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- PDB-2ci1: Crystal Structure of dimethylarginine dimethylaminohydrolase I in... -

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Basic information

Entry
Database: PDB / ID: 2ci1
TitleCrystal Structure of dimethylarginine dimethylaminohydrolase I in complex with S-nitroso-Lhomocysteine
ComponentsNG, NG-DIMETHYLARGININE DIMETHYLAMINOHYDROLASE 1
KeywordsHYDROLASE / NOS REGULATION / S-NITROSYLATION / ZINC / NO / MMA / ADMA / ACETYLATION / METAL-BINDING
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
CITRIC ACID / N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 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 Inhibitors.
Authors: Frey, D. / Braun, O. / Briand, C. / Vasak, M. / Grutter, M.G.
History
DepositionMar 17, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2006Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2May 22, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / refine / struct_conn
Item: _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod ..._pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 13, 2023Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,7192
Polymers30,5271
Non-polymers1921
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)40.664, 79.910, 44.894
Angle α, β, γ (deg.)90.00, 108.58, 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: 30526.945 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-CIT / CITRIC ACID


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


Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHYDROLYZES N(G),N(G)-DIMETHYL-L-ARGININE (ADMA) AND N(G)- MONOMETHYL-L-ARGININE (MMA) WHICH ACT AS ...HYDROLYZES N(G),N(G)-DIMETHYL-L-ARGININE (ADMA) AND N(G)- MONOMETHYL-L-ARGININE (MMA) WHICH ACT AS INHIBITORS OF NOS

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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: 1.86 Å3/Da / Density % sol: 33.9 %
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: 0.8998
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 17, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8998 Å / Relative weight: 1
ReflectionResolution: 1.08→40 Å / Num. obs: 114012 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 3.65 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.7
Reflection shellResolution: 1.08→1.12 Å / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4.1 / % possible all: 96

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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: 1.08→20 Å / Num. parameters: 25625 / Num. restraintsaints: 33348 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY NULL
RfactorNum. reflection% reflectionSelection details
Rfree0.1413 1126 1 %RANDOM
all0.1118 112848 --
obs--97.4 %-
Refine analyzeNum. disordered residues: 47 / Occupancy sum hydrogen: 2092 / Occupancy sum non hydrogen: 2611
Refinement stepCycle: LAST / Resolution: 1.08→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2150 0 13 471 2634
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0304
X-RAY DIFFRACTIONs_zero_chiral_vol0.088
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.093
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.038
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.051
X-RAY DIFFRACTIONs_approx_iso_adps0.104

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