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- PDB-3hvm: Agmatine Deiminase from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 3hvm
TitleAgmatine Deiminase from Helicobacter pylori
ComponentsAGMATINE DEIMINASE
KeywordsHYDROLASE / Agmatine Deiminase
Function / homologyputrescine biosynthetic process / Peptidyl-arginine deiminase, Porphyromonas-type / Porphyromonas-type peptidyl-arginine deiminase / protein-arginine deiminase activity / L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / Alpha Beta / Putative
Function and homology information
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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