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- PDB-6btc: SCCmec type IV LP1413 - nucleic acids binding protein -

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Basic information

Entry
Database: PDB / ID: 6btc
TitleSCCmec type IV LP1413 - nucleic acids binding protein
ComponentsLP1413 - SCCmec type IV-encoded DNA binding protein
KeywordsDNA BINDING PROTEIN
Function / homologyDomain of uncharacterized function (DUF1413)
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.17740739208 Å
AuthorsRice, P.A. / Mir-Sanchis, I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM121655 United States
CitationJournal: Structure / Year: 2018
Title: Crystal Structure of an Unusual Single-Stranded DNA-Binding Protein Encoded by Staphylococcal Cassette Chromosome Elements.
Authors: Mir-Sanchis, I. / Pigli, Y.Z. / Rice, P.A.
History
DepositionDec 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 22, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 9, 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

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Assembly

Deposited unit
A: LP1413 - SCCmec type IV-encoded DNA binding protein
B: LP1413 - SCCmec type IV-encoded DNA binding protein


Theoretical massNumber of molelcules
Total (without water)21,9652
Polymers21,9652
Non-polymers00
Water2,108117
1
A: LP1413 - SCCmec type IV-encoded DNA binding protein


Theoretical massNumber of molelcules
Total (without water)10,9821
Polymers10,9821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LP1413 - SCCmec type IV-encoded DNA binding protein


Theoretical massNumber of molelcules
Total (without water)10,9821
Polymers10,9821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.033, 97.033, 127.794
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11B-157-

HOH

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Components

#1: Protein LP1413 - SCCmec type IV-encoded DNA binding protein


Mass: 10982.456 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: CEJ93_14580, R114_18, R15_21, R17_21, R92_18, R95_21, R99_21
Production host: Escherichia coli (E. coli) / References: UniProt: Q0WXP5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 3.95 Å3/Da / Density % sol: 68.89 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop
Details: 100mM NaCitrate, pH6, 10mM MgCl2-1.8M Li2SO4-14% Glycerol-5mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.177→48.5165 Å / Num. obs: 18476 / % possible obs: 96.823 % / Redundancy: 27.9 % / Biso Wilson estimate: 29.6711641615 Å2 / Net I/σ(I): 27.3
Reflection shellResolution: 2.1774→2.2363 Å

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
REFMAC1.12_2829refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.17740739208→48.5165 Å / SU ML: 0.267310965461 / Cross valid method: FREE R-VALUE / σ(F): 0.221462839837 / Phase error: 24.9491275769
RfactorNum. reflection% reflection
Rfree0.251193461653 1850 10.0129898246 %
Rwork0.220223362636 --
obs0.223309918529 18476 96.054068105 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.0356877907 Å2
Refinement stepCycle: LAST / Resolution: 2.17740739208→48.5165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1343 0 0 117 1460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005903159767741374
X-RAY DIFFRACTIONf_angle_d0.6613124188141845
X-RAY DIFFRACTIONf_chiral_restr0.0429883280926192
X-RAY DIFFRACTIONf_plane_restr0.00420236083358232
X-RAY DIFFRACTIONf_dihedral_angle_d9.31524705713823
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1774-2.23630.396548561735940.303128133267828X-RAY DIFFRACTION64.0277777778
2.2363-2.30210.324209825251400.2910258327311234X-RAY DIFFRACTION95.020746888
2.3021-2.37640.307958746461350.269098276161256X-RAY DIFFRACTION96.3963963964
2.3764-2.46130.3061363027821400.2544058314921261X-RAY DIFFRACTION96.955017301
2.4613-2.55990.260202955491430.2653144031631287X-RAY DIFFRACTION98.3493810179
2.5599-2.67640.2945042255881440.2455261411091288X-RAY DIFFRACTION98.4869325997
2.6764-2.81740.2616117549181450.2628490542471301X-RAY DIFFRACTION99.381443299
2.8174-2.99390.2833248289371460.2454579643261311X-RAY DIFFRACTION99.7262149213
2.9939-3.22510.2857846445511490.2313230981731334X-RAY DIFFRACTION99.9326145553
3.2251-3.54950.2243496439861470.2007241973031325X-RAY DIFFRACTION99.9321113374
3.5495-4.06290.2019115647431500.1745836197161351X-RAY DIFFRACTION99.9334221039
4.0629-5.1180.1852211966691520.1633436754091375X-RAY DIFFRACTION99.6086105675
5.118-48.52850.2623569059341650.233005974611475X-RAY DIFFRACTION99.8781973203

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