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- PDB-3nkz: The crystal structure of a flagella protein from Yersinia enteroc... -

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Basic information

Entry
Database: PDB / ID: 3nkz
TitleThe crystal structure of a flagella protein from Yersinia enterocolitica subsp. enterocolitica 8081
ComponentsFlagellar protein fliTFlagellum
Keywordsstructural genomics / unknown function / PSI-2 / protein structure initiative / MCSG / Midwest Center for Structural Genomics
Function / homology
Function and homology information


negative regulation of bacterial-type flagellum assembly / bacterial-type flagellum organization / protein folding / cytosol
Similarity search - Function
Flagellar protein flit. / Flagellar protein FliT / Flagellar protein FliT / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Flagellar protein FliT
Similarity search - Component
Biological speciesYersinia enterocolitica subsp. enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.112 Å
AuthorsTan, K. / Li, H. / Feldmann, B. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a flagella protein from Yersinia enterocolitica subsp. enterocolitica 8081
Authors: Tan, K. / Li, H. / Feldmann, B. / Joachimiak, A.
History
DepositionJun 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flagellar protein fliT
B: Flagellar protein fliT
C: Flagellar protein fliT
D: Flagellar protein fliT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,51510
Polymers56,7424
Non-polymers7736
Water1,56787
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11760 Å2
ΔGint-150 kcal/mol
Surface area19080 Å2
MethodPISA
2
A: Flagellar protein fliT
B: Flagellar protein fliT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7575
Polymers28,3712
Non-polymers3863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-68 kcal/mol
Surface area10350 Å2
MethodPISA
3
C: Flagellar protein fliT
D: Flagellar protein fliT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7575
Polymers28,3712
Non-polymers3863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-64 kcal/mol
Surface area10360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.798, 66.758, 137.649
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsExperimentally unknown. The chains A and B, C and D likely form dimers, respectively.

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Components

#1: Protein
Flagellar protein fliT / Flagellum


Mass: 14185.469 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica subsp. enterocolitica (bacteria)
Strain: 8081 / Gene: fliT, YE2526 / Plasmid: pMCSG19b / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: A1JSR8
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.7 Å3/Da / Density % sol: 54.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.0M Ammonium sulfate, 0.1M Bis-Tris, 1% w/v PEG3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2010 / Details: mirror
RadiationMonochromator: Si 111 Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.112→39 Å / Num. all: 34714 / Num. obs: 34714 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 31.9
Reflection shellResolution: 2.12→2.16 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 2.44 / Num. unique all: 1740 / % possible all: 96.5

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.112→38.936 Å / σ(F): 0.02 / σ(I): 0 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1747 5.23 %random
Rwork0.1588 ---
all0.1582 33376 --
obs0.1582 33376 92.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.954 Å2 / ksol: 0.365 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.3713 Å20 Å20 Å2
2--1.402 Å2-0 Å2
3---5.9693 Å2
Refinement stepCycle: LAST / Resolution: 2.112→38.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3085 0 46 87 3218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083172
X-RAY DIFFRACTIONf_angle_d1.0514275
X-RAY DIFFRACTIONf_dihedral_angle_d19.2811229
X-RAY DIFFRACTIONf_chiral_restr0.059526
X-RAY DIFFRACTIONf_plane_restr0.003531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1132-2.18140.31151280.25082565X-RAY DIFFRACTION80
2.1814-2.25930.28521290.22672639X-RAY DIFFRACTION82
2.2593-2.34980.2461430.21242737X-RAY DIFFRACTION84
2.3498-2.45670.22351460.21262765X-RAY DIFFRACTION86
2.4567-2.58610.23321530.19932797X-RAY DIFFRACTION87
2.5861-2.7480.21421500.18872869X-RAY DIFFRACTION88
2.748-2.96010.22251630.18982883X-RAY DIFFRACTION88
2.9601-3.25760.22171600.16582980X-RAY DIFFRACTION91
3.2576-3.72820.17141540.13513090X-RAY DIFFRACTION94
3.7282-4.69430.13211510.10973168X-RAY DIFFRACTION95
4.6943-30.05080.16851750.13823212X-RAY DIFFRACTION92
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)
10.3890.1142-0.12780.10070.09060.3368-0.1272-0.02510.0068-0.0630.16490.2819-0.06240.0021-0.04210.29490.03980.05760.03370.02160.3001-6.7335-9.136734.1973
20.37790.0325-0.20431.1992-0.05210.5077-0.1677-0.1481-0.07080.29980.2018-0.33830.10950.0671-0.00890.3710.061-0.00610.05470.02580.23451.5042-13.125140.5672
30.31320.17190.00940.2792-0.09710.17740.13490.0409-0.17370.0692-0.06830.03050.06120.0043-0.04990.27450.0164-0.00370.1906-0.05650.3289.0917-23.0372-0.0456
41.57530.1520.09120.5255-0.2090.13810.1390.31570.1507-0.0105-0.05620.03060.07160.0199-0.05930.25090.0356-0.01890.2226-0.02370.22555.3466-14.6539-6.1096
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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