[English] 日本語
Yorodumi
- PDB-1hzg: CRYSTAL STRUCTURE OF THE INACTIVE C866S MUTANT OF THE CATALYTIC D... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hzg
TitleCRYSTAL STRUCTURE OF THE INACTIVE C866S MUTANT OF THE CATALYTIC DOMAIN OF E. COLI CYTOTOXIC NECROTIZING FACTOR 1
ComponentsCYTOTOXIC NECROTIZING FACTOR 1
KeywordsTOXIN / Beta Sandwich / Rho Deamidase / Rho Transglutaminase
Function / homology
Function and homology information


Cytotoxic necrotizing factor 1 (CNF1) / Cytotoxic necrotizing factor, Rho-activating domain / Cytotoxic necrotizing factor, Rho-activating domain / Domain of unknown function DUF4765 / Cytotoxic necrotizing factor, Rho-activating domain superfamily / Rho-activating domain of cytotoxic necrotizing factor / Domain of unknown function (DUF4765) / Domain of unknown function DUF6543 / Family of unknown function (DUF6543) / Cytotoxic necrotizing factor-like, catalytic ...Cytotoxic necrotizing factor 1 (CNF1) / Cytotoxic necrotizing factor, Rho-activating domain / Cytotoxic necrotizing factor, Rho-activating domain / Domain of unknown function DUF4765 / Cytotoxic necrotizing factor, Rho-activating domain superfamily / Rho-activating domain of cytotoxic necrotizing factor / Domain of unknown function (DUF4765) / Domain of unknown function DUF6543 / Family of unknown function (DUF6543) / Cytotoxic necrotizing factor-like, catalytic / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Cytotoxic necrotizing factor 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Difference Fourier / Resolution: 1.86 Å
AuthorsBuetow, L. / Flatau, G. / Chiu, K. / Boquet, P. / Ghosh, P.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Structure of the Rho-activating domain of Escherichia coli cytotoxic necrotizing factor 1.
Authors: Buetow, L. / Flatau, G. / Chiu, K. / Boquet, P. / Ghosh, P.
History
DepositionJan 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CYTOTOXIC NECROTIZING FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8323
Polymers32,6421
Non-polymers1902
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.900, 54.900, 176.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein CYTOTOXIC NECROTIZING FACTOR 1 / CNF1


Mass: 32642.375 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Mutation: C866S, L794P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: E-B35 / Plasmid: PET 28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q47106
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: sodium phosphate, potassium phosphate, 1,4-butandiol, HEPES, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K
Crystal grow
*PLUS
Temperature: 37 ℃ / pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.65 Msodium phosphate1reservoir
20.65 Mpotassium phosphate1reservoir
3100 mMHEPES1reservoir
45 %(v/v)1,4-butanediol1reservoir
52 mMdithiothreitol1reservoir
6150 mM1dropNaCl
720 mMTris1drop
82 mMdithiothreitol1drop
915 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-5 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 4, 2000 / Details: Supper mirror
RadiationMonochromator: Supper mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→15 Å / Num. all: 25165 / Num. obs: 25142 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 33.8
Reflection shellResolution: 1.86→1.91 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 3.5 / % possible all: 98.1
Reflection
*PLUS
Lowest resolution: 15 Å

-
Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: Difference Fourier
Starting model: PDB Entry 1HQ0

1hq0


Resolution: 1.86→15 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1444667.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used Maximum Likelihood Refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1241 4.9 %RANDOM
Rwork0.198 ---
all0.2 ---
obs0.2 25152 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.38 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 30.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.36 Å22.61 Å20 Å2
2--3.36 Å20 Å2
3----6.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.86→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2260 0 10 157 2427
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_mcbond_it1.531.5
X-RAY DIFFRACTIONc_mcangle_it2.522
X-RAY DIFFRACTIONc_scbond_it1.952
X-RAY DIFFRACTIONc_scangle_it2.892.5
LS refinement shellResolution: 1.86→1.98 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 166 4 %
Rwork0.258 4011 -
obs-4011 99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PHOSPHATE.PARAMPHOSPHATE.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 4.9 % / Rfactor obs: 0.198 / Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.288 / % reflection Rfree: 4 % / Rfactor Rwork: 0.258

+
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