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- PDB-3pmd: Crystal structure of the sporulation inhibitor pXO1-118 from Baci... -

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Basic information

Entry
Database: PDB / ID: 3pmd
TitleCrystal structure of the sporulation inhibitor pXO1-118 from Bacillus anthracis
ComponentsConserved domain proteinProtein domain
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 / UNDECANOIC ACID / Conserved domain protein
Function and homology information
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 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
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Conserved domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7623
Polymers18,5401
Non-polymers2222
Water1,71195
1
A: Conserved domain protein
hetero molecules

A: Conserved domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5246
Polymers37,0812
Non-polymers4434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area5030 Å2
ΔGint-60 kcal/mol
Surface area16350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.223, 89.223, 35.819
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-154-

HOH

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Components

#1: Protein Conserved domain protein / Protein domain / PXO1-118 / Plasmid pX01 (from Bacillus anthracis UM23-1) trans-acting positive regulator (Atx A)


Mass: 18540.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: GBAA_pXO1_0148, pX01-118 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q44635
#2: Chemical ChemComp-11A / UNDECANOIC ACID / Undecylic acid


Mass: 186.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H22O2 / Comment: antifungal*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.22 Å3/Da / Density % sol: 44.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.4
Details: 5% PEG1000, 40% PEG400, 0.1 M TrisHCl, pH 5.4, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9781 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: 0.9781 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 16351 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.038 / Net I/σ(I): 55.1
Reflection shellResolution: 1.76→1.82 Å / Rmerge(I) obs: 0.276 / % possible all: 96

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.76→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.063 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22316 830 5 %RANDOM
Rwork0.17792 ---
obs0.1802 15617 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.056 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å2-0.27 Å20 Å2
2---0.53 Å20 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.76→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1306 0 14 95 1415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221394
X-RAY DIFFRACTIONr_bond_other_d0.0010.02972
X-RAY DIFFRACTIONr_angle_refined_deg1.0691.961878
X-RAY DIFFRACTIONr_angle_other_deg1.61232386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9935162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.06824.72272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40215275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.496154
X-RAY DIFFRACTIONr_chiral_restr0.070.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021507
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02284
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_it1.7741.5781
X-RAY DIFFRACTIONr_mcbond_other0.6441.5313
X-RAY DIFFRACTIONr_mcangle_it2.99121277
X-RAY DIFFRACTIONr_scbond_it5.1763613
X-RAY DIFFRACTIONr_scangle_it7.7824.5597
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.762→1.807 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 47 -
Rwork0.23 1134 -
obs--98.66 %
Refinement TLS params.Method: refined / Origin x: -8.038 Å / Origin y: 32.5633 Å / Origin z: 13.4902 Å
111213212223313233
T0.0361 Å2-0.0336 Å2-0.0377 Å2-0.0727 Å20.0195 Å2--0.0801 Å2
L0.7311 °2-0.6387 °2-0.0115 °2-2.2769 °2-0.1456 °2--0.8736 °2
S-0.0576 Å °0.0339 Å °0.1393 Å °0.1743 Å °-0.0342 Å °-0.1115 Å °-0.0908 Å °0.0815 Å °0.0918 Å °

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