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- PDB-2ol5: Crystal Structure of a protease synthase and sporulation negative... -

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Basic information

Entry
Database: PDB / ID: 2ol5
TitleCrystal Structure of a protease synthase and sporulation negative regulatory protein PAI 2 from Bacillus stearothermophilus
ComponentsPAI 2 protein
KeywordsTRANSCRIPTION REGULATOR / PAI 2 protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyTranscriptional regulator PAI 2-type / Putative FMN-binding domain / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta / Transcriptional repressor of sporulation and degradative enzymes production
Function and homology information
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsBrunzelle, J.S. / Cuff, M.E. / Minasov, G. / Li, H. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proteins / Year: 2011
Title: Crystal structure of the novel PaiB transcriptional regulator from Geobacillus stearothermophilus.
Authors: Filippova, E.V. / Brunzelle, J.S. / Cuff, M.E. / Li, H. / Joachimiak, A. / Anderson, W.F.
History
DepositionJan 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 10, 2011Group: Database references
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999 SEQUENCE THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT DATABASE AT THE TIME OF DEPOSITION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PAI 2 protein
B: PAI 2 protein


Theoretical massNumber of molelcules
Total (without water)47,7062
Polymers47,7062
Non-polymers00
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-31 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.601, 77.949, 89.453
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PAI 2 protein


Mass: 23852.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5L206*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M Ammonium acetate, 0.1M Bis-Tris pH 6.0, 17% PEG 10000, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: SBC-3 / Detector: CCD / Date: Aug 20, 2003
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 34879 / Num. obs: 34879 / % possible obs: 81.7 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 8.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 2.27 / % possible all: 36.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
SHARPphasing
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→38.81 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.89 / SU B: 20.272 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.863 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27551 1556 10.2 %RANDOM
Rwork0.21281 ---
obs0.21911 13772 97.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.468 Å2
Baniso -1Baniso -2Baniso -3
1--3.91 Å20 Å20 Å2
2--7.45 Å20 Å2
3----3.54 Å2
Refinement stepCycle: LAST / Resolution: 2.5→38.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3012 0 0 108 3120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223086
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7641.9334174
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4355365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.33124.591159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1715546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1441516
X-RAY DIFFRACTIONr_chiral_restr0.1260.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022360
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.21361
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22074
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2149
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7721.51906
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20922982
X-RAY DIFFRACTIONr_scbond_it1.67531359
X-RAY DIFFRACTIONr_scangle_it2.484.51192
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 88 -
Rwork0.265 870 -
obs--86.07 %

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