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- PDB-3rhy: Crystal structure of the dimethylarginine dimethylaminohydrolase ... -

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Basic information

Entry
Database: PDB / ID: 3rhy
TitleCrystal structure of the dimethylarginine dimethylaminohydrolase adduct with 4-chloro-2-hydroxymethylpyridine
ComponentsN(G),N(G)-dimethylarginine dimethylaminohydrolase
KeywordsHYDROLASE / enzyme adduct
Function / homology
Function and homology information


dimethylargininase / dimethylargininase activity / citrulline metabolic process / arginine metabolic process / amino acid binding / positive regulation of nitric oxide biosynthetic process / metal ion binding
Similarity search - Function
: / Dimethylarginine dimethylaminohydrolase / N,N dimethylarginine dimethylhydrolase, eukaryotic / L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / Alpha Beta
Similarity search - Domain/homology
(4-chloropyridin-2-yl)methanol / N(G),N(G)-dimethylarginine dimethylaminohydrolase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsMonzingo, A.F. / Johnson, C.M. / Ke, Z. / Yoon, D.-W. / Linsky, T.W. / Guo, H. / Fast, W. / Robertus, J.D.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: On the mechanism of dimethylarginine dimethylaminohydrolase inactivation by 4-halopyridines.
Authors: Johnson, C.M. / Monzingo, A.F. / Ke, Z. / Yoon, D.W. / Linsky, T.W. / Guo, H. / Robertus, J.D. / Fast, W.
History
DepositionApr 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Database references
Revision 1.3Sep 13, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N(G),N(G)-dimethylarginine dimethylaminohydrolase
B: N(G),N(G)-dimethylarginine dimethylaminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3004
Polymers57,0132
Non-polymers2872
Water4,089227
1
A: N(G),N(G)-dimethylarginine dimethylaminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6502
Polymers28,5071
Non-polymers1441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: N(G),N(G)-dimethylarginine dimethylaminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6502
Polymers28,5071
Non-polymers1441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.800, 73.280, 149.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein N(G),N(G)-dimethylarginine dimethylaminohydrolase / Dimethylarginine dimethylaminohydrolase / DDAH / Dimethylargininase


Mass: 28506.521 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA1195 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I4E3, dimethylargininase
#2: Chemical ChemComp-HM3 / (4-chloropyridin-2-yl)methanol / 4-chloro-2-hydroxymethylpyridine


Mass: 143.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6ClNO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.21 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 20% PEG3350, 0.2 M ammonium acetate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 28, 2010 / Details: Varimax HF
RadiationMonochromator: Varimax HF optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. all: 27154 / Num. obs: 27154 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.18-2.225.90.4623.3198.4
2.22-2.261100
2.26-2.31100
2.3-2.351100
2.35-2.41100
2.4-2.461100

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Processing

Software
NameVersionClassification
StructureStudiodata collection
MOLREPphasing
CNS1.21refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H70

1h70


Resolution: 2.18→50 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2652 1266 4.8 %RANDOM
Rwork0.2091 23984 --
obs-25250 96 %-
Solvent computationBsol: 39.8845 Å2
Displacement parametersBiso max: 89.96 Å2 / Biso mean: 36.2859 Å2 / Biso min: 16.43 Å2
Baniso -1Baniso -2Baniso -3
1-12.016 Å20 Å20 Å2
2---1.499 Å20 Å2
3----10.517 Å2
Refinement stepCycle: LAST / Resolution: 2.18→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3882 0 16 227 4125
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.319
X-RAY DIFFRACTIONc_mcbond_it1.2631.5
X-RAY DIFFRACTIONc_scbond_it2.0142
X-RAY DIFFRACTIONc_mcangle_it2.0382
X-RAY DIFFRACTIONc_scangle_it2.8782.5
LS refinement shellResolution: 2.18→2.21 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.337 46 5.06 %
Rwork0.276 909 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5hmp.parhmp.top

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