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- PDB-2x49: Crystal structure of the C-terminal domain of InvA -

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Basic information

Entry
Database: PDB / ID: 2x49
TitleCrystal structure of the C-terminal domain of InvA
ComponentsINVASION PROTEIN INVA
KeywordsPROTEIN TRANSPORT / TRANSPORT / PATHOGENESIS
Function / homology
Function and homology information


protein secretion / plasma membrane
Similarity search - Function
FHIPEP family, domain 3 / FHIPEP family, domain 2 / FHIPEP family, domain 4 / FHIPEP family, domain 1 / Type III secretion protein HrcV / FHIPEP, domain 1 / FHIPEP conserved site / Bacterial export FHIPEP family signature. / Type III secretion system FHIPEP / FHIPEP, domain 3 ...FHIPEP family, domain 3 / FHIPEP family, domain 2 / FHIPEP family, domain 4 / FHIPEP family, domain 1 / Type III secretion protein HrcV / FHIPEP, domain 1 / FHIPEP conserved site / Bacterial export FHIPEP family signature. / Type III secretion system FHIPEP / FHIPEP, domain 3 / FHIPEP, domain 4 / FHIPEP family / Ribosomal Protein L9; domain 1 / Helicase, Ruva Protein; domain 3 / Glutaredoxin / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / Invasion protein InvA
Similarity search - Component
Biological speciesSALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsWorrall, L.J. / Vuckovic, M. / Strynadka, N.C.J.
CitationJournal: Protein Sci. / Year: 2010
Title: Crystal Structure of the C-Terminal Domain of the Salmonella Type III Secretion System Export Apparatus Protein Inva.
Authors: Worrall, L.J. / Vuckovic, M. / Strynadka, N.C.J.
History
DepositionJan 28, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INVASION PROTEIN INVA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9417
Polymers38,1531
Non-polymers7886
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.991, 57.413, 113.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein INVASION PROTEIN INVA / INVA


Mass: 38153.035 Da / Num. of mol.: 1 / Fragment: RESIDUES 357-685
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
Strain: LT2 / Plasmid: PET-28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A1I3
#2: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 1.94 Å3/Da / Density % sol: 36.5 % / Description: NONE
Crystal growpH: 5.5
Details: 15-20 % PEG 500, 0.05 M CACL2, 0.1 M CITRATE PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9793
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 5, 2008 / Details: VERTICALLY FOCUSSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 44795 / % possible obs: 93.3 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 11.4
Reflection shellResolution: 1.5→1.57 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.02 / Mean I/σ(I) obs: 2 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5.4.0074refinement
MOSFLMdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.5→25.51 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.382 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.22516 2279 5.1 %RANDOM
Rwork0.1918 ---
obs0.19346 42455 93.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.296 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å20 Å2
2--0.42 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 1.5→25.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2679 0 12 292 2983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222726
X-RAY DIFFRACTIONr_bond_other_d0.0020.021881
X-RAY DIFFRACTIONr_angle_refined_deg1.6511.9773678
X-RAY DIFFRACTIONr_angle_other_deg2.47834578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.755332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.55623.692130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32615515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4541525
X-RAY DIFFRACTIONr_chiral_restr0.0940.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022978
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02549
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_it0.8591.51656
X-RAY DIFFRACTIONr_mcbond_other0.2851.5673
X-RAY DIFFRACTIONr_mcangle_it1.53622685
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.77931070
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4224.5993
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 131 -
Rwork0.285 2179 -
obs--66.61 %
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)
12.378-0.23771.08383.7802-0.94345.11970.01290.13890.2463-0.09760.0580.1094-0.2991-0.0171-0.0709-0.07330.01090.0306-0.05120.0009-0.029841.9760.2628.682
22.16230.94-1.66012.577-1.95734.23440.05350.016-0.0392-0.05890.08250.20910.1335-0.1471-0.136-0.0820.0239-0.0134-0.0545-0.0131-0.049344.5456.84324.882
35.3893-1.6673-1.59162.4765-0.42243.71370.0212-0.0122-0.3497-0.1306-0.1034-0.06720.06780.43740.0822-0.05420.0066-0.0192-0.0233-0.0011-0.054660.16841.88934.627
45.65941.71.50453.23241.86187.9864-0.010.0594-0.0394-0.00510.0207-0.2471-0.02410.5305-0.0107-0.06790.02780.0183-0.05290.0335-0.053361.53643.23934.108
51.7728-0.76831.61222.5372-2.60276.5719-0.00480.09450.12740.0251-0.0927-0.0807-0.3169-0.05490.0975-0.06370.02520.0406-0.0299-0.0181-0.039251.09860.19616.353
61.6915-0.89340.06062.1395-1.65394.4970.02570.07310.197-0.0469-0.025-0.0689-0.19-0.1081-0.0008-0.0495-0.00110.0215-0.0483-0.0068-0.04645862.8551.183
75.0237-0.37164.521714.3683-0.1156.3457-0.1293-0.57690.38671.03960.1847-0.9154-0.27950.3393-0.0555-0.0012-0.0640.04010.17830.02120.026966.65548.49617.167
82.77260.96760.83751.4659-2.20886.19820.08760.4623-0.0468-0.24310.014-0.05750.14210.3878-0.10170.05120.05420.00860.0342-0.0340.033857.3835.5140.348
92.55950.0519-0.64082.9339-0.77363.5719-0.0404-0.1665-0.1887-0.0461-0.0303-0.05320.13590.0480.0708-0.05540.02070.0173-0.04610.0027-0.047762.09943.53411.648
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A353 - 380
2X-RAY DIFFRACTION2A381 - 422
3X-RAY DIFFRACTION3A423 - 447
4X-RAY DIFFRACTION4A448 - 472
5X-RAY DIFFRACTION5A473 - 510
6X-RAY DIFFRACTION6A511 - 580
7X-RAY DIFFRACTION7A581 - 593
8X-RAY DIFFRACTION8A594 - 632
9X-RAY DIFFRACTION9A633 - 685

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