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- PDB-3i4a: Crystal structure of dimethylarginine dimethylaminohydrolase-1 (D... -

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Basic information

Entry
Database: PDB / ID: 3i4a
TitleCrystal structure of dimethylarginine dimethylaminohydrolase-1 (DDAH-1) in complex with N5-(1-iminopropyl)-L-ornithine
ComponentsN(G),N(G)-dimethylarginine dimethylaminohydrolase 1
KeywordsHYDROLASE / DDAH / NITRIC OXIDE SYNTHASE REGULATION / Metal-binding
Function / homology
Function and homology information


dimethylargininase / dimethylargininase activity / : / 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 / : ...dimethylargininase / dimethylargininase activity / : / 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 / : / L-arginine catabolic process / nitric oxide metabolic process / eNOS activation / 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
N5-(1-iminopropyl)-L-ornithine / N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.898 Å
AuthorsMonzingo, A.F. / Wang, Y. / Hu, S. / Schaller, T.H. / Fast, W. / Robertus, J.D.
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
DepositionJul 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 16, 2014Group: Other
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Sep 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 1.5Nov 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 1
B: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6214
Polymers67,2472
Non-polymers3742
Water1,78399
1
A: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8112
Polymers33,6231
Non-polymers1871
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8112
Polymers33,6231
Non-polymers1871
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.600, 80.130, 73.900
Angle α, β, γ (deg.)90.000, 90.130, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11C
21D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain C or (chain A and resid 274)A - C0
211chain D or (chain B and resid 274)B - D0

NCS oper: (Code: given
Matrix: (0.999324, -0.036751, 0.0006), (-0.036748, -0.999313, -0.004775), (0.000775, 0.00475, -0.999988)
Vector: 22.808201, -38.0159, -58.340199)

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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: Chemical ChemComp-LN5 / N5-(1-iminopropyl)-L-ornithine / (2S)-2-azanyl-5-(propanimidoylamino)pentanoic acid


Mass: 187.239 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.1 Å3/Da / Density % sol: 41.31 %
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 MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: May 21, 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
Reflection twinOperator: h,-k,-l / Fraction: 0.486
ReflectionResolution: 1.898→25.12 Å / Num. obs: 42222 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.065 / Χ2: 1.078 / Net I/σ(I): 10.5
Reflection shellResolution: 1.898→1.93 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.391 / Num. unique all: 2048 / Χ2: 0.6 / % possible all: 94.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3I2E

3i2e


Resolution: 1.898→25.12 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: detwinning algorithm used during refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2041 5.03 %random
Rwork0.174 ---
obs0.178 40594 92.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.55 Å2 / ksol: 0.302 e/Å3
Displacement parametersBiso max: 60.25 Å2 / Biso mean: 30.402 Å2 / Biso min: 8.34 Å2
Baniso -1Baniso -2Baniso -3
1--2.692 Å20 Å2-2.01 Å2
2--5.599 Å20 Å2
3----2.907 Å2
Refinement stepCycle: LAST / Resolution: 1.898→25.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4178 0 26 99 4303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074270
X-RAY DIFFRACTIONf_angle_d1.115782
X-RAY DIFFRACTIONf_chiral_restr0.068678
X-RAY DIFFRACTIONf_plane_restr0.005754
X-RAY DIFFRACTIONf_dihedral_angle_d19.6831602
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A19X-RAY DIFFRACTIONPOSITIONAL0.036
12B19X-RAY DIFFRACTIONPOSITIONAL0.036
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 98 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.898-1.9310.383920.35316591751
1.931-1.9660.36760.28716531729
1.966-2.0030.31980.24518891987
2.003-2.0440.309930.24619192012
2.044-2.0890.292850.22519242009
2.089-2.1370.2841070.2219262033
2.137-2.1910.3561020.22319222024
2.191-2.250.489640.29516681732
2.25-2.3160.3811020.25216911793
2.316-2.3910.228910.20519802071
2.391-2.4760.3541140.20219512065
2.476-2.5750.246900.19620182108
2.575-2.6920.236980.19820292127
2.692-2.8340.2741100.19320592169
2.834-3.0110.2681080.17520112119
3.011-3.2430.241000.16820612161
3.243-3.5690.2241030.14820822185
3.569-4.0840.2021020.12519592061
4.084-5.1380.1571100.11521102220
5.138-25.1220.197970.14221412238

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