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- PDB-5zfr: Crystal structure of PilB, an extension ATPase motor of Type IV p... -

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Basic information

Entry
Database: PDB / ID: 5zfr
TitleCrystal structure of PilB, an extension ATPase motor of Type IV pilus, from Geobacter sulfurreducens
ComponentsType IV pilus biogenesis ATPase PilB
KeywordsTRANSPORT PROTEIN / extension motor
Function / homology
Function and homology information


pilus assembly / nucleotide binding / ATP hydrolysis activity / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
ATPase, type IV, pilus assembly, PilB / Beta-Lactamase - #90 / Type II secretion system protein GspE, N-terminal / MshEN domain / Type II secretion system protein GspE, N-terminal superfamily / Bacterial type II secretion system protein E signature. / Type II/IV secretion system protein / Type II/IV secretion system protein / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases ...ATPase, type IV, pilus assembly, PilB / Beta-Lactamase - #90 / Type II secretion system protein GspE, N-terminal / MshEN domain / Type II secretion system protein GspE, N-terminal superfamily / Bacterial type II secretion system protein E signature. / Type II/IV secretion system protein / Type II/IV secretion system protein / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Type IV pilus biogenesis ATPase PilB
Similarity search - Component
Biological speciesGeobacter sulfurreducens PCA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsThakur, K.G. / Solanki, V. / Kapoor, S.
Funding support India, 2items
OrganizationGrant numberCountry
Council of Scientific and Industrial Research India
Department of Biotechnology India
CitationJournal: FEBS J. / Year: 2018
Title: Structural insights into the mechanism of Type IVa pilus extension and retraction ATPase motors
Authors: Solanki, V. / Kapoor, S. / Thakur, K.G.
History
DepositionMar 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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 / 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

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Assembly

Deposited unit
A: Type IV pilus biogenesis ATPase PilB
B: Type IV pilus biogenesis ATPase PilB
C: Type IV pilus biogenesis ATPase PilB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,5189
Polymers193,0373
Non-polymers4816
Water86548
1
A: Type IV pilus biogenesis ATPase PilB
B: Type IV pilus biogenesis ATPase PilB
C: Type IV pilus biogenesis ATPase PilB
hetero molecules

A: Type IV pilus biogenesis ATPase PilB
B: Type IV pilus biogenesis ATPase PilB
C: Type IV pilus biogenesis ATPase PilB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)387,03718
Polymers386,0746
Non-polymers96212
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area20570 Å2
ΔGint-88 kcal/mol
Surface area94170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.301, 176.301, 138.561
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 181 through 260 or resid 268 through 568))
21(chain B and (resid 181 through 260 or resid 268 through 568))
31(chain C and (resid 181 through 260 or resid 268 through 568))

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
11ALAALAILEILE(chain A and (resid 181 through 260 or resid 268 through 568))AA181 - 260195 - 274
12METMETASPASP(chain A and (resid 181 through 260 or resid 268 through 568))AA268 - 568282 - 582
21ALAALAILEILE(chain B and (resid 181 through 260 or resid 268 through 568))BB181 - 260195 - 274
22METMETASPASP(chain B and (resid 181 through 260 or resid 268 through 568))BB268 - 568282 - 582
31ALAALAILEILE(chain C and (resid 181 through 260 or resid 268 through 568))CC181 - 260195 - 274
32METMETASPASP(chain C and (resid 181 through 260 or resid 268 through 568))CC268 - 568282 - 582

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Components

#1: Protein Type IV pilus biogenesis ATPase PilB


Mass: 64345.723 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens PCA (bacteria)
Strain: PCA / Gene: pilB, GSU1491 / Plasmid: pETDuet
Details (production host): N-terminal 6xHistidine Tag and Ampicillin resistance marker
Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q74D28
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.79 Å3/Da / Density % sol: 55.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1M succinic acid pH 7.0, 0.1M HEPES pH 7.0, 1%(w/v) Polyethylene glycol monomethyl ether 2000
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0723 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2017 / Details: Toroidal mirror
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 3.1→176.301 Å / Num. obs: 39383 / % possible obs: 98.4 % / Redundancy: 7.7 % / Biso Wilson estimate: 101.77 Å2 / Rpim(I) all: 0.044 / Rrim(I) all: 0.126 / Rsym value: 0.118 / Net I/av σ(I): 5.5 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
3.1-3.278.11.3080.657110.4851.4011.30899.4
3.27-3.477.90.777153950.2930.8340.77799
3.47-3.717.50.4051.850640.1580.4370.40598.6
3.71-48.10.2423.147450.090.2590.24298.8
4-4.387.90.148543770.0550.1580.14898.7
4.38-4.97.30.0927.839230.0350.0980.09297.6
4.9-5.6680.089835110.0320.0950.08998.4
5.66-6.937.50.0789.129660.0290.0840.07897.3
6.93-9.87.40.04312.423490.0160.0460.04397.5
9.8-46.3386.70.03515.513420.0130.0380.03595.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SCALA3.3.22data scaling
PHASER2.7.17phasing
PDB_EXTRACT3.24data extraction
iMOSFLM7.2.1data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TSG

5tsg


Resolution: 3.1→46.338 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.87
RfactorNum. reflection% reflection
Rfree0.2473 1989 5.05 %
Rwork0.2177 --
obs0.2192 39350 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 216.38 Å2 / Biso mean: 102.2735 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.1→46.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8989 0 18 48 9055
Biso mean--150.06 88.15 -
Num. residues----1154
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3483X-RAY DIFFRACTION13.119TORSIONAL
12B3483X-RAY DIFFRACTION13.119TORSIONAL
13C3483X-RAY DIFFRACTION13.119TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.17750.40871280.40042648277699
3.1775-3.26340.38761480.36792646279499
3.2634-3.35940.37881430.33622660280399
3.3594-3.46780.36511420.31322639278199
3.4678-3.59170.32891470.29452616276398
3.5917-3.73550.29471440.26292658280299
3.7355-3.90540.27091180.24392682280099
3.9054-4.11120.28861440.21892651279598
4.1112-4.36860.22721350.19982660279598
4.3686-4.70560.20851450.16952643278897
4.7056-5.17850.23121590.17822663282298
5.1785-5.92660.22581460.20822686283298
5.9266-7.46180.23811500.20792694284497
7.4618-46.34290.17561400.1752815295596
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)
10.52290.0671-0.01710.3810.47661.78930.0198-0.042-0.1348-0.01050.0049-0.10310.11170.1639-0.00740.76340.0403-0.11450.77990.00630.9313-5.9031-59.82622.8226
20.8018-0.19890.14741.24320.04960.6144-0.1548-0.18540.19940.17160.0332-0.32230.0582-0.12530.1290.85850.0132-0.15960.8703-0.05150.7776-16.9068-50.862438.0827
31.828-0.19930.02960.8487-0.38130.3753-0.08940.05970.57810.20050.02-0.2441-0.10320.0060.06040.82390.0133-0.06980.7926-0.03340.9101-41.2132-22.190925.0359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 181:568)A181 - 568
2X-RAY DIFFRACTION2(chain B and resseq 179:568)B179 - 568
3X-RAY DIFFRACTION3(chain C and resseq 180:568)C180 - 568

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