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- PDB-3k9h: Crystal structure of a plasmid partition protein from borrelia bu... -

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Basic information

Entry
Database: PDB / ID: 3k9h
TitleCrystal structure of a plasmid partition protein from borrelia burgdorferi at 2.25A resolution
ComponentsPF-32 protein
KeywordsBIOSYNTHETIC PROTEIN / SSGCID / SBRI / DECODE BIOSTRUCTURES / UW / NIH / NIAID / BORELLIA BURGDORFERI / PLASMID PARTITION PROTEIN / Plasmid / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology: / AAA domain / AAA domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta / PF-32 protein
Function and homology information
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of a plasmid partition protein from borrelia burgdorferi at 2.25A resolution
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Edwards, T. / Staker, B.
History
DepositionOct 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _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: PF-32 protein
B: PF-32 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1624
Polymers61,9702
Non-polymers1922
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-39 kcal/mol
Surface area20270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.000, 57.000, 343.610
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: HOH / End label comp-ID: HOH / Refine code: 6 / Auth seq-ID: 5 - 250 / Label seq-ID: 26

Dom-IDAuth asym-IDLabel asym-ID
1AA - E
2BB - F

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Components

#1: Protein PF-32 protein


Mass: 30984.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Strain: B31 / Gene: PF-32, BB_S35 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O68233
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: INDEX SCREEN G5: 25% PEG 3350, TRIS PH 8.5, 200MM LI2SO4, BOBUA.01478.A AT 33MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→30.2 Å / Num. all: 29899 / Num. obs: 28812 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 35.22 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 18.08
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 3.7 / Num. unique all: 2187 / % possible all: 84

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0104refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3K9G, iodide soak

3k9g


Resolution: 2.25→30.2 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.903 / SU B: 5.645 / SU ML: 0.144 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.258 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1462 5.1 %RANDOM
Rwork0.194 ---
all0.197 28814 --
obs0.197 28812 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20.23 Å2-0 Å2
2--0.46 Å2-0 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 2.25→30.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3658 0 10 217 3885
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223735
X-RAY DIFFRACTIONr_bond_other_d0.0010.022423
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.9825078
X-RAY DIFFRACTIONr_angle_other_deg0.91735994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2795460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.50925.395152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.55315672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.432156
X-RAY DIFFRACTIONr_chiral_restr0.0870.2623
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024027
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02721
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_it0.7971.52295
X-RAY DIFFRACTIONr_mcbond_other0.1621.5919
X-RAY DIFFRACTIONr_mcangle_it1.49223739
X-RAY DIFFRACTIONr_scbond_it2.21331440
X-RAY DIFFRACTIONr_scangle_it3.4184.51336
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2960 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.455
loose thermal2.2610
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 76 -
Rwork0.237 1756 -
obs--84.08 %

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