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- PDB-2jai: DDAH1 complexed with citrulline -

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Basic information

Entry
Database: PDB / ID: 2jai
TitleDDAH1 complexed with citrulline
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 / arginine catabolic 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
CITRULLINE / N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 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 / Version format compliance
Revision 1.2Feb 28, 2018Group: Database references / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / entity_src_gen
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.3May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.1Nov 6, 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

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)63,9943
Polymers63,8182
Non-polymers1751
Water2,252125
1
A: NG, NG-DIMETHYLARGININE DIMETHYLAMINOHYDROLASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0842
Polymers31,9091
Non-polymers1751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: NG, NG-DIMETHYLARGININE DIMETHYLAMINOHYDROLASE 1


Theoretical massNumber of molelcules
Total (without water)31,9091
Polymers31,9091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)44.831, 46.799, 147.787
Angle α, β, γ (deg.)90.00, 94.64, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 6 / Auth seq-ID: 8 - 280 / Label seq-ID: 13 - 285

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (-0.871, -0.043, -0.489), (-0.041, 0.999, -0.015), (0.489, 0.007, -0.872)
Vector: 50.21154, 27.1546, 56.20957)

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Components

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


Mass: 31909.217 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): B834(DE3) / References: UniProt: O94760, dimethylargininase
#2: Chemical ChemComp-CIR / CITRULLINE


Type: L-peptide linking / Mass: 175.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13N3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 2.42 Å3/Da / Density % sol: 50 %
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: Jul 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.3→7.27 Å / Num. obs: 25580 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.3
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 8.8 / % possible all: 65.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.877 / SU B: 12.091 / SU ML: 0.156 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.337 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1301 5.1 %RANDOM
Rwork0.198 ---
obs0.201 24273 92.8 %-
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: 34.33 Å2
Baniso -1Baniso -2Baniso -3
1-2.17 Å20 Å2-1.28 Å2
2--0.31 Å20 Å2
3----2.69 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3901 0 12 125 4038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223992
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.521.9795432
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6185539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.42824.184141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33815609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7651520
X-RAY DIFFRACTIONr_chiral_restr0.0980.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022961
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.21708
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22708
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2214
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7121.52778
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.02224287
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.86331336
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7564.51143
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
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1791 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.295
loose thermal2.1110
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.254 59
Rwork0.163 1101
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)
11.36490.21910.11591.82-0.13472.30590.01680.1234-0.0138-0.06720.0674-0.03220.02570.0436-0.0842-0.32790.00150.0506-0.1889-0.0074-0.120117.098-0.31655.958
21.8111-1.511.90655.6965-2.9839.258-0.03030.2150.1411-0.2901-0.338-0.2812-0.46420.74630.36820.2424-0.2186-0.05850.11680.0841-0.08117.26724.70815.689
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 280
2X-RAY DIFFRACTION2B5 - 280

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