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- PDB-6szq: Crystal structure of human DDAH-1 -

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Basic information

Entry
Database: PDB / ID: 6szq
TitleCrystal structure of human DDAH-1
ComponentsN(G),N(G)-dimethylarginine dimethylaminohydrolase 1
KeywordsHYDROLASE / dimethylarginine dimethylaminohydrolase / guanidine inhibitor / induced fit / prodrug
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 / nitric oxide mediated signal transduction ...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 / nitric oxide mediated signal transduction / catalytic activity / 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
N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.412 Å
AuthorsHennig, S. / Vetter, I.R. / Schade, D.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Discovery ofN-(4-Aminobutyl)-N'-(2-methoxyethyl)guanidine as the First Selective, Nonamino Acid, Catalytic Site Inhibitor of Human Dimethylarginine Dimethylaminohydrolase-1 (hDDAH-1).
Authors: Lunk, I. / Litty, F.A. / Hennig, S. / Vetter, I.R. / Kotthaus, J. / Altmann, K.S. / Ott, G. / Havemeyer, A. / Carillo Garcia, C. / Clement, B. / Schade, D.
History
DepositionOct 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
B: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
C: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
D: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
E: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
F: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1


Theoretical massNumber of molelcules
Total (without water)195,4106
Polymers195,4106
Non-polymers00
Water6,846380
1
A: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1


Theoretical massNumber of molelcules
Total (without water)32,5681
Polymers32,5681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1


Theoretical massNumber of molelcules
Total (without water)32,5681
Polymers32,5681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1


Theoretical massNumber of molelcules
Total (without water)32,5681
Polymers32,5681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1


Theoretical massNumber of molelcules
Total (without water)32,5681
Polymers32,5681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1


Theoretical massNumber of molelcules
Total (without water)32,5681
Polymers32,5681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1


Theoretical massNumber of molelcules
Total (without water)32,5681
Polymers32,5681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.146, 76.153, 116.839
Angle α, β, γ (deg.)90.000, 95.470, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 8 through 282)
21(chain B and resid 8 through 282)
31(chain C and resid 8 through 282)
41(chain D and resid 8 through 282)
51(chain E and resid 8 through 282)
61(chain F and resid 8 through 282)

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 / Auth seq-ID: 8 - 282 / Label seq-ID: 20 - 294

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 8 through 282)AA
2(chain B and resid 8 through 282)BB
3(chain C and resid 8 through 282)CC
4(chain D and resid 8 through 282)DD
5(chain E and resid 8 through 282)EE
6(chain F and resid 8 through 282)FF

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Components

#1: Protein
N(G),N(G)-dimethylarginine dimethylaminohydrolase 1


Mass: 32568.309 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDAH1, DDAH / Plasmid: pQE-30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pREP4 / References: UniProt: O94760, dimethylargininase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.14 Å3/Da / Density % sol: 42.66 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M NaAc, 0.1M Tris pH 8,5, 30% PEG4000, cryo: reservoir+20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99985 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99985 Å / Relative weight: 1
ReflectionResolution: 2.41→46.646 Å / Num. obs: 59837 / % possible obs: 99.1 % / Redundancy: 5.913 % / Biso Wilson estimate: 50.723 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.118 / Rrim(I) all: 0.13 / Χ2: 1.032 / Net I/σ(I): 9.89
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.41-2.475.7781.0111.824285441842030.7551.10995.1
2.47-2.546.1170.8562.2526432433643210.8320.93599.7
2.54-2.626.0230.6622.8625181420741810.890.72599.4
2.62-2.75.9140.6043.1223994407140570.9130.66299.7
2.7-2.795.6120.5093.4822124396339420.9320.56299.5
2.79-2.885.8070.4294.1621903379737720.9470.47299.3
2.88-2.996.1930.3385.1922993373737130.970.36999.4
2.99-3.116.2140.2387.1521793352835070.9830.2699.4
3.11-3.256.1250.198.7620941343934190.9880.20899.4
3.25-3.416.070.1411.1119789327932600.9920.15399.4
3.41-3.65.5990.1113.5117301310930900.9950.12299.4
3.6-3.815.6850.09815.516675295029330.9950.10899.4
3.81-4.086.1550.0771917062277827720.9970.08499.8
4.08-4.46.0270.06920.6215471258725670.9970.07699.2
4.4-4.825.8610.06122.2513907239023730.9980.06799.3
4.82-5.395.4750.06420.3811749216421460.9970.0799.2
5.39-6.235.7780.06219.9610937190618930.9980.06899.3
6.23-7.636.0070.05621.429785163816290.9980.06299.5
7.63-10.795.4690.04324.436945128112700.9990.04799.1
10.79-46.6465.7760.03722.7640667217040.9990.04197.6

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I2E

3i2e


Resolution: 2.412→46.646 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.8 / Phase error: 32.97
RfactorNum. reflection% reflection
Rfree0.2702 2095 3.5 %
Rwork0.223 --
obs0.2246 59837 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.41 Å2 / Biso mean: 48.8041 Å2 / Biso min: 23.14 Å2
Refinement stepCycle: final / Resolution: 2.412→46.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12862 0 0 380 13242
Biso mean---44.73 -
Num. residues----1680
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5010X-RAY DIFFRACTION8.606TORSIONAL
12B5010X-RAY DIFFRACTION8.606TORSIONAL
13C5010X-RAY DIFFRACTION8.606TORSIONAL
14D5010X-RAY DIFFRACTION8.606TORSIONAL
15E5010X-RAY DIFFRACTION8.606TORSIONAL
16F5010X-RAY DIFFRACTION8.606TORSIONAL
LS refinement shellResolution: 2.4123→2.4684 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.4084 132 -
Rwork0.3319 3635 -
obs--95.1 %

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