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- PDB-4mbq: TPR3 of FimV from P. aeruginosa (PAO1) -

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Basic information

Entry
Database: PDB / ID: 4mbq
TitleTPR3 of FimV from P. aeruginosa (PAO1)
ComponentsMotility protein FimV
KeywordsUNKNOWN FUNCTION / TPR
Function / homology
Function and homology information


type IV pilus / type II protein secretion system complex / peptidoglycan binding / plasma membrane
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2200 / Motility protein FimV, C-terminal / Motility protein FimV, N-terminal / FimV, C-terminal domain superfamily / Lysin motif / LysM domain superfamily / LysM domain profile. / LysM domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Tetratricopeptide-like helical domain superfamily ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2200 / Motility protein FimV, C-terminal / Motility protein FimV, N-terminal / FimV, C-terminal domain superfamily / Lysin motif / LysM domain superfamily / LysM domain profile. / LysM domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Tetratricopeptide-like helical domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Motility hub protein FimV
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.006 Å
AuthorsNguyen, Y. / Zhang, K. / Daniel-Ivad, M. / Robinson, H. / Wolfram, F. / Sugiman-Marangos, S.N. / Junop, M.S. / Burrows, L.L. / Howell, P.L.
CitationJournal: To be Published
Title: Crystal structure of TPR2 from FimV
Authors: Daniel-Ivad, M. / Nguyen, Y. / Zhang, K. / Buensuceso, R. / Robinson, H. / Wolfram, F. / Sugiman-Marangos, S.N. / Junop, M.S. / Howell, P.L. / Burrows, L.L.
History
DepositionAug 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Structure summary
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Motility protein FimV
B: Motility protein FimV
C: Motility protein FimV
D: Motility protein FimV
E: Motility protein FimV
F: Motility protein FimV


Theoretical massNumber of molelcules
Total (without water)41,7156
Polymers41,7156
Non-polymers00
Water1,53185
1
A: Motility protein FimV
B: Motility protein FimV
E: Motility protein FimV


Theoretical massNumber of molelcules
Total (without water)20,8573
Polymers20,8573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-16 kcal/mol
Surface area7270 Å2
MethodPISA
2
C: Motility protein FimV
D: Motility protein FimV
F: Motility protein FimV


Theoretical massNumber of molelcules
Total (without water)20,8573
Polymers20,8573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-18 kcal/mol
Surface area7540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.026, 58.514, 136.695
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

#1: Protein
Motility protein FimV /


Mass: 6952.441 Da / Num. of mol.: 6 / Fragment: TPR2, unp residues 862-919
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: fimV, PA3115 / Plasmid: pET151-D-topo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HZA6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 1.63 Å3/Da / Density % sol: 24.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1M ammonium phosphate, 100mM tri-sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 14, 2012
RadiationMonochromator: Si(III) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 18054 / Num. obs: 18054 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Biso Wilson estimate: 32.6 Å2 / Rsym value: 0.151 / Net I/σ(I): 20.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 10.6 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 1394 / Rsym value: 0.781 / % possible all: 76.2

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIX(AutoMR)model building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(AutoMR)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.006→44.449 Å / SU ML: 0.25 / σ(F): 0 / Phase error: 30.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1754 10.08 %Random
Rwork0.2076 ---
obs0.2126 17404 91.48 %-
all-17404 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.75 Å2
Refinement stepCycle: LAST / Resolution: 2.006→44.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2143 0 0 85 2228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022161
X-RAY DIFFRACTIONf_angle_d0.5412916
X-RAY DIFFRACTIONf_dihedral_angle_d11.876786
X-RAY DIFFRACTIONf_chiral_restr0.034346
X-RAY DIFFRACTIONf_plane_restr0.001401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0065-2.06070.3627990.268881X-RAY DIFFRACTION70
2.0607-2.12140.32991050.2573957X-RAY DIFFRACTION73
2.1214-2.18990.30561170.24221027X-RAY DIFFRACTION80
2.1899-2.26810.28061280.23511117X-RAY DIFFRACTION86
2.2681-2.35890.29141330.23521180X-RAY DIFFRACTION93
2.3589-2.46630.31041410.23191241X-RAY DIFFRACTION95
2.4663-2.59630.31561410.21391263X-RAY DIFFRACTION97
2.5963-2.75890.27981420.20591262X-RAY DIFFRACTION97
2.7589-2.97190.27331460.21741295X-RAY DIFFRACTION99
2.9719-3.27090.29861470.21091317X-RAY DIFFRACTION99
3.2709-3.7440.22981460.19081323X-RAY DIFFRACTION99
3.744-4.71620.19211490.1671345X-RAY DIFFRACTION100
4.7162-44.46040.2521600.22051442X-RAY DIFFRACTION100
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)
12.00780.5331-2.13346.13720.37724.19850.1218-0.66120.1212-0.0709-0.0571-0.20010.2080.2765-0.26210.39020.0286-0.04970.2959-0.00920.209-1.0058-1.41699.825
25.27290.3943-2.35141.46330.5627.6778-0.3661-0.01791.10670.3060.34550.1776-0.9444-0.4862-0.01030.5110.0937-0.06930.22780.00070.2452-6.390.40824.3752
36.64040.43920.24725.3471-0.56883.9658-0.3450.5055-0.1328-0.76650.35930.03990.84480.0656-0.12540.3058-0.0153-0.02770.2569-0.01230.154-1.7924-8.3211.5664
48.236-0.3085-4.78092.09540.10597.0181-0.67820.1613-0.43-0.35660.24110.47960.99080.4293-0.27560.49060.0228-0.16770.24-0.03930.1256-0.5412-1.528818.6647
56.25351.1407-1.05064.2051-0.38233.6109-0.1793-0.04750.41960.22540.1087-0.0669-0.21210.21450.03140.4890.0277-0.06290.2285-0.00980.1861.5580.760726.2649
66.50240.1385-1.25224.4443-1.17886.8778-0.0018-0.2431-1.45030.9017-0.1989-0.45270.98480.62120.18020.63050.0727-0.13130.2309-0.01510.29052.6478-8.823827.5327
72.32191.1939-0.20582.75391.25374.14790.0657-0.01050.0836-0.1575-0.07820.88080.0102-0.0787-0.06780.6095-0.04050.08060.209-0.04740.28467.022-26.59227.283
82.9483-0.83240.01473.6548-0.842.6840.0818-0.36030.020.97170.0446-0.1925-0.2780.2991-0.04750.7097-0.0617-0.0160.313-0.03160.1849-1.835-25.12931.575
94.399-0.9068-0.91466.04542.90243.6048-0.0854-0.2137-0.59941.255-0.46510.60130.1068-1.00110.19920.48590.21340.20310.4020.20390.26886.235-25.464514.1794
103.91212.152.15826.3064.3066.43810.4853-0.17020.07720.6294-0.2271-0.44770.6916-0.0417-0.21880.33320.04110.11820.23330.01690.209110.294-20.5098.7992
112.70030.62910.26145.74130.89783.82110.0025-0.0573-0.1472-0.1888-0.34250.5649-0.255-0.94370.13180.28680.07020.08820.35170.05230.29460.7364-20.60545.5973
125.7219-2.161-0.56954.53330.67864.23180.14380.12280.4149-0.42570.0180.04890.1955-0.3953-0.21740.4854-0.0286-0.01140.17350.02140.2476-6.478310.37117.0944
136.21152.1485-3.14777.0891-3.89223.34960.0369-0.34270.82431.09240.6137-0.1577-0.70480.1595-0.51830.4679-0.05570.00190.2986-0.00340.3451-6.307717.596123.671
144.454-2.2843-0.87993.4955-0.91531.6209-0.1657-0.70490.08330.23120.1719-0.3022-0.05530.0702-0.0030.4170.05460.04970.37340.07370.308418.9636-29.52618.3501
153.24270.45071.7217.06167.34098.08090.0047-0.0831-0.3989-0.47580.5567-1.1594-1.28880.8881-0.10310.5580.25210.14880.39680.13360.336426.3831-28.270512.4255
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 869:885 )B869 - 885
2X-RAY DIFFRACTION2( CHAIN B AND RESID 886:902 )B886 - 902
3X-RAY DIFFRACTION3( CHAIN B AND RESID 903:918 )B903 - 918
4X-RAY DIFFRACTION4( CHAIN A AND RESID 871:886 )A871 - 886
5X-RAY DIFFRACTION5( CHAIN A AND RESID 887:902 )A887 - 902
6X-RAY DIFFRACTION6( CHAIN A AND RESID 903:919 )A903 - 919
7X-RAY DIFFRACTION7( CHAIN C AND RESID 868:902 )C868 - 902
8X-RAY DIFFRACTION8( CHAIN C AND RESID 903:918 )C903 - 918
9X-RAY DIFFRACTION9( CHAIN D AND RESID 869:885 )D869 - 885
10X-RAY DIFFRACTION10( CHAIN D AND RESID 886:902 )D886 - 902
11X-RAY DIFFRACTION11( CHAIN D AND RESID 903:919 )D903 - 919
12X-RAY DIFFRACTION12( CHAIN E AND RESID 869:902 )E869 - 902
13X-RAY DIFFRACTION13( CHAIN E AND RESID 903:918 )E903 - 918
14X-RAY DIFFRACTION14( CHAIN F AND RESID 869:902 )F869 - 902
15X-RAY DIFFRACTION15( CHAIN F AND RESID 903:918 )F903 - 918

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