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- PDB-2ooi: The crystal structure of gene product SA0254 from Staphylocococcu... -

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Basic information

Entry
Database: PDB / ID: 2ooi
TitleThe crystal structure of gene product SA0254 from Staphylocococcus aureus subsp. aureus N315
ComponentsSA0254 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Staphylocococcus aureus / PSI-2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


transaminase activity / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
UTRA / UbiC transcription regulator-associated / UTRA domain / Chorismate lyase / Chorismate lyase-like / Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family ...UTRA / UbiC transcription regulator-associated / UTRA domain / Chorismate lyase / Chorismate lyase-like / Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SA0254 protein / SA0254 protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsZhang, R. / Duggan, E. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of gene product SA0254 from Staphylocococcus aureus subsp. aureus N315
Authors: Zhang, R. / Duggan, E. / Gu, M. / Joachimiak, A.
History
DepositionJan 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SA0254 protein
B: SA0254 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1004
Polymers37,9692
Non-polymers1312
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-89 kcal/mol
Surface area14590 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)116.104, 116.104, 86.185
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsThis protein existed as dimer. The deposited coords. of MolA and MolB represent the dimer in the asymmetric unit.

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Components

#1: Protein SA0254 protein


Mass: 18984.523 Da / Num. of mol.: 2 / Fragment: Residues 73-234
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Species: Staphylococcus aureus / Strain: N315 / Gene: SA0254 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7A7U1, UniProt: A0A0H3JL95*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 4.42 Å3/Da / Density % sol: 72.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 2M Ammonium sulfate, 0.1M CAPS, 0.2M Lithium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 2, 2006 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 19411 / Num. obs: 19380 / % possible obs: 99.84 % / Observed criterion σ(I): 2 / Redundancy: 14.5 % / Biso Wilson estimate: 50.1 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 28.57
Reflection shellResolution: 2.6→2.668 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2 / % possible all: 98.61

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→48.17 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.906 / SU B: 19.317 / SU ML: 0.203 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.332 / ESU R Free: 0.267
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The N-terminal of Mol.A (residues 73-86) and Mol.B (residues 73-88) can not be refined very well due to the lack of the density of the sidechains.
RfactorNum. reflection% reflectionSelection details
Rfree0.27002 1038 5.1 %RANDOM
Rwork0.22361 ---
obs0.22595 19380 99.84 %-
all-19380 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.097 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0.04 Å20 Å2
2---0.08 Å20 Å2
3---0.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.045 Å0.042 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.6→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2592 0 2 49 2643
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222704
X-RAY DIFFRACTIONr_bond_other_d0.0010.021853
X-RAY DIFFRACTIONr_angle_refined_deg1.7981.9553647
X-RAY DIFFRACTIONr_angle_other_deg1.07434500
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4275318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73723.897136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.20615480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4961514
X-RAY DIFFRACTIONr_chiral_restr0.1160.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022971
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02587
X-RAY DIFFRACTIONr_nbd_refined0.2370.2580
X-RAY DIFFRACTIONr_nbd_other0.2050.21992
X-RAY DIFFRACTIONr_nbtor_refined0.1970.21246
X-RAY DIFFRACTIONr_nbtor_other0.0910.21542
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.293
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1660.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1950.215
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0710.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0111.52040
X-RAY DIFFRACTIONr_mcbond_other0.1191.5642
X-RAY DIFFRACTIONr_mcangle_it1.20322598
X-RAY DIFFRACTIONr_scbond_it1.61531310
X-RAY DIFFRACTIONr_scangle_it2.4114.51049
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 67 -
Rwork0.336 1422 -
obs--98.61 %
Refinement TLS params.Method: refined / Origin x: 19.811 Å / Origin y: 44.744 Å / Origin z: 57.401 Å
111213212223313233
T0.1201 Å20.1106 Å2-0.009 Å2-0.1793 Å2-0.0092 Å2---0.0402 Å2
L1.1385 °2-0.2523 °21.5851 °2-0.2805 °2-0.7105 °2--3.2025 °2
S0.083 Å °-0.1248 Å °-0.1777 Å °0.0195 Å °0.0793 Å °0.1004 Å °0.1184 Å °-0.2299 Å °-0.1623 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA73 - 911 - 19
2X-RAY DIFFRACTION1AA92 - 14020 - 68
3X-RAY DIFFRACTION1AA141 - 18069 - 108
4X-RAY DIFFRACTION1AA181 - 233109 - 161
5X-RAY DIFFRACTION1BB73 - 911 - 19
6X-RAY DIFFRACTION1BB92 - 14020 - 68
7X-RAY DIFFRACTION1BB141 - 18069 - 108
8X-RAY DIFFRACTION1BB181 - 233109 - 161

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