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- PDB-2c6z: crystal structure of dimethylarginine dimethylaminohydrolase I in... -

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Basic information

Entry
Database: PDB / ID: 2c6z
Titlecrystal structure of dimethylarginine dimethylaminohydrolase I in complex with citrulline
ComponentsNG, NG-DIMETHYLARGININE DIMETHYLAMINOHYDROLASE 1
KeywordsHYDROLASE / DDAH I / NO / NOS / ADMA / MMA / ACETYLATION / METAL-BINDING / S-NITROSYLATION / ZINC
Function / homology
Function and homology information


protein nitrosylation / eNOS activation / dimethylargininase / dimethylargininase activity / citrulline metabolic process / arginine metabolic process / amino acid binding / nitric oxide biosynthetic process / positive regulation of nitric oxide biosynthetic process / zinc ion binding
Similarity search - Function
Dimethylarginine dimethylaminohydrolase / Arginine deiminase / L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / Alpha Beta
Similarity search - Domain/homology
CITRULLINE / CITRIC ACID / N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsFrey, D. / Braun, O. / Briand, C. / Vasak, M. / Grutter, M.G.
CitationJournal: Structure / Year: 2006
Title: Structure of the Mammalian Nos Regulator Dimethylarginine Dimethylaminohydrolase: A Basis for the Design of Specific Inbitors
Authors: Frey, D. / Braun, O. / Briand, C. / Vasak, M. / Grutter, M.G.
History
DepositionNov 16, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 2.1Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,5663
Polymers31,1991
Non-polymers3672
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)40.652, 80.134, 44.932
Angle α, β, γ (deg.)90.00, 108.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 31198.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: BRAIN / References: UniProt: P56965, 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: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O
Compound detailsINVOLVED IN NITRIC OXIDE GENERATION.

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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: 1.87 Å3/Da / Density % sol: 34.2 %
Crystal growpH: 5
Details: 100 MM CITRIC ACID/NAOH, 20-40% PEG 8000, 2 MM TCEP, PH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.000087
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 25, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000087 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. obs: 91675 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 2.98 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.8
Reflection shellResolution: 1.16→1.2 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2 / % possible all: 77.9

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H70

1h70


Resolution: 1.2→20 Å / Num. parameters: 24342 / Num. restraintsaints: 30825 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1688 2580 3.1 %RANDOM
all0.1211 81946 --
obs0.1215 -96.2 %-
Refine analyzeNum. disordered residues: 33 / Occupancy sum hydrogen: 2084.3 / Occupancy sum non hydrogen: 2526.15
Refinement stepCycle: LAST / Resolution: 1.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2108 0 25 395 2528
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0296
X-RAY DIFFRACTIONs_zero_chiral_vol0.073
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.081
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.022
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.052
X-RAY DIFFRACTIONs_approx_iso_adps0.099

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