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- PDB-6juz: Crystal Structure of N-terminal domain of ArgZ(N71S) covalently b... -

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Basic information

Entry
Database: PDB / ID: 6juz
TitleCrystal Structure of N-terminal domain of ArgZ(N71S) covalently bond to a reaction intermediate
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 / 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 / Arginine deiminase / 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: 1.21 Å
AuthorsZhuang, N. / Li, L. / Wu, X. / Zhuang, 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

Downloads & links

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Assembly

Deposited unit
A: Sll1336 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,34512
Polymers34,5491
Non-polymers79611
Water4,738263
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)40.530, 87.549, 43.196
Angle α, β, γ (deg.)90.000, 93.740, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sll1336 protein


Mass: 34549.410 Da / Num. of mol.: 1 / Fragment: N terminal domain of ArgZ / Mutation: N71S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: sll1336 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta (DE3) / References: UniProt: P74535
#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.38 Å3/Da / Density % sol: 48.24 %
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: BL17U1 / Wavelength: 0.97916 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 1.21→50 Å / Num. obs: 89713 / % possible obs: 98.2 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.027 / Rrim(I) all: 0.061 / Χ2: 0.856 / Net I/σ(I): 18.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.21-1.233.80.48944560.8040.2760.5640.97297.2
1.23-1.254.30.45245300.860.2420.5150.96199.5
1.25-1.284.40.41245350.8830.2180.4680.97899.5
1.28-1.34.50.35745440.9110.1860.4030.96499.4
1.3-1.334.60.30644660.9250.1610.3470.95599.1
1.33-1.364.60.25845170.9340.1350.2920.94298.8
1.36-1.44.50.21345140.9460.1130.2430.94498.1
1.4-1.434.40.17542860.9590.0930.1990.91994.7
1.43-1.484.70.1443640.9760.0720.1580.87896.3
1.48-1.524.90.11645280.9810.0590.130.87799.5
1.52-1.5850.09545210.9860.0470.1070.86299.5
1.58-1.644.90.07845390.9890.0390.0870.81599.4
1.64-1.7250.06845290.990.0340.0760.8198.9
1.72-1.814.90.05745450.9910.0290.0640.76499.1
1.81-1.924.70.05344030.990.0270.060.84496.6
1.92-2.0750.04843430.9930.0230.0530.80795.3
2.07-2.285.50.04645910.9940.0220.0510.81399.7
2.28-2.615.40.04445520.9940.0210.0490.76999.5
2.61-3.285.30.04145150.9950.0190.0450.69998.4
3.28-504.80.04244350.9930.0220.0480.68995.1

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JV0

6jv0


Resolution: 1.21→25.026 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 17.84
RfactorNum. reflection% reflection
Rfree0.1754 4408 4.95 %
Rwork0.1656 --
obs0.1661 89094 97.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 63.01 Å2 / Biso mean: 19.2384 Å2 / Biso min: 9.92 Å2
Refinement stepCycle: final / Resolution: 1.21→25.026 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2183 0 51 263 2497
Biso mean--24.19 31.53 -
Num. residues----272
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2104-1.22410.24091350.2262574270988
1.2241-1.23850.23791400.21922802294297
1.2385-1.25360.22781410.22062814295598
1.2536-1.26950.21491470.21252881302898
1.2695-1.28620.21271550.21352776293198
1.2862-1.30380.22761510.21042898304999
1.3038-1.32250.23321450.20962778292399
1.3225-1.34220.2121640.20152841300599
1.3422-1.36320.24931340.19712857299199
1.3632-1.38550.18671500.19562836298698
1.3855-1.40940.20531530.18442786293997
1.4094-1.4350.18821560.18112685284193
1.435-1.46260.20591390.18362725286494
1.4626-1.49250.19181420.175928733015100
1.4925-1.52490.17021370.17528723009100
1.5249-1.56040.21291330.173528883021100
1.5604-1.59940.16841510.16852890304199
1.5994-1.64270.1881570.16452824298199
1.6427-1.6910.18931520.16722894304699
1.691-1.74560.18661470.16392863301099
1.7456-1.80790.1751380.16562882302099
1.8079-1.88030.17361240.16392815293997
1.8803-1.96580.16021350.16462689282493
1.9658-2.06940.16121760.15862789296598
2.0694-2.1990.16141810.161628663047100
2.199-2.36870.18791360.158629193055100
2.3687-2.60680.17111190.16812907302699
2.6068-2.98350.17211170.16692886300399
2.9835-3.75690.17181940.15942750294495
3.7569-25.03150.15341590.14362826298596

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