515-0.18930.00960.2888-0.1209-0.33640.07160.282-0.01-0.07160.46140.08480.2875-18.180713.4116-15.1373
52.7078-0.5178-0.60763.28681.76437.165-0.01350.2068-0.12030.09920.1776-0.22030.4520.712-0.20430.27460.0157-0.03630.36620.04720.3365-12.87029.2093-6.1634
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 118 )
3X-RAY DIFFRACTION3chain 'A' and (resid 119 through 143 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 57 )
5X-RAY DIFFRACTION5chain 'B' and (resid 58 through 143 )

+
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