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- PDB-3k9g: CRYSTAL STRUCTURE OF A PLASMID PARTITION PROTEIN FROM BORRELIA BU... -

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Basic information

Entry
Database: PDB / ID: 3k9g
TitleCRYSTAL STRUCTURE OF A PLASMID PARTITION PROTEIN FROM BORRELIA BURGDORFERI AT 2.25A RESOLUTION, iodide soak
ComponentsPF-32 protein
KeywordsBIOSYNTHETIC PROTEIN / SSGCID / SBRI / DECODE BIOSTRUCTURES / UW / NIH / NIAID / BORELLIA BURGDORFERI / PLASMID PARTITION PROTEIN / IODIDE / SAD PHASING / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


: / AAA domain / AAA domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / PF-32 protein
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: J Struct Funct Genomics / Year: 2011
Title: SAD phasing using iodide ions in a high-throughput structural genomics environment.
Authors: Abendroth, J. / Gardberg, A.S. / Robinson, J.I. / Christensen, J.S. / Staker, B.L. / Myler, P.J. / Stewart, L.J. / Edwards, T.E.
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 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_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

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Assembly

Deposited unit
A: PF-32 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,53114
Polymers30,9851
Non-polymers1,54613
Water1,63991
1
A: PF-32 protein
hetero molecules

A: PF-32 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,06128
Polymers61,9702
Non-polymers3,09226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5730 Å2
ΔGint-34 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.810, 55.810, 200.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-299-

HOH

21A-301-

HOH

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Components

#1: Protein PF-32 protein / Plasmid partition protein


Mass: 30984.820 Da / Num. of mol.: 1
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: INDEX SCREEN A10: 3M NACL, 100MM BISTRIS PH 6.5 EXCHANGED IN 2M NACL, 1M KI, 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: Oct 5, 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: 16030 / Num. obs: 15985 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 25 % / Biso Wilson estimate: 41.45 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 34.53
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 13 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 5 / Num. unique all: 1158 / % possible all: 100

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0104refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.25→30.2 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.891 / SU B: 5.088 / SU ML: 0.133 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.266 795 5 %RANDOM
Rwork0.223 ---
all0.225 15915 --
obs0.225 15985 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å2-0 Å2-0 Å2
2--0.7 Å20 Å2
3----1.41 Å2
Refinement stepCycle: LAST / Resolution: 2.25→30.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1749 0 13 91 1853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221784
X-RAY DIFFRACTIONr_bond_other_d0.0010.021132
X-RAY DIFFRACTIONr_angle_refined_deg1.361.9792431
X-RAY DIFFRACTIONr_angle_other_deg0.91832804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2425226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.31625.50769
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.75615306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.343153
X-RAY DIFFRACTIONr_chiral_restr0.080.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021947
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02343
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_it0.9441.51131
X-RAY DIFFRACTIONr_mcbond_other0.1681.5453
X-RAY DIFFRACTIONr_mcangle_it1.7121832
X-RAY DIFFRACTIONr_scbond_it2.2253653
X-RAY DIFFRACTIONr_scangle_it3.534.5598
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 54 -
Rwork0.26 1080 -
obs--99.91 %

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