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- PDB-6juy: Crystal Structure of ArgZ, apo structure, an Arginine Dihydrolase... -

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Basic information

Entry
Database: PDB / ID: 6juy
TitleCrystal Structure of ArgZ, apo structure, an Arginine Dihydrolase from the Ornithine-Ammonia Cycle in Cyanobacteria
ComponentsSll1336 protein
KeywordsHYDROLASE / arginine dihydrolase / amidino-transferase domain / alpha/beta propeller fold / LOR/SDH superfamily
Function / homology
Function and homology information


arginine dihydrolase / ornithine cyclodeaminase / lyase activity / hydrolase activity / nucleotide binding
Similarity search - Function
putative lor/sdh protein like domains / 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 / Arginine deiminase ...putative lor/sdh protein like domains / 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 / Arginine deiminase / L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Bifunctional arginine dihydrolase/ornithine cyclodeaminase ArgZ
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 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 / 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

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Assembly

Deposited unit
A: Sll1336 protein
B: Sll1336 protein
C: Sll1336 protein
D: Sll1336 protein


Theoretical massNumber of molelcules
Total (without water)314,1754
Polymers314,1754
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13930 Å2
ΔGint-62 kcal/mol
Surface area98760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.865, 105.439, 165.905
Angle α, β, γ (deg.)90.000, 113.180, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 4 through 6 and (name N...
21(chain B and ((resid 4 through 6 and (name N...
31(chain C and (resid 4 through 12 or (resid 34...
41(chain D and ((resid 4 through 6 and (name N...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 4 through 6 and (name N...A0
211(chain B and ((resid 4 through 6 and (name N...B0
311(chain C and (resid 4 through 12 or (resid 34...C0
411(chain D and ((resid 4 through 6 and (name N...D4 - 6
421(chain D and ((resid 4 through 6 and (name N...D3 - 696
431(chain D and ((resid 4 through 6 and (name N...D3 - 696
441(chain D and ((resid 4 through 6 and (name N...D3 - 696
451(chain D and ((resid 4 through 6 and (name N...D3 - 696

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Components

#1: Protein
Sll1336 protein


Mass: 78543.867 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: sll1336 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P74535
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.24 M ammonium formate, 17% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979176 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979176 Å / Relative weight: 1
ReflectionResolution: 2.97→48.74 Å / Num. obs: 60551 / % possible obs: 97.3 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.02 / Rrim(I) all: 0.044 / Net I/σ(I): 18.4 / Num. measured all: 263617 / Scaling rejects: 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.97-3.054.50.5642054045240.8660.2920.637299
13.28-48.744.20.02429467040.9990.0130.02842.795.1

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
XDSdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C2Q, 3MGJ, 6JV0

3c2q

3mgj

6jv0


Resolution: 2.97→41.06 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2747 1987 3.28 %
Rwork0.2341 58522 -
obs0.2354 60509 97.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 191.72 Å2 / Biso mean: 109.3208 Å2 / Biso min: 58.32 Å2
Refinement stepCycle: final / Resolution: 2.97→41.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18514 0 0 5 18519
Biso mean---78.98 -
Num. residues----2555
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A9856X-RAY DIFFRACTION17.734TORSIONAL
12B9856X-RAY DIFFRACTION17.734TORSIONAL
13C9856X-RAY DIFFRACTION17.734TORSIONAL
14D9856X-RAY DIFFRACTION17.734TORSIONAL
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 (%)
2.97-3.040.39161500.3674211436199
3.04-3.130.34461430.32594260440399
3.13-3.220.32781430.28794187433098
3.22-3.320.33751510.28434183433498
3.32-3.440.35321250.28934011413694
3.44-3.580.37791420.2894116425895
3.58-3.740.33171480.2684219436799
3.74-3.940.31991370.26154238437599
3.94-4.190.28131440.24284236438098
4.19-4.510.26051430.21654183432698
4.51-4.960.25181340.21164160429496
4.96-5.680.28411400.23744065420594
5.68-7.150.30441420.2524285442799
7.15-41.060.20011450.18574168431394

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