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- PDB-8dtq: Crystal Structure of Staphylococcus aureus pSK41 Cop -

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Basic information

Entry
Database: PDB / ID: 8dtq
TitleCrystal Structure of Staphylococcus aureus pSK41 Cop
ComponentsHelix-turn-helix domain
KeywordsDNA BINDING PROTEIN / transcriptional regulator / conjugation
Function / homology
Function and homology information


Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Helix-turn-helix domain
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsWalton, W.G. / Eakes, T.C. / Redinbo, M.R. / McLaughlin, K.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Plasmid / Year: 2023
Title: pSK41/pGO1-family conjugative plasmids of Staphylococcus aureus encode a cryptic repressor of replication.
Authors: Sarosh, A. / Kwong, S.M. / Jensen, S.O. / Northern, F. / Walton, W.G. / Eakes, T.C. / Redinbo, M.R. / Firth, N. / McLaughlin, K.J.
History
DepositionJul 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 6, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Helix-turn-helix domain
B: Helix-turn-helix domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4749
Polymers21,2752
Non-polymers1987
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-67 kcal/mol
Surface area8570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.460, 56.261, 46.018
Angle α, β, γ (deg.)90.000, 104.344, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 2 through 5 and (name N...
d_2ens_1(chain "B" and (resid 2 through 6 or resid 8...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASNILEA2 - 6
d_12ens_1LYSTYRA8 - 10
d_13ens_1TYRGLNA12 - 22
d_14ens_1ILELEUA24 - 35
d_15ens_1VALGLYA37 - 40
d_16ens_1LEUPROA42 - 51
d_17ens_1ILEVALA53 - 60
d_18ens_1SERALAA62 - 76
d_19ens_1GLUGLUA78 - 84
d_21ens_1ASNILEB1 - 5
d_22ens_1LYSTYRB7 - 9
d_23ens_1TYRGLNB11 - 21
d_24ens_1ILELEUB23 - 34
d_25ens_1VALGLYB36 - 39
d_26ens_1LEUPROB41 - 50
d_27ens_1ILEVALB52 - 59
d_28ens_1SERALAB61 - 75
d_29ens_1GLUGLUB77 - 83

NCS oper: (Code: givenMatrix: (0.0492094633824, -0.932536964232, -0.357705520023), (-0.924367706722, -0.178175985902, 0.337339088779), (-0.378315703459, 0.314051155689, -0.870774999714)Vector: 55. ...NCS oper: (Code: given
Matrix: (0.0492094633824, -0.932536964232, -0.357705520023), (-0.924367706722, -0.178175985902, 0.337339088779), (-0.378315703459, 0.314051155689, -0.870774999714)
Vector: 55.1641864704, 39.2592474568, 59.6519002052)

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Components

#1: Protein Helix-turn-helix domain / Helix-turn-helix domain protein / Helix-turn-helix domain-containing protein


Mass: 10637.744 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: BN1321_460002, FA040_14490, GO782_04310, GQX37_01460, SAMEA2078260_02861, SAMEA2078588_02856, SAMEA2081063_02868, SAMEA2081470_02943, SAP014A_023, SAP015H_002, SAP068A_002, SAP069A_028, SAP079A_ ...Gene: BN1321_460002, FA040_14490, GO782_04310, GQX37_01460, SAMEA2078260_02861, SAMEA2078588_02856, SAMEA2081063_02868, SAMEA2081470_02943, SAP014A_023, SAP015H_002, SAP068A_002, SAP069A_028, SAP079A_025, SAP080A_043, SAP082A_020, VRA0062
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O87366
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 3M sodium chloride, 0.1M sodium acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97942 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 2, 2012
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.45→44.58 Å / Num. obs: 33440 / % possible obs: 99.45 % / Redundancy: 2 % / Biso Wilson estimate: 18.43 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.07654 / Rrim(I) all: 0.1082 / Net I/σ(I): 14.4
Reflection shellResolution: 1.45→1.504 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.72 / Num. unique obs: 3284 / CC1/2: 0.673 / Rrim(I) all: 0.7004 / % possible all: 98.44

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
SCALAdata scaling
Cootmodel building
JBluIce-EPICSdata collection
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→44.58 Å / SU ML: 0.1632 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.449
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2227 1999 5.98 %
Rwork0.1883 31437 -
obs0.1903 33436 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.93 Å2
Refinement stepCycle: LAST / Resolution: 1.45→44.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1350 0 7 140 1497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651442
X-RAY DIFFRACTIONf_angle_d0.79131949
X-RAY DIFFRACTIONf_chiral_restr0.0758213
X-RAY DIFFRACTIONf_plane_restr0.0065251
X-RAY DIFFRACTIONf_dihedral_angle_d18.0679205
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.920860555007 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.490.36181400.2832209X-RAY DIFFRACTION98.33
1.49-1.530.26941400.25172212X-RAY DIFFRACTION98.58
1.53-1.570.26131400.22212200X-RAY DIFFRACTION98.82
1.57-1.620.26171430.19632252X-RAY DIFFRACTION99.25
1.62-1.680.25561420.19122224X-RAY DIFFRACTION99.12
1.68-1.750.25341420.17822238X-RAY DIFFRACTION99.42
1.75-1.830.2351420.17112241X-RAY DIFFRACTION99.42
1.83-1.930.23461440.1772249X-RAY DIFFRACTION99.71
1.93-2.050.19731410.17482220X-RAY DIFFRACTION99.75
2.05-2.20.2081440.16082273X-RAY DIFFRACTION99.92
2.21-2.430.19011460.17642274X-RAY DIFFRACTION100
2.43-2.780.22021430.19312249X-RAY DIFFRACTION100
2.78-3.50.24351460.19672286X-RAY DIFFRACTION100
3.5-44.580.20471460.18662310X-RAY DIFFRACTION99.96

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