[English] 日本語
Yorodumi
- PDB-3hvm: Agmatine Deiminase from Helicobacter pylori -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hvm
TitleAgmatine Deiminase from Helicobacter pylori
ComponentsAGMATINE DEIMINASE
KeywordsHYDROLASE / Agmatine Deiminase
Function / homology
Function and homology information


agmatine deiminase activity / putrescine biosynthetic process / protein-arginine deiminase activity
Similarity search - Function
Peptidyl-arginine deiminase, Porphyromonas-type / Porphyromonas-type peptidyl-arginine deiminase / L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / Alpha Beta
Similarity search - Domain/homology
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJones, J. / Lovelace, L. / Lebioda, L. / Thompson, P.
CitationJournal: Bioorg.Chem. / Year: 2010
Title: Characterization and inactivation of an agmatine deiminase from Helicobacter pylori.
Authors: Jones, J.E. / Causey, C.P. / Lovelace, L. / Knuckley, B. / Flick, H. / Lebioda, L. / Thompson, P.R.
History
DepositionJun 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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: AGMATINE DEIMINASE


Theoretical massNumber of molelcules
Total (without water)37,6141
Polymers37,6141
Non-polymers00
Water2,954164
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.082, 52.082, 246.398
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein AGMATINE DEIMINASE


Mass: 37614.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: J99 / Gene: HPAG1_0045, jhp_0042 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ZN18
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMUTATIONS OCCURRED DURING CLONING OF HPAGD

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 52.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% PEG 4K, 10 mM sodium citrate pH 5.6, and 7% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 24, 2007
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30.37 Å / Num. obs: 18081 / % possible obs: 76 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.043 / Χ2: 1.374 / Net I/σ(I): 31.053
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 16.5 / Num. unique all: 1384 / Χ2: 0.82 / % possible all: 59.8

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
SERGUIguidata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CMU

2cmu


Resolution: 2.1→30.37 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.233 / WRfactor Rwork: 0.226 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.84 / SU B: 9.861 / SU ML: 0.121 / SU R Cruickshank DPI: 0.374 / SU Rfree: 0.228 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.324 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.259 916 5.1 %RANDOM
Rwork0.2 ---
obs0.202 18041 76.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.93 Å2 / Biso mean: 29.966 Å2 / Biso min: 8.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20.42 Å20 Å2
2--0.85 Å20 Å2
3----1.27 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2640 0 0 164 2804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222710
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.9673669
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7255331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.66525.726124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.12415495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.415156
X-RAY DIFFRACTIONr_chiral_restr0.130.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022015
X-RAY DIFFRACTIONr_nbd_refined0.2150.21250
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21820
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2198
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.26
X-RAY DIFFRACTIONr_mcbond_it1.1031.51707
X-RAY DIFFRACTIONr_mcangle_it1.73122674
X-RAY DIFFRACTIONr_scbond_it2.86931150
X-RAY DIFFRACTIONr_scangle_it3.9954.5995
LS refinement shellResolution: 2.1→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 50 -
Rwork0.198 945 -
all-995 -
obs--57.71 %
Refinement TLS params.Method: refined / Origin x: -8.5798 Å / Origin y: -0.6163 Å / Origin z: -17.9363 Å
111213212223313233
T-0.0213 Å20.0472 Å20.0044 Å2--0.0602 Å20.006 Å2---0.0428 Å2
L0.4165 °2-0.2493 °20.1388 °2-1.3127 °20.3324 °2--1.5693 °2
S0.1205 Å °0.0092 Å °-0.0191 Å °-0.1962 Å °-0.0355 Å °-0.0655 Å °-0.0619 Å °-0.1005 Å °-0.0851 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 330
2X-RAY DIFFRACTION1A333 - 494

+
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