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- PDB-3jvv: Crystal Structure of P. aeruginosa PilT with bound AMP-PCP -

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Basic information

Entry
Database: PDB / ID: 3jvv
TitleCrystal Structure of P. aeruginosa PilT with bound AMP-PCP
ComponentsTwitching mobility protein
KeywordsATP binding protein / HEXAMERIC P-LOOP ATPASE / SECRETION ATPASE / ATP-binding / Fimbrium / Nucleotide-binding / Transport
Function / homology
Function and homology information


pilus retraction / type IV pilus / type IV pilus-dependent motility / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Pilus retraction protein PilT/PilU / Beta-Lactamase - #90 / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase ...Pilus retraction protein PilT/PilU / Beta-Lactamase - #90 / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / CITRIC ACID / Type IV pilus retractation ATPase PilT
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMisic, A.M. / Satyshur, K.A. / Forest, K.T.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: P. aeruginosa PilT structures with and without nucleotide reveal a dynamic type IV pilus retraction motor.
Authors: Misic, A.M. / Satyshur, K.A. / Forest, K.T.
History
DepositionSep 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _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: Twitching mobility protein
B: Twitching mobility protein
C: Twitching mobility protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,02410
Polymers118,2433
Non-polymers1,7817
Water1,60389
1
A: Twitching mobility protein
B: Twitching mobility protein
C: Twitching mobility protein
hetero molecules

A: Twitching mobility protein
B: Twitching mobility protein
C: Twitching mobility protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,04720
Polymers236,4866
Non-polymers3,56114
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area24190 Å2
ΔGint-86.1 kcal/mol
Surface area78970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.483, 119.552, 185.535
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C
13A
23C
33B
14A
24B
34C
15A
25B
35C
16A
26B
36C
17A
27B
37C
18A
28B
38C
19A
29B
39C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A1 - 34
2113B1 - 34
3113C1 - 34
1123A36 - 51
2123B36 - 51
3123C36 - 51
1133A53 - 80
2133C53 - 80
3133B53 - 80
1143A105 - 130
2143B105 - 130
3143C105 - 130
1153A140 - 155
2153B140 - 155
3153C140 - 155
1163A165 - 190
2163B165 - 190
3163C165 - 190
1173A210 - 220
2173B210 - 220
3173C210 - 220
1183A230 - 238
2183B230 - 238
3183C230 - 238
1193A240 - 343
2193B240 - 343
3193C240 - 343

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9

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Components

#1: Protein Twitching mobility protein


Mass: 39414.328 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA103 / Gene: PA0395, pilT / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P24559
#2: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.54 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: mother liquor: 10% PEG 6000, 0.1 M HEPES, protein buffer contains NaCl, MES, glycerol, MgCl and citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2006 / Details: Bent Conical Si Mirror (Rh coated)
RadiationMonochromator: Bent Ge111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→29.12 Å / Num. all: 33594 / Num. obs: 35387 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 68.8 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 32.6
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2445 / % possible all: 93.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.4.0067refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EWV
Resolution: 2.6→29.12 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.898 / SU B: 28.123 / SU ML: 0.295 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 1.368 / ESU R Free: 0.382 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: Anisotropic B values from TLS matrices
RfactorNum. reflection% reflectionSelection details
Rfree0.29136 1759 5 %RANDOM
Rwork0.24435 ---
obs0.24667 33594 94.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 60.994 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å20 Å20 Å2
2--5.66 Å20 Å2
3----4.58 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7741 0 109 89 7939
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227962
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.99110756
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3785988
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.35323.652345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.551151455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.021569
X-RAY DIFFRACTIONr_chiral_restr0.0790.21248
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215827
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.80124943
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40137983
X-RAY DIFFRACTIONr_scbond_it0.76923019
X-RAY DIFFRACTIONr_scangle_it1.2332773
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A135tight positional0.040.05
12B135tight positional0.030.05
13C135tight positional0.030.05
21A64tight positional0.030.05
22B64tight positional0.020.05
23C64tight positional0.030.05
31A112tight positional0.020.05
32B112tight positional0.020.05
33C112tight positional0.020.05
41A104tight positional0.030.05
42B104tight positional0.020.05
43C104tight positional0.030.05
51A64tight positional0.030.05
52B64tight positional0.030.05
53C64tight positional0.040.05
61A104tight positional0.030.05
62B104tight positional0.030.05
63C104tight positional0.030.05
71A44tight positional0.030.05
72B44tight positional0.040.05
73C44tight positional0.030.05
81A36tight positional0.030.05
82B36tight positional0.030.05
83C36tight positional0.030.05
91A356tight positional0.030.05
92B356tight positional0.030.05
93C356tight positional0.030.05
11A112loose positional0.075
12B112loose positional0.055
13C112loose positional0.15
21A68loose positional0.145
22B68loose positional0.095
23C68loose positional0.165
31A124loose positional0.15
32B124loose positional0.075
33C124loose positional0.15
41A91loose positional0.045
42B91loose positional0.035
43C91loose positional0.045
51A70loose positional0.045
52B70loose positional0.045
53C70loose positional0.065
61A109loose positional0.15
62B109loose positional0.075
63C109loose positional0.115
71A36loose positional0.095
72B36loose positional0.165
73C36loose positional0.095
81A26loose positional0.035
82B26loose positional0.035
83C26loose positional0.045
91A322loose positional0.095
92B322loose positional0.095
93C322loose positional0.095
11A135tight thermal1.7925
12B135tight thermal1.5825
13C135tight thermal1.4225
21A64tight thermal2.1725
22B64tight thermal2.225
23C64tight thermal2.0125
31A112tight thermal2.3325
32B112tight thermal2.8325
33C112tight thermal2.5225
41A104tight thermal2.4525
42B104tight thermal1.7425
43C104tight thermal2.5625
51A64tight thermal1.6825
52B64tight thermal1.8325
53C64tight thermal0.8325
61A104tight thermal1.925
62B104tight thermal3.4625
63C104tight thermal1.9625
71A44tight thermal2.0525
72B44tight thermal3.2625
73C44tight thermal3.9325
81A36tight thermal125
82B36tight thermal1.6825
83C36tight thermal1.8225
91A356tight thermal3.7725
92B356tight thermal2.7925
93C356tight thermal4.1425
11A112loose thermal2.1650
12B112loose thermal1.7450
13C112loose thermal1.8150
21A68loose thermal2.3450
22B68loose thermal2.150
23C68loose thermal2.3250
31A124loose thermal2.6450
32B124loose thermal2.9850
33C124loose thermal2.4850
41A91loose thermal2.4150
42B91loose thermal2.150
43C91loose thermal2.5150
51A70loose thermal2.6450
52B70loose thermal2.3650
53C70loose thermal1.8250
61A109loose thermal2.350
62B109loose thermal3.7150
63C109loose thermal2.5150
71A36loose thermal2.7350
72B36loose thermal3.3550
73C36loose thermal4.1850
81A26loose thermal1.250
82B26loose thermal1.850
83C26loose thermal1.4150
91A322loose thermal4.1850
92B322loose thermal2.9250
93C322loose thermal4.3550
LS refinement shellResolution: 2.6→2.664 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 126 -
Rwork0.352 2319 -
obs--90.15 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.34170.1879-1.87913.1458-1.97679.105-0.05090.28390.4416-0.29210.4473-0.2628-0.11670.1508-0.3964-0.0466-0.008-0.0975-0.06050.03310.0305-7.651339.561336.0612
23.34372.81741.18882.60850.20413.1346-0.47050.11731.0090.04160.2592-0.178-0.7947-0.33040.21130.14730.1319-0.0951-0.11810.02230.0087-12.810343.399440.116
36.0131-0.4813-5.34545.05431.151710.3596-0.12690.52460.49790.01110.22440.0566-0.042-0.5802-0.0976-0.06850.011-0.152-0.07760.0740.0442-22.290442.102834.0215
40.14530.07170.61961.96890.09872.66430.0992-0.0498-0.0570.232-0.0954-0.15720.16110.2177-0.0038-0.19170.05040.0471-0.0117-0.0535-0.111-28.222918.69626.0533
57.25572.24250.45386.05231.67450.46760.16760.45780.6034-0.45990.11770.9525-0.68970.1325-0.2854-0.1310.02850.0949-0.01060.1190.0091-39.194137.99322.4126
64.2563-1.1897-2.54480.8349-0.75495.80120.1596-0.25760.82510.32410.1263-0.0723-0.9053-0.2483-0.286-0.02060.12420.1211-0.1472-0.05160.0886-36.957141.818.6717
73.2315-1.19784.88754.32450.96619.4618-0.2907-0.12320.67210.20130.16940.2106-0.2968-0.52020.1213-0.03240.06140.20150.07170.03470.0278-46.549842.578914.6095
82.5048-0.33690.77311.2399-0.02491.06240.1934-0.0623-0.3968-0.0877-0.05520.03150.38930.3012-0.1381-0.06410.0866-0.0004-0.11550.0103-0.105-59.513820.359616.0282
99.6787-0.7406-4.0923.47960.33253.4904-0.1712-0.1860.2593-0.09720.0730.5931-0.4002-0.57740.0982-0.15370.0691-0.0145-0.06880.0163-0.16-85.084940.081812.3291
103.27880.0491.85892.50181.81484.8679-0.0583-0.35370.11140.31720.1212-0.3617-0.7268-0.5558-0.06290.04140.0902-0.043-0.2369-0.0157-0.174-78.334243.726513.862
1110.1654-1.133-1.06392.2676-0.32262.3561-0.1586-0.75480.02510.28920.26740.1006-0.3485-0.1957-0.10880.0590.0853-0.00720.008-0.0486-0.017-78.391144.693925.167
121.86740.2138-1.31580.3695-0.36541.1316-0.0761-0.099-0.2376-0.0635-0.0811-0.04260.12280.15190.1572-0.0547-0.0385-0.0437-0.0590.061-0.0334-86.12220.661534.0123
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 25
2X-RAY DIFFRACTION2A26 - 61
3X-RAY DIFFRACTION3A62 - 79
4X-RAY DIFFRACTION4A80 - 341
5X-RAY DIFFRACTION5B1 - 25
6X-RAY DIFFRACTION6B26 - 61
7X-RAY DIFFRACTION7B62 - 79
8X-RAY DIFFRACTION8B80 - 341
9X-RAY DIFFRACTION9C1 - 25
10X-RAY DIFFRACTION10C26 - 61
11X-RAY DIFFRACTION11C62 - 79
12X-RAY DIFFRACTION12C80 - 341

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