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- PDB-2jaj: DDAH1 complexed with L-257 -

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Basic information

Entry
Database: PDB / ID: 2jaj
TitleDDAH1 complexed with L-257
ComponentsNG, NG-DIMETHYLARGININE DIMETHYLAMINOHYDROLASE 1
KeywordsHYDROLASE / DDAH / NITRIC OXIDE SYNTHASE INHIBITOR
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 / catalytic activity ...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 / catalytic activity / nitric oxide mediated signal transduction / 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
Chem-D20 / N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMurray-Rust, J. / O'Hara, B.P. / Rossiter, S. / Leiper, J.M. / Vallance, P. / McDonald, N.Q.
CitationJournal: Nat. Med. / Year: 2007
Title: Disruption of methylarginine metabolism impairs vascular homeostasis.
Authors: Leiper, J. / Nandi, M. / Torondel, B. / Murray-Rust, J. / Malaki, M. / O'Hara, B. / Rossiter, S. / Anthony, S. / Madhani, M. / Selwood, D. / Smith, C. / Wojciak-Stothard, B. / Rudiger, A. / ...Authors: Leiper, J. / Nandi, M. / Torondel, B. / Murray-Rust, J. / Malaki, M. / O'Hara, B. / Rossiter, S. / Anthony, S. / Madhani, M. / Selwood, D. / Smith, C. / Wojciak-Stothard, B. / Rudiger, A. / Stidwill, R. / McDonald, N.Q. / Vallance, P.
History
DepositionNov 29, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 4, 2013Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Source and taxonomy
Revision 1.3Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.5May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NG, NG-DIMETHYLARGININE DIMETHYLAMINOHYDROLASE 1
B: NG, NG-DIMETHYLARGININE DIMETHYLAMINOHYDROLASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4394
Polymers62,9742
Non-polymers4652
Water5,062281
1
A: NG, NG-DIMETHYLARGININE DIMETHYLAMINOHYDROLASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7192
Polymers31,4871
Non-polymers2321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: NG, NG-DIMETHYLARGININE DIMETHYLAMINOHYDROLASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7192
Polymers31,4871
Non-polymers2321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)44.849, 46.914, 147.612
Angle α, β, γ (deg.)90.00, 94.56, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.8724, -0.04606, -0.48661), (-0.04354, 0.99892, -0.0165), (0.48684, 0.00679, -0.87346)
Vector: 50.12644, 27.42638, 56.14977)

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Components

#1: Protein NG, NG-DIMETHYLARGININE DIMETHYLAMINOHYDROLASE 1 / DIMETHYLARGININASE-1 / DIMETHYLARGININE DIMETHYLAMINOHYDROLASE 1 / DDAHI / DDAH-1


Mass: 31487.166 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O94760, dimethylargininase
#2: Chemical ChemComp-D20 / N~5~-{IMINO[(2-METHOXYETHYL)AMINO]METHYL}-L-ORNITHINE


Mass: 232.280 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H20N4O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL VECTOR-DERIVED SEQUENCE GPLGM IN CHAIN B

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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: 2.46 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 289 K / Method: microbatch
Details: PROTEIN: 20MG/ML IN 20MM TRIS-HCL PH 8.0, 150MM NACL, 1MM DTT. PRECIPITANT: 50MM TRIS-HCL PH 8.5, 150-300MM SODIUM ACETATE, 20-30% W/V PEG4000, 1MM DTT CO-CRYSTALLISED WITH 10MM LIGAND IN ...Details: PROTEIN: 20MG/ML IN 20MM TRIS-HCL PH 8.0, 150MM NACL, 1MM DTT. PRECIPITANT: 50MM TRIS-HCL PH 8.5, 150-300MM SODIUM ACETATE, 20-30% W/V PEG4000, 1MM DTT CO-CRYSTALLISED WITH 10MM LIGAND IN PRECIPITATING SOLUTION EXPT:SITTING DROPS UNDER MINERAL OIL AT 16DEG C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→33.9 Å / Num. obs: 39147 / % possible obs: 94.1 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.2
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 2.2 / % possible all: 86.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PART-REFINED DDAH1, IN-HOUSE COORDINATES

Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.897 / SU B: 8.264 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2005 5.1 %RANDOM
Rwork0.211 ---
obs0.214 37137 93.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.64 Å2
Baniso -1Baniso -2Baniso -3
1-2.58 Å20 Å2-1.07 Å2
2---0.16 Å20 Å2
3----2.59 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4058 0 32 281 4371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224164
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.9845659
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9975552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.07425162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.09815660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8871519
X-RAY DIFFRACTIONr_chiral_restr0.1130.2678
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023111
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.21871
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22821
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2379
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.229
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9671.52833
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.41924417
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.40831458
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.584.51240
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.23 129
Rwork0.224 2502
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.92090.19830.10231.0515-0.0531.29820.01320.0483-0.0027-0.04430.0102-0.0260.00810.0104-0.0234-0.18610.01460.0308-0.1134-0.0011-0.080217.1262-0.448855.8326
20.3221-0.16850.15630.8122-0.09430.80350.01980.00190.0204-0.0265-0.032-0.0581-0.00770.06520.01220.0008-0.03020.00380.04910.02540.03417.771425.065515.84
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 281
2X-RAY DIFFRACTION2B8 - 281

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