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

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Basic information

Entry
Database: PDB / ID: 4mal
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 / SAD / Resolution: 2.05 Å
AuthorsNguyen, Y. / Zhang, K. / Daniel-Ivad, M. / 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 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Structure summary

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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


Theoretical massNumber of molelcules
Total (without water)13,9992
Polymers13,9992
Non-polymers00
Water63135
1
A: Motility protein FimV


Theoretical massNumber of molelcules
Total (without water)6,9991
Polymers6,9991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Motility protein FimV


Theoretical massNumber of molelcules
Total (without water)6,9991
Polymers6,9991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.325, 42.325, 139.481
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsTHE AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

#1: Protein Motility protein FimV /


Mass: 6999.336 Da / Num. of mol.: 2 / Fragment: TPR2
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.: 35 / 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: 2.23 Å3/Da / Density % sol: 44.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 1.6 M ammonium phosphate, 0.6 M potassium phosphate, 0.1 M phosphate citrate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 26, 2013
RadiationMonochromator: Si(III) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 8648 / Num. obs: 8648 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.2 % / Biso Wilson estimate: 26.2 Å2 / Rsym value: 0.072 / Net I/σ(I): 33.9
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 6.2 / Rsym value: 0.478 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIX(AutoSol)model building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(AutoSol)phasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→40.501 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 24.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2424 825 9.92 %
Rwork0.2151 --
obs0.2178 8314 96.78 %
all-8648 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.7 Å2
Refinement stepCycle: LAST / Resolution: 2.05→40.501 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms914 0 0 35 949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013960
X-RAY DIFFRACTIONf_angle_d1.0421300
X-RAY DIFFRACTIONf_dihedral_angle_d14.97363
X-RAY DIFFRACTIONf_chiral_restr0.077145
X-RAY DIFFRACTIONf_plane_restr0.004182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.17850.27811040.24631008X-RAY DIFFRACTION81
2.1785-2.34670.28971400.22721252X-RAY DIFFRACTION100
2.3467-2.58280.27031380.24171252X-RAY DIFFRACTION100
2.5828-2.95640.31231420.24731279X-RAY DIFFRACTION100
2.9564-3.72440.24371450.20831305X-RAY DIFFRACTION100
3.7244-40.50930.18811560.18991393X-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)
12.0917-0.24540.26685.093-4.59274.1557-0.68040.6630.37240.12810.64130.22690.0077-1.26490.09250.6277-0.050.10070.70990.06590.776447.123636.83477.3859
29.70514.1215-1.53036.2247-1.26848.68110.34780.13350.13160.3313-0.3463-0.15030.05870.5802-0.05810.22230.0945-0.02530.16250.00860.152141.868116.107277.1283
36.67152.1261-1.68127.066-0.37395.1605-0.0037-0.1412-0.2163-0.3989-0.00580.06620.57710.82240.00120.1860.106-0.03230.3224-0.01820.146740.763211.224371.032
46.573-1.2726-3.60666.63031.71756.1470.06510.7495-1.3403-0.1164-0.2671-0.41131.36150.8754-0.07940.46110.1495-0.02030.4791-0.05120.614621.291931.672756.5062
56.3551-0.12912.47178.2162-3.60483.7913-0.43870.24550.18390.24380.0821-0.4153-0.66860.07430.27040.22820.0179-0.01040.23650.02970.174839.141322.346954.7631
64.9828-2.94830.10153.8529-2.2845.44170.02990.0059-0.7158-0.14760.38720.42010.2996-0.9616-0.24270.27850.0089-0.00560.42410.05560.226733.686315.669559.7695
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 861 through 868 )
2X-RAY DIFFRACTION2chain 'A' and (resid 869 through 885 )
3X-RAY DIFFRACTION3chain 'A' and (resid 886 through 919 )
4X-RAY DIFFRACTION4chain 'B' and (resid 856 through 871 )
5X-RAY DIFFRACTION5chain 'B' and (resid 872 through 902 )
6X-RAY DIFFRACTION6chain 'B' and (resid 903 through 919 )

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