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- PDB-5eou: Pseudomonas aeruginosa PilM:PilN1-12 bound to ATP -

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Basic information

Entry
Database: PDB / ID: 5eou
TitlePseudomonas aeruginosa PilM:PilN1-12 bound to ATP
ComponentsType 4 fimbrial biogenesis protein PilM,Type 4 fimbrial biogenesis protein PilN
KeywordsPEPTIDE BINDING PROTEIN / PilM / PilN / Type IV Pilus / T4P
Function / homology
Function and homology information


type IV pilus assembly / type IV pilus / type IV pilus-dependent motility / cell division / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Dna Ligase; domain 1 - #300 / Type IV pilus inner membrane component PilN / Fimbrial assembly protein (PilN) / : / Type IV pilus inner membrane component PilM / Type IV pilus assembly protein PilM; / SHS2 domain inserted in FtsA / Cell division protein FtsA / : / Dna Ligase; domain 1 ...Dna Ligase; domain 1 - #300 / Type IV pilus inner membrane component PilN / Fimbrial assembly protein (PilN) / : / Type IV pilus inner membrane component PilM / Type IV pilus assembly protein PilM; / SHS2 domain inserted in FtsA / Cell division protein FtsA / : / Dna Ligase; domain 1 / ATPase, nucleotide binding domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Type IV pilus inner membrane component PilM / Type IV pilus inner membrane component PilN
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMcCallum, M. / Tammam, S. / Robinson, H. / Shah, M. / Calmettes, C. / Moraes, T. / Burrows, L. / Howell, L.P.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: PilN Binding Modulates the Structure and Binding Partners of the Pseudomonas aeruginosa Type IVa Pilus Protein PilM.
Authors: McCallum, M. / Tammam, S. / Little, D.J. / Robinson, H. / Koo, J. / Shah, M. / Calmettes, C. / Moraes, T.F. / Burrows, L.L. / Howell, P.L.
History
DepositionNov 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 2.0Sep 27, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _atom_site.occupancy / _citation.journal_id_CSD ..._atom_site.occupancy / _citation.journal_id_CSD / _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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.value / _pdbx_struct_oper_list.symmetry_operation / _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 4 fimbrial biogenesis protein PilM,Type 4 fimbrial biogenesis protein PilN
B: Type 4 fimbrial biogenesis protein PilM,Type 4 fimbrial biogenesis protein PilN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,60119
Polymers80,0892
Non-polymers1,51217
Water1,820101
1
A: Type 4 fimbrial biogenesis protein PilM,Type 4 fimbrial biogenesis protein PilN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6089
Polymers40,0451
Non-polymers5638
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Type 4 fimbrial biogenesis protein PilM,Type 4 fimbrial biogenesis protein PilN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,99410
Polymers40,0451
Non-polymers9499
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)131.790, 131.790, 78.993
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11B-523-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Type 4 fimbrial biogenesis protein PilM,Type 4 fimbrial biogenesis protein PilN


Mass: 40044.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria), (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: pilM, PA5044, pilN, PA5043 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: G3XD28, UniProt: G3XD30

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Non-polymers , 6 types, 118 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: ammonium sulphate, tris / PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 37322 / % possible obs: 100 % / Redundancy: 19.9 % / Rsym value: 0.135 / Net I/σ(I): 21.2

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Processing

Software
NameVersionClassification
PHENIXdev_1639refinement
Cootmodel building
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EOY

5eoy


Resolution: 2.4→39.497 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2387 1600 5.1 %
Rwork0.2123 --
obs0.2137 29964 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→39.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4904 0 79 101 5084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035021
X-RAY DIFFRACTIONf_angle_d0.6396835
X-RAY DIFFRACTIONf_dihedral_angle_d11.2271750
X-RAY DIFFRACTIONf_chiral_restr0.025844
X-RAY DIFFRACTIONf_plane_restr0.004868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.43760.33861780.31482550X-RAY DIFFRACTION100
2.4376-2.47750.33241850.29622521X-RAY DIFFRACTION100
2.4775-2.52021000000000.27542687X-RAY DIFFRACTION100
2.5202-2.56610.29751860.25652542X-RAY DIFFRACTION100
2.5661-2.61540.27941860.27892527X-RAY DIFFRACTION100
2.6154-2.66880.32331830.27332553X-RAY DIFFRACTION100
2.6688-2.72681000000000.26422714X-RAY DIFFRACTION100
2.7268-2.79020.25931820.26592561X-RAY DIFFRACTION100
2.7902-2.860.31121820.26832564X-RAY DIFFRACTION100
2.86-2.93730.31081800.27672512X-RAY DIFFRACTION100
2.9373-3.02371000000000.26092757X-RAY DIFFRACTION100
3.0237-3.12120.33851860.26842540X-RAY DIFFRACTION100
3.1212-3.23270.29481780.25352524X-RAY DIFFRACTION100
3.2327-3.36210.26181840.23462567X-RAY DIFFRACTION100
3.3621-3.5151000000000.22872729X-RAY DIFFRACTION100
3.515-3.70020.22751840.20692525X-RAY DIFFRACTION100
3.7002-3.93190.23721780.19132580X-RAY DIFFRACTION100
3.9319-4.23510.20271820.18392528X-RAY DIFFRACTION100
4.2351-4.66070.17931700.16622586X-RAY DIFFRACTION100
4.6607-5.33371000000000.17692708X-RAY DIFFRACTION100
5.3337-6.71460.23081740.19622572X-RAY DIFFRACTION100
6.7146-39.50180.18571610.17632543X-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)
14.80181.04730.65845.12851.00485.6875-0.1119-0.1163-0.168-0.0043-0.1035-0.34010.00690.13350.23810.2803-0.05540.00070.594-0.06640.4932332.4295217.7378179.3715
28.48630.99781.590610.2971-4.35986.53730.57060.26480.1101-0.3192-0.02911.2491-0.833-1.5708-0.34320.67810.30560.13540.8442-0.1580.6693323.0865242.9331171.6443
37.83024.46284.83743.3290.96822.3344-0.2486-0.06560.64730.0134-0.13780.4539-0.0294-0.60510.3940.3478-0.0070.05670.6418-0.08730.4922329.8025226.9749176.0108
48.8516-1.0568-0.18786.4956-2.5316.36920.02770.68050.282-0.27990.25150.1838-0.951-0.0902-0.32250.46190.01420.05360.52970.05840.5072311.9424225.6468179.0365
58.9452-1.75771.85267.1122-2.27018.8754-0.2795-0.0249-0.15041.9526-0.2965-0.75210.84250.5430.44421.02080.0327-0.02841.02170.13210.671316.5019211.731201.0026
610.335-0.50661.37358.89980.05447.69080.0779-0.36850.00820.09930.11451.0736-0.4146-0.681-0.2940.3168-0.0010.04380.53530.00550.4657305.3907221.7692185.0142
77.61133.4-0.52026.6693-3.00226.7331-0.29880.5028-0.3186-0.4850.3790.04720.5997-0.3078-0.09230.3191-0.05230.03510.6301-0.18180.4464323.2577212.9322173.4313
82.34480.11430.91892.9494-0.54484.9087-0.1015-0.1040.3298-0.0178-0.03640.3803-0.2993-0.28970.16520.2704-0.0276-0.05930.3734-0.0540.4704355.4461238.8668179.5549
93.66711.7833-3.58264.76871.38539.9931-0.5368-0.5465-0.8329-0.4173-0.2352-0.20530.9731.01240.80170.65280.1398-0.08540.60480.14670.8568363.514211.9026171.1587
108.01321.6556-1.65081.56680.0240.5438-0.0201-0.0704-0.3645-0.1237-0.05170.14130.0785-0.00670.080.3397-0.0125-0.09930.5653-0.06060.4695357.8679229.7845176.0171
119.3854-0.51110.87815.45395.45053.79520.12740.8134-0.217-0.42530.07170.1741.0820.7377-0.2020.4350.1313-0.07930.4634-0.06240.4308376.0325230.7078179.1276
129.9843-3.3951-5.59966.31552.55279.0538-0.0497-0.28560.77770.5049-0.08910.4318-0.4617-0.12060.15170.30290.0349-0.04160.2764-0.050.5972371.8144244.046201.484
139.8477-1.68830.88562.470.37828.5333-0.07590.226-0.1060.09090.047-0.31240.50371.0328-0.02030.31370.0091-0.05130.44850.01150.3567382.7851234.3321184.6878
145.29543.31793.63356.8708-2.87524.0119-0.62470.64660.2737-0.20660.356-0.0622-0.98080.18580.31950.4146-0.0517-0.08170.4979-0.00730.5146364.5619243.546173.5751
152.17795.9106-1.53722.2256-4.44266.03780.22961.4041-1.5097-2.0301-0.6297-0.4109-1.03611.46230.44940.74420.20870.09960.9318-0.11650.874333.0507234.7527168.8169
169.56980.1907-2.64557.1665-6.918.120.02081.5952-1.248-1.03410.1021-1.34250.6614-0.73920.30510.5706-0.051-0.14120.5047-0.24910.8239357.8423223.3802168.8835
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 81)
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 147 )
3X-RAY DIFFRACTION3chain 'A' and (resid 148 through 182 )
4X-RAY DIFFRACTION4chain 'A' and (resid 183 through 223 )
5X-RAY DIFFRACTION5chain 'A' and (resid 224 through 265 )
6X-RAY DIFFRACTION6chain 'A' and (resid 266 through 318 )
7X-RAY DIFFRACTION7chain 'A' and (resid 319 through 354 )
8X-RAY DIFFRACTION8chain 'B' and (resid 10 through 81)
9X-RAY DIFFRACTION9chain 'B' and (resid 82 through 147 )
10X-RAY DIFFRACTION10chain 'B' and (resid 148 through 182 )
11X-RAY DIFFRACTION11chain 'B' and (resid 183 through 223 )
12X-RAY DIFFRACTION12chain 'B' and (resid 224 through 265 )
13X-RAY DIFFRACTION13chain 'B' and (resid 266 through 318 )
14X-RAY DIFFRACTION14chain 'B' and (resid 319 through 355 )
15X-RAY DIFFRACTION15chain 'A' and (resid 359 through 367)
16X-RAY DIFFRACTION16chain 'B' and (resid 358 through 366)

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