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- PDB-4ok0: Crystal structure of putative nucleotidyltransferase from H. pylori -

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Basic information

Entry
Database: PDB / ID: 4ok0
TitleCrystal structure of putative nucleotidyltransferase from H. pylori
ComponentsPutative
KeywordsTRANSFERASE / Nucleotidyltransferase
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: 2.17 Å
AuthorsYoon, J.Y. / Lee, S.J. / Lee, B. / Yang, J.K. / Suh, S.W.
CitationJournal: Proteins / Year: 2014
Title: Crystal structure of JHP933 from Helicobacter pylori J99 shows two-domain architecture with a DUF1814 family nucleotidyltransferase domain and a helical bundle domain.
Authors: Yoon, J.Y. / Lee, S.J. / Kim, D.J. / Lee, B.J. / Yang, J.K. / Suh, S.W.
History
DepositionJan 21, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative
B: Putative


Theoretical massNumber of molelcules
Total (without water)60,0672
Polymers60,0672
Non-polymers00
Water4,630257
1
A: Putative


Theoretical massNumber of molelcules
Total (without water)30,0331
Polymers30,0331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative


Theoretical massNumber of molelcules
Total (without water)30,0331
Polymers30,0331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.533, 82.533, 155.276
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Putative


Mass: 30033.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: J99 / ATCC 700824 / Gene: jhp_0933 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ZKK2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 200mM ammonium citrate, 20%(w/v) PEG3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Type: OTHER / Wavelength: 0.99999 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.17→20 Å / Num. obs: 31472 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.17→2.25 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.17→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.105 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23974 1585 5 %RANDOM
Rwork0.19029 ---
obs0.19276 29828 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.867 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20.38 Å2-0 Å2
2--0.76 Å2-0 Å2
3----1.14 Å2
Refinement stepCycle: LAST / Resolution: 2.17→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3660 0 0 257 3917
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.023716
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.9784992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8975450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.43724.835182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86915742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1961522
X-RAY DIFFRACTIONr_chiral_restr0.0830.2566
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022724
LS refinement shellResolution: 2.17→2.228 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 122 -
Rwork0.23 2101 -
obs--98.23 %

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