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- PDB-5tvk: Crystal Structure of putative plasmid partition protein (BB_S35) ... -

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Basic information

Entry
Database: PDB / ID: 5tvk
TitleCrystal Structure of putative plasmid partition protein (BB_S35) from Borrelia burgdorferi B31 bound to AMPPNP
ComponentsPF-32 protein
KeywordsCELL CYCLE / Structural Genomics / SSGCID / NTPase / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


AAA domain / AAA domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / PF-32 protein
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal Structure of putative plasmid partition protein (BB_S35) from Borrelia burgdorferi B31 bound to AMPPNP
Authors: SSGCID / Delker, S.L. / Yano, J.K. / Lorimer, D. / Edwards, T.E.
History
DepositionNov 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / struct_ncs_dom_lim
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_ncs_dom_lim.end_label_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)62,9966
Polymers61,9702
Non-polymers1,0264
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-11 kcal/mol
Surface area20610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.320, 57.320, 343.570
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 12 or resid 14...
21(chain B and (resid 5 through 12 or resid 14...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSALAALA(chain A and (resid 5 through 12 or resid 14...AA5 - 1226 - 33
12ILEILEVALVAL(chain A and (resid 5 through 12 or resid 14...AA14 - 7635 - 97
13ILEILEALAALA(chain A and (resid 5 through 12 or resid 14...AA78 - 15599 - 176
14GLUGLULYSLYS(chain A and (resid 5 through 12 or resid 14...AA156 - 157177 - 178
15LYSLYSILEILE(chain A and (resid 5 through 12 or resid 14...AA4 - 24625 - 267
16LYSLYSILEILE(chain A and (resid 5 through 12 or resid 14...AA4 - 24625 - 267
17LYSLYSILEILE(chain A and (resid 5 through 12 or resid 14...AA4 - 24625 - 267
18LYSLYSILEILE(chain A and (resid 5 through 12 or resid 14...AA4 - 24625 - 267
21LYSLYSALAALA(chain B and (resid 5 through 12 or resid 14...BB5 - 1226 - 33
22ILEILETYRTYR(chain B and (resid 5 through 12 or resid 14...BB14 - 5335 - 74
23GLUGLUGLUGLU(chain B and (resid 5 through 12 or resid 14...BB5475
24LYSLYSILEILE(chain B and (resid 5 through 12 or resid 14...BB5 - 24626 - 267
25LYSLYSILEILE(chain B and (resid 5 through 12 or resid 14...BB5 - 24626 - 267
26LYSLYSILEILE(chain B and (resid 5 through 12 or resid 14...BB5 - 24626 - 267
27LYSLYSILEILE(chain B and (resid 5 through 12 or resid 14...BB5 - 24626 - 267

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Components

#1: Protein PF-32 protein / BobuA.01478.a.A1


Mass: 30984.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (strain ATCC 35210 / B31 / CIP 102532 / DSM 4680) (bacteria)
Strain: ATCC 35210 / B31 / CIP 102532 / DSM 4680 / Gene: BB_S35, PF-32 / Plasmid: BobuA.01478.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H7C7Q1
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Li
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus F2: 10% w/v PEG8000, 20% v/v ethylene glycol, 0.2 M D-glucose, 0.2 M D-mannose, 0.2 M D-galactose, 0.2 M L-fucose, 0.2 M D-xylose, 0.2 M N-acetyl-D-glucosamine, 0.1 M MES/imidazole, ...Details: Morpheus F2: 10% w/v PEG8000, 20% v/v ethylene glycol, 0.2 M D-glucose, 0.2 M D-mannose, 0.2 M D-galactose, 0.2 M L-fucose, 0.2 M D-xylose, 0.2 M N-acetyl-D-glucosamine, 0.1 M MES/imidazole, pH 6.5, direct cryoprotection, BobuA.01478.a.A1 PS00305 at 20 mg/mL, Tray268926f2, puck llm2-10, supplemented with 3 mM AMPPNP, 3 mM magnesium chloride, NDPs (possibly co-purified with the protein, as suggested by electron density)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 5, 2016 / Details: beryllium lenses
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.3→49.6 Å / Num. all: 215618 / Num. obs: 76639 / % possible obs: 90.4 % / Observed criterion σ(I): -3 / Redundancy: 2.81 % / Biso Wilson estimate: 48.35 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.32
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allCC1/2% possible all
2.3-2.360.4852.251584957500.88493
2.36-2.420.3782.830.91592.8
2.42-2.490.3163.310.92792.8
2.49-2.570.2454.160.95491.9
2.57-2.660.1895.330.96791.9
2.66-2.750.1576.260.97891.6
2.75-2.850.11980.98691.5
2.85-2.970.09110.270.9990.8
2.97-3.10.07612.320.99191
3.1-3.250.05914.90.99590.2
3.25-3.430.05117.010.99689.8
3.43-3.640.04519.770.99689.5
3.64-3.890.04221.30.99688.7
3.89-4.20.03723.760.99788.4
4.2-4.60.03425.760.99788.1
4.6-5.140.03226.910.99887.1
5.14-5.940.03126.420.99886.7
5.94-7.270.03126.560.99885.6
7.27-10.290.0329.080.99785.1
10.290.0328.040.99776.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3K9G

3k9g


Resolution: 2.4→28.269 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 25.43
RfactorNum. reflection% reflection
Rfree0.218 2065 8.35 %
Rwork0.1687 --
obs0.1729 24742 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 174.32 Å2 / Biso mean: 62.0199 Å2 / Biso min: 26.48 Å2
Refinement stepCycle: final / Resolution: 2.4→28.269 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3741 0 64 77 3882
Biso mean--72.03 56.33 -
Num. residues----479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083891
X-RAY DIFFRACTIONf_angle_d0.8995322
X-RAY DIFFRACTIONf_chiral_restr0.056657
X-RAY DIFFRACTIONf_plane_restr0.005654
X-RAY DIFFRACTIONf_dihedral_angle_d13.8172308
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2104X-RAY DIFFRACTION8.442TORSIONAL
12B2104X-RAY DIFFRACTION8.442TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4001-2.45590.32671110.218315211632100
2.4559-2.51730.28111390.216715051644100
2.5173-2.58530.26851270.208915281655100
2.5853-2.66130.24951170.201515301647100
2.6613-2.74720.27531630.211115201683100
2.7472-2.84530.2891430.201314961639100
2.8453-2.95910.28511550.200614631618100
2.9591-3.09360.2651410.196115191660100
3.0936-3.25640.2271200.199115261646100
3.2564-3.46010.28411140.192715351649100
3.4601-3.72680.23311290.174515251654100
3.7268-4.10080.18341320.152215671699100
4.1008-4.69180.17211430.126614921635100
4.6918-5.90240.18491510.142614961647100
5.9024-28.27120.1921800.15351454163498
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.6360.1528-2.87114.6971-0.6612.5888-0.16470.0041-0.15160.01320.0952-0.29740.09410.28360.13260.38160.0536-0.00050.4254-0.03650.288-15.309914.9742-12.5119
28.6028-3.3116-4.63239.85176.65827.09280.1290.47890.2589-0.55420.1406-0.5501-0.59540.6059-0.26080.4097-0.0777-0.00760.6307-0.01150.3322-7.388727.5362-20.7102
34.2660.41140.95844.95461.96154.643-0.11870.1010.1635-0.1646-0.0197-0.0039-0.5281-0.04240.13170.4242-0.02420.01850.38640.03110.2687-14.518227.8724-15.3895
42.25990.75090.17212.18060.23427.90720.0402-0.2384-0.140.1587-0.0368-0.11310.06640.00880.04510.26970.03370.00210.4515-0.08560.3436-19.913219.9911-7.8653
54.39090.43651.0775.4609-0.26329.80680.2885-0.7477-0.37760.8812-0.20560.97960.6612-0.6544-0.0340.4858-0.11290.01480.6788-0.0540.3893-23.511120.496.2764
63.5352-0.5024-0.97992.73840.13496.1746-0.2043-0.0965-0.10350.4968-0.2492-0.40251.06270.04830.41290.54870.0173-0.02990.53460.04940.5871-22.247911.86920.1891
78.85811.9421.46815.3584-1.81452.52970.14-0.59690.16290.7608-0.2160.36821.8198-0.8923-0.00681.1439-0.15370.20970.8162-0.02890.7353-23.57573.86445.0676
89.5651.9689-6.52716.0332-3.06784.9725-1.01940.01820.0247-0.8217-0.3197-1.30732.42440.78451.00911.34980.29270.27311.13070.10221.1565-8.08911.1724-9.9415
98.0221-2.0644-2.13458.40560.85237.5102-0.5499-0.1054-1.65080.78070.11950.43251.5628-0.24780.27720.7817-0.19340.06190.5381-0.05580.5401-22.14032.833-9.8184
102.2609-0.7369-0.94722.0782-1.68152.8096-0.06980.1663-0.0582-0.16180.05650.15240.3344-0.15690.00090.4220.0741-0.0910.4359-0.10690.30563.81322.53712.3286
118.1265-4.80265.27094.8802-6.31398.0867-0.03-0.4518-0.19190.68530.01720.57670.1379-0.9037-0.04220.4458-0.08370.04120.5914-0.09190.3277-10.435323.213921.1797
122.7968-0.50541.71383.3371-0.24774.4755-0.1521-0.22820.0990.24020.12890.393-0.3597-0.56850.05030.35520.05880.01940.498-0.07630.3262-6.746129.926416.3303
131.9807-0.9857-1.33472.33890.5237.49490.01470.3742-0.1781-0.23130.10520.07680.1272-0.231-0.13310.37660.0134-0.08420.4298-0.10350.34322.503230.06398.7869
144.6572-1.61031.29911.3763-1.5715.64040.02130.5609-0.1416-0.15320.1808-0.120.35720.9764-0.19510.4846-0.0332-0.00480.6762-0.10750.364110.880426.6775-3.4417
153.47522.92480.51463.8693-1.60892.9296-0.8265-1.2373-0.22720.1431-0.62771.47841.20210.44830.54881.48530.1281-0.18240.9454-0.02171.11926.99047.175110.9218
167.82294.343-3.67623.5744-4.51848.0696-0.0001-0.1087-0.2621-0.8711-0.618-0.60930.6390.65420.57180.43610.1839-0.06380.6974-0.11380.462717.783621.29119.0717
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 52 )A4 - 52
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 77 )A53 - 77
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 119 )A78 - 119
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 158 )A120 - 158
5X-RAY DIFFRACTION5chain 'A' and (resid 159 through 172 )A159 - 172
6X-RAY DIFFRACTION6chain 'A' and (resid 173 through 189 )A173 - 189
7X-RAY DIFFRACTION7chain 'A' and (resid 190 through 208 )A190 - 208
8X-RAY DIFFRACTION8chain 'A' and (resid 209 through 229 )A209 - 229
9X-RAY DIFFRACTION9chain 'A' and (resid 230 through 246 )A230 - 246
10X-RAY DIFFRACTION10chain 'B' and (resid 5 through 52 )B5 - 52
11X-RAY DIFFRACTION11chain 'B' and (resid 53 through 77 )B53 - 77
12X-RAY DIFFRACTION12chain 'B' and (resid 78 through 119 )B78 - 119
13X-RAY DIFFRACTION13chain 'B' and (resid 120 through 158 )B120 - 158
14X-RAY DIFFRACTION14chain 'B' and (resid 159 through 212 )B159 - 212
15X-RAY DIFFRACTION15chain 'B' and (resid 213 through 229 )B213 - 229
16X-RAY DIFFRACTION16chain 'B' and (resid 230 through 246 )B230 - 246

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