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- PDB-3pmc: Crystal structure of the sporulation inhibitor pXO2-61 from Bacil... -

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Basic information

Entry
Database: PDB / ID: 3pmc
TitleCrystal structure of the sporulation inhibitor pXO2-61 from Bacillus anthracis
ComponentsUncharacterized protein pXO2-61/BXB0075/GBAA_pXO2_0075
KeywordsLIPID BINDING PROTEIN / globin fold / non-heme globin / sporulation / Bacillus anthracis / kinase sensor domain / chloride coordination / fatty acid-binding protein
Function / homologyHistidine kinase N-terminal domain / Histidine kinase, N-terminal / Histidine kinase N terminal / Globin-like / Orthogonal Bundle / Mainly Alpha / IODIDE ION / Uncharacterized protein pXO2-61/BXB0075/GBAA_pXO2_0075
Function and homology information
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsStranzl, G.R. / Santelli, E. / Bankston, L.A. / La Clair, C. / Bobkov, A. / Schwarzenbacher, R. / Godzik, A. / Perego, M. / Grynberg, M. / Liddington, R.C.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural Insights into Inhibition of Bacillus anthracis Sporulation by a Novel Class of Non-heme Globin Sensor Domains.
Authors: Stranzl, G.R. / Santelli, E. / Bankston, L.A. / La Clair, C. / Bobkov, A. / Schwarzenbacher, R. / Godzik, A. / Perego, M. / Grynberg, M. / Liddington, R.C.
History
DepositionNov 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
SupersessionFeb 23, 2011ID: 1YKU
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Uncharacterized protein pXO2-61/BXB0075/GBAA_pXO2_0075
B: Uncharacterized protein pXO2-61/BXB0075/GBAA_pXO2_0075
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,50536
Polymers33,4652
Non-polymers4,04034
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7630 Å2
ΔGint-35 kcal/mol
Surface area13360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.110, 62.620, 124.760
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 Uncharacterized protein pXO2-61/BXB0075/GBAA_pXO2_0075


Mass: 16732.479 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: BXB0075, GBAA_pXO2_0075, pX02-61, pXO2-61 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RMX2
#2: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.57 Å3/Da / Density % sol: 52.22 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5
Details: 20% PEG3350, 1M NaI, 0.1 M TrisHCl, pH 7.5, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 13, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.49→34.64 Å / Num. obs: 56717 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 43.8
Reflection shellResolution: 1.49→1.54 Å / Rmerge(I) obs: 0.032 / % possible all: 94.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→34.64 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.756 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20846 2866 5.1 %RANDOM
Rwork0.17406 ---
obs0.17582 53809 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.304 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2---0.37 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.49→34.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 34 363 2641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222315
X-RAY DIFFRACTIONr_bond_other_d0.0010.021634
X-RAY DIFFRACTIONr_angle_refined_deg1.2071.9653112
X-RAY DIFFRACTIONr_angle_other_deg1.92734010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6935268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.22324.741116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.14215485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3781512
X-RAY DIFFRACTIONr_chiral_restr0.0730.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022468
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02454
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.10821332
X-RAY DIFFRACTIONr_mcbond_other0.7532528
X-RAY DIFFRACTIONr_mcangle_it3.31932178
X-RAY DIFFRACTIONr_scbond_it4.7794983
X-RAY DIFFRACTIONr_scangle_it7.0946932
X-RAY DIFFRACTIONr_rigid_bond_restr1.71133949
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.492→1.531 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 207 -
Rwork0.178 3837 -
obs--97.14 %

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