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- PDB-4o8s: Crystal structure of JHP933 from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 4o8s
TitleCrystal structure of JHP933 from Helicobacter pylori
ComponentsPutative
KeywordsHYDROLASE / nucleotidyl transferase
Function / homology
Function and homology information


JHP933, helical tail domain / JHP933, nucleotidyltransferase-like core domain / Nucleotidyl transferase AbiEii toxin, Type IV TA system / Nucleotidyl transferase AbiEii toxin, Type IV TA system / Nuclear Transport Factor 2; Chain: A, / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Roll / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsZhao, Y.H. / Su, Y.T. / Sun, L.F. / Wu, Y.
CitationJournal: Plos One / Year: 2014
Title: Crystal Structure Confirmation of JHP933 as a Nucleotidyltransferase Superfamily Protein from Helicobacter pylori Strain J99
Authors: Zhao, Y. / Ye, X. / Su, Y. / Sun, L. / She, F. / Wu, Y.
History
DepositionDec 30, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative


Theoretical massNumber of molelcules
Total (without water)26,9351
Polymers26,9351
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.056, 90.056, 70.867
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Detailsbiological unit is the same as asym.

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Components

#1: Protein Putative


Mass: 26935.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: J99 / ATCC 700824 / Gene: 933, jhp_0933 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZKK2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 3.08 Å3/Da / Density % sol: 60.06 % / Mosaicity: 0.23 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Potassium Sodium tartarate, 0.1M Tris-HCl, 32%(v/w) PEG4000, pH 7.5, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 3, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 20549 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.139 / Χ2: 1.821 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.05-2.126.30.93220360.8051100
2.12-2.216.30.58520400.8891100
2.21-2.316.30.44320431.0121100
2.31-2.436.30.30420601.1461100
2.43-2.586.30.23620341.4561100
2.58-2.786.30.18520471.6891100
2.78-3.066.30.14520622.0171100
3.06-3.516.30.11620622.2891100
3.51-4.426.30.11920733.0451100
4.42-506.10.11820923.9199

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→38.005 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8335 / SU ML: 0.21 / σ(F): 0 / Phase error: 24.09 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 1829 9.66 %RANDOM
Rwork0.2043 ---
all0.207 ---
obs0.207 18941 98.74 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.442 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso max: 125.43 Å2 / Biso mean: 47.0548 Å2 / Biso min: 21.66 Å2
Baniso -1Baniso -2Baniso -3
1-1.7633 Å2-0 Å2-0 Å2
2--1.7633 Å2-0 Å2
3----3.5265 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1867 0 0 76 1943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081893
X-RAY DIFFRACTIONf_angle_d1.1372543
X-RAY DIFFRACTIONf_chiral_restr0.082290
X-RAY DIFFRACTIONf_plane_restr0.004327
X-RAY DIFFRACTIONf_dihedral_angle_d14.209732
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.15680.29331310.26871269140095
2.1568-2.22030.30131380.24931287142598
2.2203-2.29190.28331400.24711297143798
2.2919-2.37380.28681400.23561306144699
2.3738-2.46890.25281390.22611292143198
2.4689-2.58120.28751390.22791330146999
2.5812-2.71720.32521430.23031315145899
2.7172-2.88740.25951370.229913201457100
2.8874-3.11030.25841430.214313471490100
3.1103-3.42310.24671410.212513101451100
3.4231-3.9180.2181480.19413481496100
3.918-4.93460.15861480.167113251473100
4.9346-38.01140.20911420.18721366150899

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