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- PDB-6c5d: N-terminal domain of Helicobacter pylori LlaJI.R1 -

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Basic information

Entry
Database: PDB / ID: 6c5d
TitleN-terminal domain of Helicobacter pylori LlaJI.R1
ComponentsLlaJI.R1
KeywordsDNA BINDING PROTEIN / B3 domain / restriction endonuclease
Function / homology: / ATPase, dynein-related, AAA domain / AAA domain (dynein-related subfamily) / ATP hydrolysis activity / P-loop containing nucleoside triphosphate hydrolase / ATP binding / Restriction enzyme
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsHosford, C.J. / Chappie, J.S.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: The crystal structure of theHelicobacter pyloriLlaJI.R1 N-terminal domain provides a model for site-specific DNA binding.
Authors: Hosford, C.J. / Chappie, J.S.
History
DepositionJan 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: LlaJI.R1
D: LlaJI.R1
B: LlaJI.R1
C: LlaJI.R1


Theoretical massNumber of molelcules
Total (without water)68,0254
Polymers68,0254
Non-polymers00
Water4,414245
1
A: LlaJI.R1
B: LlaJI.R1


Theoretical massNumber of molelcules
Total (without water)34,0122
Polymers34,0122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-15 kcal/mol
Surface area12700 Å2
MethodPISA
2
D: LlaJI.R1
C: LlaJI.R1


Theoretical massNumber of molelcules
Total (without water)34,0122
Polymers34,0122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-13 kcal/mol
Surface area13050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.526, 43.771, 85.091
Angle α, β, γ (deg.)97.87, 93.86, 97.77
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
LlaJI.R1 / Putative restriction enzyme


Mass: 17006.238 Da / Num. of mol.: 4 / Fragment: N-terminal domain (UNP residues 1-137)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: J99 / ATCC 700824 / Gene: jhp_0164 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9ZMQ4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.01 Å3/Da / Density % sol: 38.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MMT, pH 6.5, 25% v/v PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 21, 2017
RadiationMonochromator: Cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.97→83.97 Å / Num. obs: 152937 / % possible obs: 93.6 % / Redundancy: 3.68 % / CC1/2: 0.997 / Rrim(I) all: 0.096 / Net I/σ(I): 9
Reflection shellResolution: 1.97→2.1 Å / Redundancy: 1.91 % / Mean I/σ(I) obs: 1.56 / Num. unique obs: 23180 / CC1/2: 0.709 / Rrim(I) all: 0.624 / % possible all: 90.1

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→83.97 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs152937 93.6 %
Refinement stepCycle: LAST / Resolution: 1.97→83.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4124 0 0 245 4369

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