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- PDB-3bpb: Crystal structure of the dimethylarginine dimethylaminohydrolase ... -

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Basic information

Entry
Database: PDB / ID: 3bpb
TitleCrystal structure of the dimethylarginine dimethylaminohydrolase H162G adduct with S-methyl-L-thiocitrulline
Componentsdimethylarginine dimethylaminohydrolase
KeywordsHYDROLASE / enzyme adduct
Function / homology
Function and homology information


dimethylargininase / dimethylargininase activity / citrulline metabolic process / arginine metabolic process / amino acid binding / positive regulation of nitric oxide biosynthetic process / metal ion binding
Similarity search - Function
: / Dimethylarginine dimethylaminohydrolase / N,N dimethylarginine dimethylhydrolase, eukaryotic / L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / Alpha Beta
Similarity search - Domain/homology
Chem-SMZ / N(G),N(G)-dimethylarginine dimethylaminohydrolase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.81 Å
AuthorsMonzingo, A.F. / Linsky, T.W. / Stone, E.M. / Fast, W. / Robertus, J.D.
CitationJournal: Chem.Biol. / Year: 2008
Title: Promiscuous partitioning of a covalent intermediate common in the pentein superfamily.
Authors: Linsky, T.W. / Monzingo, A.F. / Stone, E.M. / Robertus, J.D. / Fast, W.
History
DepositionDec 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: dimethylarginine dimethylaminohydrolase
B: dimethylarginine dimethylaminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2614
Polymers56,8512
Non-polymers4112
Water1,06359
1
A: dimethylarginine dimethylaminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6312
Polymers28,4251
Non-polymers2051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: dimethylarginine dimethylaminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6312
Polymers28,4251
Non-polymers2051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.258, 127.532, 47.339
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A,B, using restrain
21chain A,B, using restrain

NCS ensembles :
IDDetails
1A B
2A B

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Components

#1: Protein dimethylarginine dimethylaminohydrolase


Mass: 28425.424 Da / Num. of mol.: 2 / Mutation: H162G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA1195 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I4E3, dimethylargininase
#2: Chemical ChemComp-SMZ / N~5~-[(E)-imino(methylsulfanyl)methyl]-L-ornithine / S-methyl-L-thiocitrulline


Mass: 205.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H15N3O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG4000, 0.1 M Tris-HCl, 0.2 M sodium acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 22, 2006 / Details: Blue Max-Flux confocal
RadiationMonochromator: Blue Max-Flux confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.81→50 Å / Num. obs: 12825 / % possible obs: 96.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.137 / Χ2: 1.129 / Net I/σ(I): 5.4
Reflection shellResolution: 2.81→2.91 Å / Redundancy: 3 % / Rmerge(I) obs: 0.465 / Num. unique all: 1236 / Χ2: 0.664 / % possible all: 95

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.373 / Cor.coef. Fo:Fc: 0.655
Highest resolutionLowest resolution
Rotation4 Å39.46 Å
Translation4 Å39.46 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1H70

1h70


Resolution: 2.81→20 Å / FOM work R set: 0.774 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.297 573 4.3 %random
Rwork0.233 ---
obs-11429 85.3 %-
Solvent computationBsol: 10 Å2
Displacement parametersBiso mean: 29.823 Å2
Baniso -1Baniso -2Baniso -3
1--11.575 Å20 Å20 Å2
2--8.495 Å20 Å2
3---3.08 Å2
Refinement stepCycle: LAST / Resolution: 2.81→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3978 0 22 59 4059
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.373
X-RAY DIFFRACTIONc_mcbond_it0.9841.5
X-RAY DIFFRACTIONc_scbond_it1.3862
X-RAY DIFFRACTIONc_mcangle_it1.6922
X-RAY DIFFRACTIONc_scangle_it2.1942.5
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDRmsTypeWeight
11BX-RAY DIFFRACTION0.028restrain300
12BX-RAY DIFFRACTION0.082restrain100
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5smtc.parsmtc.top

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