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- PDB-2ci5: Crystal structure of Dimethylarginine Dimethylaminohydrolase I in... -

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Basic information

Entry
Database: PDB / ID: 2ci5
TitleCrystal structure of Dimethylarginine Dimethylaminohydrolase I in complex with L-homocysteine
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 / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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
DepositionMar 17, 2006Deposition 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 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 2.0Mar 6, 2024Group: Atomic model / Structure summary / Category: atom_site / chem_comp
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _chem_comp.pdbx_synonyms

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)62,8605
Polymers62,3972
Non-polymers4623
Water11,656647
1
A: NG, NG-DIMETHYLARGININE DIMETHYLAMINOHYDROLASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3342
Polymers31,1991
Non-polymers1351
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)31,5263
Polymers31,1991
Non-polymers3272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)44.603, 79.363, 78.617
Angle α, β, γ (deg.)90.00, 104.80, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99999, 0.00489, -0.0023), (-0.00515, 0.99176, -0.12803), (0.00165, 0.12804, 0.99177)
Vector: -12.18182, -10.19773, -37.26404)

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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.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: BRAIN / References: UniProt: P56965, dimethylargininase
#2: Chemical ChemComp-HCS / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / L-Homocysteine


Type: L-peptide linking / Mass: 135.185 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO2S
#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.: 647 / Source method: isolated from a natural source / Formula: H2O

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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: 2.16 Å3/Da / Density % sol: 43 %
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: 0.9793
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 11, 2003 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 48415 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 3.25 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.5
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.2 / % possible all: 90.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H70

1h70


Resolution: 1.79→29.2 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1453876.18 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.211 2422 5 %RANDOM
Rwork0.176 ---
obs0.176 48394 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.7133 Å2 / ksol: 0.348887 e/Å3
Displacement parametersBiso mean: 15 Å2
Baniso -1Baniso -2Baniso -3
1--2.9 Å20 Å2-1.18 Å2
2--2.26 Å20 Å2
3---0.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.79→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4209 0 29 647 4885
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it1.782
X-RAY DIFFRACTIONc_scbond_it2.292
X-RAY DIFFRACTIONc_scangle_it3.442.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.085 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.409 23 3.8 %
Rwork0.269 588 -
obs--6.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3HCY.PARHCY.TOP
X-RAY DIFFRACTION4CITRATE.PARCITRATE.TOP

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