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- PDB-3i2e: Crystal structure of human dimethylarginine dymethylaminohydrolas... -

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Basic information

Entry
Database: PDB / ID: 3i2e
TitleCrystal structure of human dimethylarginine dymethylaminohydrolase-1 (DDAH-1)
ComponentsN(G),N(G)-dimethylarginine dimethylaminohydrolase 1
KeywordsHYDROLASE / DDAH / NITRIC OXIDE SYNTHASE REGULATOR / Metal-binding / Zinc
Function / homology
Function and homology information


dimethylargininase / dimethylargininase activity / citrulline metabolic process / negative regulation of cellular response to hypoxia / arginine metabolic process / regulation of systemic arterial blood pressure / negative regulation of vascular permeability / nitric oxide metabolic process / amino acid binding / nitric oxide mediated signal transduction ...dimethylargininase / dimethylargininase activity / citrulline metabolic process / negative regulation of cellular response to hypoxia / arginine metabolic process / regulation of systemic arterial blood pressure / negative regulation of vascular permeability / nitric oxide metabolic process / amino acid binding / nitric oxide mediated signal transduction / catalytic activity / eNOS activation / arginine catabolic process / positive regulation of angiogenesis / positive regulation of nitric oxide biosynthetic process / negative regulation of cell population proliferation / extracellular exosome / metal ion binding / cytosol
Similarity search - Function
Dimethylarginine dimethylaminohydrolase / N,N dimethylarginine dimethylhydrolase, eukaryotic / Arginine deiminase / L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / Alpha Beta
Similarity search - Domain/homology
N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.03 Å
AuthorsMonzingo, A.F. / Wang, Y. / Hu, S. / Schaller, T.H. / Robertus, J.D. / Fast, W.
CitationJournal: Biochemistry / Year: 2009
Title: Developing dual and specific inhibitors of dimethylarginine dimethylaminohydrolase-1 and nitric oxide synthase: toward a targeted polypharmacology to control nitric oxide.
Authors: Wang, Y. / Monzingo, A.F. / Hu, S. / Schaller, T.H. / Robertus, J.D. / Fast, W.
History
DepositionJun 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
B: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1


Theoretical massNumber of molelcules
Total (without water)67,2472
Polymers67,2472
Non-polymers00
Water9,512528
1
A: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1


Theoretical massNumber of molelcules
Total (without water)33,6231
Polymers33,6231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1


Theoretical massNumber of molelcules
Total (without water)33,6231
Polymers33,6231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.995, 47.926, 90.318
Angle α, β, γ (deg.)90.00, 94.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 33623.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDAH, DDAH1 / Plasmid: pET28a-hDDAH-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O94760, dimethylargininase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 528 / 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: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25% (w/v) PEG 6000, 0.1 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 1, 2007 / Details: Blue Max-Flux Optical System
RadiationMonochromator: Blue Max-Flux Optical System / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.03→36.4 Å / Num. obs: 40755 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.074 / Χ2: 1.088 / Net I/σ(I): 20.99
Reflection shellResolution: 2.03→2.1 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.225 / Num. unique all: 4021 / Χ2: 0.938 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.408 / Cor.coef. Fo:Fc: 0.712
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMR2.5phasing
CNSrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2JAI

2jai


Resolution: 2.03→20 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.827 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1838 4.3 %random
Rwork0.189 ---
obs-37241 87.7 %-
Solvent computationBsol: 40.179 Å2
Displacement parametersBiso max: 48.91 Å2 / Biso mean: 17.744 Å2 / Biso min: 4.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å2-2.354 Å2
2--0.458 Å20 Å2
3----1.088 Å2
Refinement stepCycle: LAST / Resolution: 2.03→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4195 0 0 528 4723
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.309
X-RAY DIFFRACTIONc_mcbond_it1.2581.5
X-RAY DIFFRACTIONc_scbond_it2.162
X-RAY DIFFRACTIONc_mcangle_it1.9372
X-RAY DIFFRACTIONc_scangle_it3.1962.5
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

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