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- PDB-1xsv: X-ray crystal structure of conserved hypothetical UPF0122 protein... -

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Basic information

Entry
Database: PDB / ID: 1xsv
TitleX-ray crystal structure of conserved hypothetical UPF0122 protein SAV1236 from Staphylococcus aureus subsp. aureus Mu50
ComponentsHypothetical UPF0122 protein SAV1236
KeywordsUNKNOWN FUNCTION / helix-turn-helix / putative DNA-binding protein / signal recognition particle / UPF0122
Function / homology
Function and homology information


Putative helix-turn-helix protein, YlxM/p13-like / : / Putative helix-turn-helix protein, YlxM / p13 like / RNA polymerase sigma factor, region 3/4-like / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
UPF0122 protein SAV1236
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsWalker, J.R. / Xu, X. / Virag, C. / McDonald, M.-L. / Houston, S. / Buzadzija, K. / Vedadi, M. / Dharamsi, A. / Fiebig, K.M. / Savchenko, A.
CitationJournal: To be Published
Title: 1.7 Angstrom Crystal Structure of Conserved Hypothetical UPF0122 Protein SAV1236 From Staphylococcus aureus
Authors: Walker, J.R. / Xu, X. / Virag, C. / McDonald, M.-L. / Houston, S. / Buzadzija, K. / Vedadi, M. / Dharamsi, A. / Fiebig, K.M. / Savchenko, A.
History
DepositionOct 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 UPF0122 protein SAV1236
B: Hypothetical UPF0122 protein SAV1236


Theoretical massNumber of molelcules
Total (without water)27,9442
Polymers27,9442
Non-polymers00
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-16 kcal/mol
Surface area12090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.096, 67.784, 87.978
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer, consisting of Chains A and B.

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Components

#1: Protein Hypothetical UPF0122 protein SAV1236


Mass: 13972.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Species: Staphylococcus aureus / Strain: subsp. aureus / Gene: SAV1236 / Plasmid: pPW2 / Production host: Escherichia coli (E. coli) / References: UniProt: P67248
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M Sodium Acetate, 2.0M Ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97936 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 6, 2004
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97936 Å / Relative weight: 1
ReflectionResolution: 1.7→32 Å / Num. all: 24963 / Num. obs: 24963 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.68 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.054
Reflection shellResolution: 1.7→1.78 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.23 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→32.54 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1237412.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1241 5 %RANDOM
Rwork0.187 ---
obs0.187 24963 99.4 %-
all-24963 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.5857 Å2 / ksol: 0.409932 e/Å3
Displacement parametersBiso mean: 21.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2---4.47 Å20 Å2
3---4.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.03 Å
Refinement stepCycle: LAST / Resolution: 1.7→32.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 0 272 2130
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.421.5
X-RAY DIFFRACTIONc_mcangle_it2.072
X-RAY DIFFRACTIONc_scbond_it2.812
X-RAY DIFFRACTIONc_scangle_it4.322.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.231 180 4.4 %
Rwork0.183 3893 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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