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- PDB-5tsh: PilB from Geobacter metallireducens bound to AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 5tsh
TitlePilB from Geobacter metallireducens bound to AMP-PNP
ComponentsType IV pilus biogenesis ATPase PilB
KeywordsATP-BINDING PROTEIN / PilB / Pilus / Type IVa Pilus / Extension
Function / homology
Function and homology information


pilus assembly / nucleotide binding / ATP hydrolysis activity / metal ion binding / cytoplasm
Similarity search - Function
ATPase, type IV, pilus assembly, PilB / Type II secretion system protein GspE, N-terminal / MshEN domain / Beta-Lactamase - #90 / 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 / Type II secretion system protein GspE, N-terminal / MshEN domain / Beta-Lactamase - #90 / 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
ADENOSINE-5'-DIPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Type IV pilus biogenesis ATPase PilB
Similarity search - Component
Biological speciesGeobacter metallireducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMcCallum, M. / Tammam, S. / Khan, A. / Burrows, L. / Howell, P.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP 93585 Canada
CitationJournal: Nat Commun / Year: 2017
Title: The molecular mechanism of the type IVa pilus motors.
Authors: McCallum, M. / Tammam, S. / Khan, A. / Burrows, L.L. / Howell, P.L.
History
DepositionOct 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
D: Type IV pilus biogenesis ATPase PilB
E: Type IV pilus biogenesis ATPase PilB
F: Type IV pilus biogenesis ATPase PilB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)392,63220
Polymers389,3126
Non-polymers3,32014
Water9,494527
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22840 Å2
ΔGint-98 kcal/mol
Surface area90930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.320, 99.960, 109.790
Angle α, β, γ (deg.)112.99, 106.60, 88.91
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Type IV pilus biogenesis ATPase PilB


Mass: 64885.250 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210) (bacteria)
Strain: GS-15 / ATCC 53774 / DSM 7210 / Gene: pilB, Gmet_1393 / Production host: Escherichia coli (E. coli) / References: UniProt: Q39VU7

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Non-polymers , 5 types, 541 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / 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: 1.84 Å3/Da / Density % sol: 33.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3350, magnesium formate, Tris pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949322119492 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949322119492 Å / Relative weight: 1
ReflectionResolution: 2.3→48 Å / Num. obs: 253982 / % possible obs: 96 % / Redundancy: 2.1 % / CC1/2: 0.995 / Rsym value: 0.056 / Net I/σ(I): 5.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2 / CC1/2: 0.639 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P9R

1p9r


Resolution: 2.3→45.755 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.9
RfactorNum. reflection% reflection
Rfree0.2184 2018 1.67 %
Rwork0.1838 --
obs0.1843 120967 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→45.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17216 0 186 527 17929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00417715
X-RAY DIFFRACTIONf_angle_d0.53423996
X-RAY DIFFRACTIONf_dihedral_angle_d14.82510791
X-RAY DIFFRACTIONf_chiral_restr0.0432862
X-RAY DIFFRACTIONf_plane_restr0.0043060
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35750.34051310.27298319X-RAY DIFFRACTION96
2.3575-2.42130.30781470.24918505X-RAY DIFFRACTION98
2.4213-2.49250.28141470.23378399X-RAY DIFFRACTION98
2.4925-2.5730.25281470.2258535X-RAY DIFFRACTION98
2.573-2.66490.24081430.22358445X-RAY DIFFRACTION98
2.6649-2.77160.24181370.22128508X-RAY DIFFRACTION98
2.7716-2.89770.2911460.22788450X-RAY DIFFRACTION98
2.8977-3.05050.24051420.21618532X-RAY DIFFRACTION98
3.0505-3.24150.28191440.20438582X-RAY DIFFRACTION98
3.2415-3.49170.23141440.18448443X-RAY DIFFRACTION98
3.4917-3.8430.17231490.16718549X-RAY DIFFRACTION99
3.843-4.39870.20191490.15058544X-RAY DIFFRACTION99
4.3987-5.54030.16621420.15058525X-RAY DIFFRACTION99
5.5403-45.76410.19731500.16328613X-RAY DIFFRACTION99
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)
10.8267-0.40730.6681.2094-0.24231.43880.12210.107-0.21490.0101-0.00930.40060.1368-1.1801-00.46590.0111-0.0380.9501-0.00660.624184.070419.00124.1933
21.13360.00020.18982.98040.69341.2039-0.0671-0.04390.0815-0.14410.01080.045-0.1171-0.0196-00.27550.0175-0.01790.3936-0.01390.32103.25431.41018.4289
31.6439-1.61220.29162.594-0.3790.1679-0.2077-0.10230.57510.04120.1487-0.6381-0.21570.0585-0.00010.4037-0.0039-0.04450.4047-0.07650.5097112.949919.283313.2568
41.03631.03020.01141.13280.90650.96730.2676-0.1693-0.34450.1012-0.0815-0.19810.4165-0.0894-00.6602-0.0155-0.04310.48560.10650.6232119.9488-40.121922.6175
51.09180.4402-0.89862.2998-0.67032.4204-0.06890.1886-0.048-0.0824-0.05410.03180.1176-0.104-00.41290.0218-0.0230.42410.00680.3891132.0079-27.282148.8897
60.96270.0164-0.97271.04410.12782.55470.0060.07110.02520.1255-0.0399-0.1596-0.13390.0648-00.34250.0028-0.01930.42650.0330.4247142.0744-15.408931.174
71.66440.80730.24742.1578-0.19060.86940.0604-0.1309-0.0550.164-0.07990.02230.2384-0.211100.53560.0043-0.02540.39050.03810.4461129.8038-41.386767.3044
81.418-1.2816-0.45232.5519-0.15770.99390.1051-0.05990.0241-0.1337-0.1233-0.30630.03710.213500.4594-0.008-0.04970.3610.00820.4016138.0736-13.9473.5526
92.18070.15780.21241.42721.29011.57650.06740.1902-0.2244-0.058-0.11810.54530.0793-0.469600.4915-0.01060.02150.5878-0.03240.515590.684815.88969.5026
100.78650.2931-0.10680.2704-0.52350.50930.10890.01430.17890.0556-0.1060.1415-0.3856-0.066500.6181-0.01840.03180.4868-0.04430.4255106.718923.529847.4684
112.2758-0.3702-0.06671.31460.50972.0427-0.0284-0.2076-0.23380.167-0.05510.25370.1359-0.3305-00.4449-0.00340.02090.4975-00.476298.792215.814938.3954
120.94950.32890.67631.73841.19192.3647-0.01310.18170.05210.05180.0624-0.0656-0.11970.118500.4437-0.00350.0080.3830.0410.3343121.028924.011950.279
132.71260.1501-0.25571.98220.13972.2573-0.0435-0.0314-0.286-0.1295-0.05530.2850.0221-0.2571-00.2856-0.0126-0.03120.4103-0.04670.352194.2153-17.8155-0.0912
141.81780.3511-0.08181.0839-0.19482.0153-0.05630.2252-0.2585-0.1123-0.0227-0.04310.219-0.0755-00.39550.01750.03960.4347-0.03220.4098121.5861-24.9024.8986
151.6115-0.05121.02390.9087-0.292.3828-0.09730.40360.2958-0.2631-0.1222-0.0127-0.1630.354300.37370.03270.04480.49230.03640.4415127.3367-9.9414-6.1626
161.1817-0.2236-0.47381.0903-0.05921.49720.0196-0.0553-0.23020.1445-0.04060.55610.2934-0.4798-00.5466-0.11760.07940.52050.06880.6079108.0057-12.856293.0507
170.6820.15670.20340.3434-0.28390.26960.1177-0.21170.0185-0.0369-0.29180.4134-0.243-0.282800.6591-0.10250.0940.57460.02730.5024111.86733.323692.5272
182.8303-0.4770.11351.3448-0.11111.32110.1116-0.1075-0.0969-0.0289-0.09720.04410.0546-0.055100.4199-0.01510.0260.313-0.0170.3183112.67814.485477.95
190.4997-0.58990.31731.5679-0.78940.9521-0.0242-0.19470.06110.21290.1014-0.067-0.01010.0700.4138-0.0146-0.02540.3556-0.0140.3525129.392311.41894.6781
201.0604-0.28140.37240.80030.49140.7568-0.07230.05540.1564-0.06650.0708-0.1676-0.06170.259-00.3777-0.0293-0.0230.3709-0.03620.3991133.673218.141288.4068
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 182 through 303 )
2X-RAY DIFFRACTION2chain 'A' and (resid 304 through 398 )
3X-RAY DIFFRACTION3chain 'A' and (resid 399 through 567 )
4X-RAY DIFFRACTION4chain 'B' and (resid 181 through 303 )
5X-RAY DIFFRACTION5chain 'B' and (resid 304 through 423 )
6X-RAY DIFFRACTION6chain 'B' and (resid 424 through 568 )
7X-RAY DIFFRACTION7chain 'C' and (resid 180 through 303 )
8X-RAY DIFFRACTION8chain 'C' and (resid 304 through 567 )
9X-RAY DIFFRACTION9chain 'D' and (resid 182 through 277 )
10X-RAY DIFFRACTION10chain 'D' and (resid 278 through 330 )
11X-RAY DIFFRACTION11chain 'D' and (resid 331 through 423 )
12X-RAY DIFFRACTION12chain 'D' and (resid 424 through 567 )
13X-RAY DIFFRACTION13chain 'E' and (resid 182 through 288 )
14X-RAY DIFFRACTION14chain 'E' and (resid 289 through 398 )
15X-RAY DIFFRACTION15chain 'E' and (resid 399 through 568 )
16X-RAY DIFFRACTION16chain 'F' and (resid 180 through 277 )
17X-RAY DIFFRACTION17chain 'F' and (resid 278 through 303 )
18X-RAY DIFFRACTION18chain 'F' and (resid 304 through 423 )
19X-RAY DIFFRACTION19chain 'F' and (resid 424 through 512 )
20X-RAY DIFFRACTION20chain 'F' and (resid 513 through 567 )

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