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- PDB-1ku9: X-ray Structure of a Methanococcus jannaschii DNA-Binding Protein... -

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Basic information

Entry
Database: PDB / ID: 1ku9
TitleX-ray Structure of a Methanococcus jannaschii DNA-Binding Protein: Implications for Antibiotic Resistance in Staphylococcus aureus
Componentshypothetical protein MJ223Hypothesis
KeywordsDNA BINDING PROTEIN / putative transcription factor / homodimeric winged-helix fold / STRUCTURAL GENOMICS / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
DNA-binding protein, MJ1563 type / Helix hairpin bin / Bacterial regulatory protein, arsR family / ArsR-type HTH domain profile. / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helix Hairpins / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...DNA-binding protein, MJ1563 type / Helix hairpin bin / Bacterial regulatory protein, arsR family / ArsR-type HTH domain profile. / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helix Hairpins / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Putative HTH-type transcriptional regulator MJ1563
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsRay, S.S. / Bonanno, J.B. / Chen, H. / de Lencastre, H. / Wu, S. / Tomasz, A. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Proteins / Year: 2002
Title: X-ray structure of an M. jannaschii DNA-binding protein: implications for antibiotic resistance in S. aureus
Authors: Ray, S.S. / Bonanno, J.B. / Chen, H. / de Lencastre, H. / Wu, S. / Tomasz, A. / Burley, S.K.
History
DepositionJan 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein MJ223
B: hypothetical protein MJ223


Theoretical massNumber of molelcules
Total (without water)35,7512
Polymers35,7512
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-52 kcal/mol
Surface area17200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.939, 56.939, 209.515
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Detailsasymmetric unit represents the putative biological assembly

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Components

#1: Protein hypothetical protein MJ223 / Hypothesis / HYPOTHETICAL PROTEIN MJ1563


Mass: 17875.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: NYSGRC target T088
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: Mj223 / Plasmid details: variation on pET18B / Plasmid: pSKB2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q58958
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.74 Å3/Da / Density % sol: 55.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% dioxane, 30% PEG 8000, TRIS pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 MTris1reservoirpH8.0
230 %PEG80001reservoir
310 %dioxane1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9793, 0.9790, 0.9686
DetectorType: BRANDEIS - B1 / Detector: CCD / Date: Jan 19, 2001
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.9791
30.96861
ReflectionResolution: 2.8→30 Å / Num. all: 9501 / Num. obs: 9454 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 66 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 38.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 7.7 / Num. unique all: 941 / Rsym value: 0.208 / % possible all: 99.4
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 9469 / % possible obs: 99.7 % / Num. measured all: 137127
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 6.9

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Processing

Software
NameVersionClassification
MARMADdata collection
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
MLPHAREphasing
DMmodel building
CNS1refinement
MARMADdata reduction
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Data were twinned and appeared to have P6(5)22 symmetry. Refined as space group P6(5) with twinning fraction of 0.485.
RfactorNum. reflectionSelection details
Rfree0.28 849 random
Rwork0.241 --
all0.245 9426 -
obs0.245 9257 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.299 Å2-9.42 Å20 Å2
2--0.299 Å20 Å2
3----0.599 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2452 0 0 86 2538
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.47
X-RAY DIFFRACTIONc_mcbond_it1.15
X-RAY DIFFRACTIONc_scbond_it1.83
X-RAY DIFFRACTIONc_mcangle_it2.02
X-RAY DIFFRACTIONc_scangle_it3
Refinement
*PLUS
Lowest resolution: 28.5 Å / Num. reflection obs: 11373 / Num. reflection Rfree: 1056 / % reflection Rfree: 9 % / Rfactor Rfree: 0.293 / Rfactor Rwork: 0.262
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.38

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