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- PDB-6nib: Crystal Structure of Medicago truncatula Agmatine Iminohydrolase ... -

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Basic information

Entry
Database: PDB / ID: 6nib
TitleCrystal Structure of Medicago truncatula Agmatine Iminohydrolase (Deiminase)
ComponentsPorphyromonas-type peptidyl-arginine deiminase
KeywordsHYDROLASE / Polyamine metabolism / Putrescine biosynthesis
Function / homology
Function and homology information


agmatine deiminase / agmatine deiminase activity / putrescine biosynthetic process from arginine / protein-arginine deiminase activity
Similarity search - Function
Agmatine deiminase / 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
DI(HYDROXYETHYL)ETHER / Agmatine deiminase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsSekula, B. / Dauter, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)The Intramural Research Program United States
CitationJournal: Front Plant Sci / Year: 2019
Title: Structural Study of Agmatine Iminohydrolase FromMedicago truncatula, the Second Enzyme of the Agmatine Route of Putrescine Biosynthesis in Plants.
Authors: Sekula, B. / Dauter, Z.
History
DepositionDec 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Porphyromonas-type peptidyl-arginine deiminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6777
Polymers41,2491
Non-polymers4286
Water10,539585
1
A: Porphyromonas-type peptidyl-arginine deiminase
hetero molecules

A: Porphyromonas-type peptidyl-arginine deiminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,35514
Polymers82,4982
Non-polymers85712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)146.996, 75.504, 47.103
Angle α, β, γ (deg.)90.00, 108.56, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-401-

GOL

21A-1050-

HOH

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Components

#1: Protein Porphyromonas-type peptidyl-arginine deiminase / Putative agmatine deiminase


Mass: 41249.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Tissue: Leaves / Gene: 11445422, MTR_4g112810, MtrunA17_Chr4g0061951 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G7JT50, agmatine deiminase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 585 / 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: 3 Å3/Da / Density % sol: 59.05 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Sodium Acetate, 20% PEG 3350, cryoprotected with 25% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 4, 2017
RadiationMonochromator: Si (1111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→39.96 Å / Num. obs: 121248 / % possible obs: 93.8 % / Observed criterion σ(I): -3 / Redundancy: 3.63 % / CC1/2: 1 / Rmerge(I) obs: 0.031 / Rpim(I) all: 0.019 / Rrim(I) all: 0.036 / Net I/σ(I): 19.1
Reflection shellResolution: 1.2→1.28 Å / Redundancy: 3.12 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 5584 / CC1/2: 0.758 / Rpim(I) all: 0.309 / Rrim(I) all: 0.56 / % possible all: 58.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
STARANISOdata scaling
XDSVERSION Jan 26, 2018data reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VKP

1vkp


Resolution: 1.2→34.695 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.07
RfactorNum. reflection% reflectionSelection details
Rfree0.1367 1568 1.29 %RANDOM
Rwork0.1116 ---
obs0.112 121247 79.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.2→34.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2745 0 27 585 3357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143028
X-RAY DIFFRACTIONf_angle_d1.3974145
X-RAY DIFFRACTIONf_dihedral_angle_d20.3681146
X-RAY DIFFRACTIONf_chiral_restr0.104443
X-RAY DIFFRACTIONf_plane_restr0.01540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1971-1.23570.178260.18741483X-RAY DIFFRACTION11
1.2357-1.27990.2093620.17983662X-RAY DIFFRACTION27
1.2799-1.33120.1653920.1617231X-RAY DIFFRACTION53
1.3312-1.39170.20191600.141211334X-RAY DIFFRACTION83
1.3917-1.46510.14031830.127613640X-RAY DIFFRACTION100
1.4651-1.55690.15451430.111313734X-RAY DIFFRACTION100
1.5569-1.67710.13661830.104113672X-RAY DIFFRACTION100
1.6771-1.84590.14051840.101513678X-RAY DIFFRACTION100
1.8459-2.1130.14341820.102113704X-RAY DIFFRACTION99
2.113-2.6620.12851660.106813715X-RAY DIFFRACTION99
2.662-34.70960.12151870.11113826X-RAY DIFFRACTION99

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