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- PDB-3p8e: Crystal structure of human DIMETHYLARGININE DIMETHYLAMINOHYDROLAS... -

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Basic information

Entry
Database: PDB / ID: 3p8e
TitleCrystal structure of human DIMETHYLARGININE DIMETHYLAMINOHYDROLASE-1 (DDAH-1) covalently bound with N5-(1-iminopentyl)-L-ornithine
ComponentsN(G),N(G)-dimethylarginine dimethylaminohydrolase 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / DDAH / NITRIC OXIDE SYNTHASE REGULATION / HYDROLASE-HYDROLASE INHIBITOR complex
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 / amino acid binding / catalytic activity / 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 / amino acid binding / catalytic activity / nitric oxide mediated signal transduction / L-arginine catabolic process / eNOS activation / nitric oxide metabolic 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~5~-[(1S)-1-aminopentyl]-L-ornithine / N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4946 Å
AuthorsLluis, M. / Wang, Y. / Monzingo, A.F. / Fast, W. / Robertus, J.D.
CitationJournal: Chemmedchem / Year: 2011
Title: Characterization of C-Alkyl Amidines as Bioavailable Covalent Reversible Inhibitors of Human DDAH-1.
Authors: Lluis, M. / Wang, Y. / Monzingo, A.F. / Fast, W. / Robertus, J.D.
History
DepositionOct 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6824
Polymers67,2472
Non-polymers4352
Water88349
1
A: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8412
Polymers33,6231
Non-polymers2171
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8412
Polymers33,6231
Non-polymers2171
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.210, 80.900, 74.090
Angle α, β, γ (deg.)90.00, 90.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein N(G),N(G)-dimethylarginine dimethylaminohydrolase 1 / DDAH-1 / Dimethylarginine dimethylaminohydrolase 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: Chemical ChemComp-LN7 / N~5~-[(1S)-1-aminopentyl]-L-ornithine


Mass: 217.309 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H23N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Compound detailsIN LINKING N5-(1-IMINOPENTYL)-L-ORNITHINE TO CYS 274 THE HYBRIDIZATION STATE OF CZ CHANGES FROM SP2 TO SP3
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: 2.1 Å3/Da / Density % sol: 41.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 20% polyethyleneglycol 6000, 0.1 M Tris-HCl, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: May 11, 2009 / Details: varimax high flux optics
RadiationMonochromator: varimax high flux optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4946→73.794 Å / Num. all: 18983 / Num. obs: 18983 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 5.9
Reflection shellResolution: 2.4946→2.59 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 1.97 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3I2E

3i2e


Resolution: 2.4946→35.752 Å / SU ML: 0.78 / Cross valid method: THROUGHOUT / σ(F): 0.06 / Phase error: 31.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3083 951 5.16 %random
Rwork0.2119 ---
obs0.2168 18442 94.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.76 Å2 / ksol: 0.283 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.9302 Å20 Å2-0.4373 Å2
2--3.3176 Å20 Å2
3----5.2478 Å2
Refinement stepCycle: LAST / Resolution: 2.4946→35.752 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4182 0 30 49 4261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084276
X-RAY DIFFRACTIONf_angle_d1.1955776
X-RAY DIFFRACTIONf_dihedral_angle_d19.031628
X-RAY DIFFRACTIONf_chiral_restr0.07672
X-RAY DIFFRACTIONf_plane_restr0.004750
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4946-2.62610.40211360.26832457X-RAY DIFFRACTION94
2.6261-2.79060.36551310.26492517X-RAY DIFFRACTION96
2.7906-3.0060.39431130.25712553X-RAY DIFFRACTION97
3.006-3.30830.33491570.24012591X-RAY DIFFRACTION98
3.3083-3.78650.31151300.22252189X-RAY DIFFRACTION83
3.7865-4.76880.26351310.17972550X-RAY DIFFRACTION95
4.7688-35.75570.25631530.16612634X-RAY DIFFRACTION98

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