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- PDB-6b10: C. Jejuni Agmatine Deiminase -

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Basic information

Entry
Database: PDB / ID: 6b10
TitleC. Jejuni Agmatine Deiminase
ComponentsPutative peptidyl-arginine deiminase family protein
KeywordsHYDROLASE / polyamine biosynthesis / agmatine iminohydrolase / putrescine / N-carbamoylputrescine
Function / homology
Function and homology information


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
: / PHOSPHATE ION / Peptidyl-arginine deiminase family protein
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 Å
AuthorsShek, R. / Hicks, K.A. / French, J.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM124898 United States
CitationJournal: Biochemistry / Year: 2017
Title: Structural and Functional Basis for Targeting Campylobacter jejuni Agmatine Deiminase To Overcome Antibiotic Resistance.
Authors: Shek, R. / Dattmore, D.A. / Stives, D.P. / Jackson, A.L. / Chatfield, C.H. / Hicks, K.A. / French, J.B.
History
DepositionSep 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative peptidyl-arginine deiminase family protein
B: Putative peptidyl-arginine deiminase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4818
Polymers78,0232
Non-polymers4586
Water5,278293
1
A: Putative peptidyl-arginine deiminase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2404
Polymers39,0111
Non-polymers2293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative peptidyl-arginine deiminase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2404
Polymers39,0111
Non-polymers2293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.400, 80.296, 83.923
Angle α, β, γ (deg.)90.000, 97.360, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative peptidyl-arginine deiminase family protein


Mass: 39011.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) (Campylobacter)
Strain: ATCC 700819 / NCTC 11168 / Gene: Cj0949c / Production host: Escherichia coli (E. coli) / References: UniProt: Q0P9V0
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.22 % / Description: rod-shaped
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.2M potassium phosphate, pH 4.6 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 40360 / % possible obs: 96.7 % / Redundancy: 4 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.038 / Rrim(I) all: 0.077 / Χ2: 1.181 / Net I/σ(I): 11.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.09-2.143.50.24416630.9380.1440.2840.8680.8
2.14-2.183.60.22717520.9580.1320.2640.84684.1
2.18-2.223.70.22918250.960.1310.2650.86488.2
2.22-2.263.70.20618840.9660.1190.2390.87291
2.26-2.313.70.19719900.9720.1140.2290.89695.9
2.31-2.373.80.18620240.9740.1080.2160.93597.2
2.37-2.423.90.16520680.9810.0940.190.97898.4
2.42-2.4940.15320370.9840.0870.1770.97298.8
2.49-2.5640.13420750.9880.0760.1541.04599.3
2.56-2.654.10.12320680.9890.0690.1421.12699.9
2.65-2.744.10.10920680.9910.0610.1251.10699.9
2.74-2.854.10.09521030.9920.0530.1091.182100
2.85-2.984.20.08520850.9930.0480.0981.277100
2.98-3.144.20.07520850.9950.0410.0851.499100
3.14-3.334.20.06620930.9950.0370.0761.571100
3.33-3.594.20.05820770.9950.0320.0671.44100
3.59-3.954.20.05320870.9960.0290.0611.556100
3.95-4.524.20.05221060.9960.0290.061.676100
4.52-5.74.20.0521100.9950.0280.0581.587100
5.7-5040.04621600.9960.0260.0530.7899.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HVM

3hvm


Resolution: 2.09→47.6 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.856 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.249 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2495 1967 4.9 %RANDOM
Rwork0.1999 ---
obs0.2023 38374 95.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.95 Å2 / Biso mean: 37.985 Å2 / Biso min: 19.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å2-4.15 Å2
2---2.93 Å20 Å2
3---4.68 Å2
Refinement stepCycle: final / Resolution: 2.09→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5176 0 22 293 5491
Biso mean--72.16 41.19 -
Num. residues----646
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0195323
X-RAY DIFFRACTIONr_bond_other_d0.0010.024971
X-RAY DIFFRACTIONr_angle_refined_deg1.0221.9547198
X-RAY DIFFRACTIONr_angle_other_deg0.709311421
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.875645
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.4125.15266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0615926
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.041519
X-RAY DIFFRACTIONr_chiral_restr0.0610.2787
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026025
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021254
LS refinement shellResolution: 2.09→2.139 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 118 -
Rwork0.268 2123 -
all-2241 -
obs--72.2 %

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