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- PDB-6jv1: Crystal Structure of N-terminal domain of ArgZ, C264S mutant, bou... -

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Basic information

Entry
Database: PDB / ID: 6jv1
TitleCrystal Structure of N-terminal domain of ArgZ, C264S mutant, bound to Substrate, an arginine dihydrolase from the Ornithine-Ammonia Cycle in Cyanobacteria
ComponentsSll1336 protein
KeywordsHYDROLASE / arginine dihydrolase / amidino-transferase domain / alpha/beta propeller fold
Function / homology
Function and homology information


arginine dihydrolase / ornithine cyclodeaminase / hydrolase activity / lyase activity / nucleotide binding
Similarity search - Function
Conserved hypothetical protein CHP00300 / LOR/SDH bifunctional enzyme, conserved domain / : / : / LOR/SDH bifunctional enzyme conserved region / Arginine dihydrolase ArgZ-like, C-terminal, Rossmann fold / Arginine dihydrolase ArgZ-like, C-terminal, first region / N,N dimethylarginine dimethylhydrolase, eukaryotic / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
ARGININE / Bifunctional arginine dihydrolase/ornithine cyclodeaminase ArgZ
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsZhuang, N. / Li, L. / Wu, X. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31822001 China
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Crystal structures and biochemical analyses of the bacterial arginine dihydrolase ArgZ suggests a "bond rotation" catalytic mechanism.
Authors: Zhuang, N. / Zhang, H. / Li, L. / Wu, X. / Yang, C. / Zhang, Y.
History
DepositionApr 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 26, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Nov 22, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sll1336 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7362
Polymers34,5601
Non-polymers1751
Water5,801322
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.346, 87.256, 42.818
Angle α, β, γ (deg.)90.000, 93.190, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sll1336 protein


Mass: 34560.371 Da / Num. of mol.: 1 / Fragment: N-terminal domain of ArgZ / Mutation: C264S
Source method: isolated from a genetically manipulated source
Details: substrate
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: sll1336 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P74535
#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H15N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.2 M KI, 0.1 M MES pH 6.5, 19% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.16→50 Å / Num. obs: 98683 / % possible obs: 97 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.038 / Rrim(I) all: 0.101 / Χ2: 0.942 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.16-1.185.60.74747500.7240.3350.8210.78893.7
1.18-1.260.6847130.770.2960.7430.80493.5
1.2-1.226.70.60248480.8380.2470.6510.81594.9
1.22-1.256.80.53748520.8620.220.5810.84296
1.25-1.286.70.44348590.8990.1830.480.89896.2
1.28-1.316.60.38748610.9120.1610.420.92495.8
1.31-1.346.40.32249200.9340.1350.3490.96796.4
1.34-1.386.30.27848060.9490.1180.3031.03295.6
1.38-1.426.90.2449040.9580.0970.2591.05496.9
1.42-1.466.90.20949280.9690.0850.2261.07496.9
1.46-1.516.90.18749280.9690.0770.2031.11196.9
1.51-1.576.80.16749580.9740.0690.1811.1397.8
1.57-1.656.40.15249810.9770.0640.1651.13797.7
1.65-1.736.80.1449820.9830.0570.1511.197.9
1.73-1.847.10.12750020.9830.0510.1371.04798.5
1.84-1.9870.11750330.9850.0480.127199.1
1.98-2.186.80.10750580.9870.0440.1160.93199.2
2.18-2.56.50.150670.9880.0420.1090.84699
2.5-3.157.20.08950850.9920.0360.0960.70499.8
3.15-506.80.08151480.9890.0340.0880.61199.1

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JV0

6jv0


Resolution: 1.2→43.63 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1816 2014 2.25 %
Rwork0.1721 87625 -
obs0.1724 89639 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.3 Å2 / Biso mean: 19.7262 Å2 / Biso min: 9.68 Å2
Refinement stepCycle: final / Resolution: 1.2→43.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2181 0 12 322 2515
Biso mean--13.06 30.79 -
Num. residues----271
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.230.25961530.23756092624595
1.23-1.260.2581310.236179631095
1.26-1.30.24181530.22376123627696
1.3-1.340.22981250.21096191631696
1.34-1.390.24841320.20676121625395
1.39-1.450.19811540.1956182633697
1.45-1.510.22571440.19256238638297
1.51-1.590.20491490.18446278642798
1.59-1.690.17981400.17736249638997
1.69-1.820.2011620.17716313647599
1.82-2.010.1771350.17166391652699
2.01-2.30.18631410.17016363650499
2.3-2.890.18591450.17216436658199
2.89-43.630.14931500.15246469661999

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