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- PDB-3kxy: Crystal Structure of the ExsC-ExsE Complex -

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Basic information

Entry
Database: PDB / ID: 3kxy
TitleCrystal Structure of the ExsC-ExsE Complex
Components
  • Exoenzyme S synthesis protein C
  • ExsE
KeywordsCHAPERONE/TRANSCRIPTION INHIBITOR / type-three secretion system / TTSS / T3SS / chaperone-effector complex / chaperone / effector / CHAPERONE-TRANSCRIPTION INHIBITOR complex
Function / homology
Function and homology information


protein secretion by the type III secretion system / negative regulation of protein secretion / cellular response to calcium ion / protein-folding chaperone binding / positive regulation of DNA-templated transcription / extracellular region / cytoplasm
Similarity search - Function
Dna Ligase; domain 1 - #10 / Type III secretion system ExsE / Type III secretion system ExsE / Dna Ligase; domain 1 / Tir chaperone protein (CesT) family / Tir chaperone protein (CesT) family / Yope Regulator; Chain: A, - #10 / Yope Regulator; Chain: A, / Other non-globular / Special ...Dna Ligase; domain 1 - #10 / Type III secretion system ExsE / Type III secretion system ExsE / Dna Ligase; domain 1 / Tir chaperone protein (CesT) family / Tir chaperone protein (CesT) family / Yope Regulator; Chain: A, - #10 / Yope Regulator; Chain: A, / Other non-globular / Special / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcriptional anti-antiactivator ExsC / Type III secretion regulatory protein ExsE
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.804 Å
AuthorsVogelaar, N.J. / Robinson, H.H. / Schubot, F.D.
CitationJournal: Biochemistry / Year: 2010
Title: Analysis of the Crystal Structure of the ExsC.ExsE Complex Reveals Distinctive Binding Interactions of the Pseudomonas aeruginosa Type III Secretion Chaperone ExsC with ExsE and ExsD.
Authors: Vogelaar, N.J. / Jing, X. / Robinson, H.H. / Schubot, F.D.
History
DepositionDec 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 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: Exoenzyme S synthesis protein C
B: Exoenzyme S synthesis protein C
T: ExsE
C: Exoenzyme S synthesis protein C
D: Exoenzyme S synthesis protein C
U: ExsE
E: Exoenzyme S synthesis protein C
F: Exoenzyme S synthesis protein C
V: ExsE
G: Exoenzyme S synthesis protein C
H: Exoenzyme S synthesis protein C
W: ExsE
I: Exoenzyme S synthesis protein C
J: Exoenzyme S synthesis protein C
X: ExsE
K: Exoenzyme S synthesis protein C
L: Exoenzyme S synthesis protein C
Y: ExsE


Theoretical massNumber of molelcules
Total (without water)222,41518
Polymers222,41518
Non-polymers00
Water1,62190
1
G: Exoenzyme S synthesis protein C
H: Exoenzyme S synthesis protein C
W: ExsE


Theoretical massNumber of molelcules
Total (without water)37,0693
Polymers37,0693
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-16 kcal/mol
Surface area15920 Å2
MethodPISA
2
A: Exoenzyme S synthesis protein C
B: Exoenzyme S synthesis protein C
T: ExsE


Theoretical massNumber of molelcules
Total (without water)37,0693
Polymers37,0693
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-12 kcal/mol
Surface area15560 Å2
MethodPISA
3
C: Exoenzyme S synthesis protein C
D: Exoenzyme S synthesis protein C
U: ExsE


Theoretical massNumber of molelcules
Total (without water)37,0693
Polymers37,0693
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-22 kcal/mol
Surface area16490 Å2
MethodPISA
4
E: Exoenzyme S synthesis protein C
F: Exoenzyme S synthesis protein C
V: ExsE


Theoretical massNumber of molelcules
Total (without water)37,0693
Polymers37,0693
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Exoenzyme S synthesis protein C
J: Exoenzyme S synthesis protein C
X: ExsE


Theoretical massNumber of molelcules
Total (without water)37,0693
Polymers37,0693
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Exoenzyme S synthesis protein C
L: Exoenzyme S synthesis protein C
Y: ExsE


Theoretical massNumber of molelcules
Total (without water)37,0693
Polymers37,0693
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.313, 124.973, 228.126
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
Exoenzyme S synthesis protein C


Mass: 14971.155 Da / Num. of mol.: 12 / Fragment: sequence datbase residues 1-133 / Mutation: A59V, D132A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: exsC, PA1710 / Plasmid: HISMBP Gateway DEST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus RIL / References: UniProt: P26995
#2: Protein
ExsE


Mass: 7126.873 Da / Num. of mol.: 6 / Fragment: sequence database residues 16-81 / Mutation: A17T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: exsE, PA1711 / Plasmid: HISMBP Gateway DEST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus RIL / References: UniProt: Q9I322
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 3.09 Å3/Da / Density % sol: 60.2 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.0M sodium potassium tartrate, 0.2M lithium sulfate, 0.1M CHES, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 3, 2007
Details: vertically-focusing mirror and horizontally-focusing monochromator
RadiationMonochromator: Si(1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 66241 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 7.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 1.6 / % possible all: 83.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIX(phaser)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.804→30 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.34 / Isotropic thermal model: TLS by chain / σ(F): 0.11 / Phase error: 26.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2566 1999 3.28 %
Rwork0.2174 --
obs0.2187 60940 89.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.898 Å2 / ksol: 0.304 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.2231 Å20 Å2-0 Å2
2--19.3346 Å20 Å2
3----11.1116 Å2
Refine analyzeLuzzati coordinate error obs: 0.47 Å
Refinement stepCycle: LAST / Resolution: 2.804→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14927 0 0 90 15017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215171
X-RAY DIFFRACTIONf_angle_d0.47720508
X-RAY DIFFRACTIONf_dihedral_angle_d12.2175493
X-RAY DIFFRACTIONf_chiral_restr0.0342348
X-RAY DIFFRACTIONf_plane_restr0.0012679
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8035-2.87360.36761040.31753070X-RAY DIFFRACTION66
2.8736-2.95120.34331160.30783403X-RAY DIFFRACTION73
2.9512-3.0380.34061240.27063669X-RAY DIFFRACTION79
3.038-3.13590.31831350.25913959X-RAY DIFFRACTION85
3.1359-3.24790.27131400.23814155X-RAY DIFFRACTION89
3.2479-3.37780.26331460.2344289X-RAY DIFFRACTION91
3.3778-3.53130.23691450.22154257X-RAY DIFFRACTION91
3.5313-3.71710.2891470.21824369X-RAY DIFFRACTION93
3.7171-3.94950.25831510.19764427X-RAY DIFFRACTION94
3.9495-4.25370.24251520.18414507X-RAY DIFFRACTION96
4.2537-4.68030.18581570.17034615X-RAY DIFFRACTION98
4.6803-5.35420.23431570.17744630X-RAY DIFFRACTION97
5.3542-6.73320.26131590.22694652X-RAY DIFFRACTION97
6.7332-30.00170.23741660.21124939X-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)
10.8313-0.05120.95422.60080.20552.97680.09020.0074-0.0609-0.0034-0.2424-0.17310.1221-0.00670.14720.05490.02860.01820.32290.06020.2662-39.351933.6498-16.4294
24.95582.0629-0.25121.5407-0.96281.8272-0.027-0.06980.9009-0.0272-0.10720.0779-0.06320.35120.18110.25990.007-0.08110.40140.13280.5753-24.361550.8421-14.4998
32.1042-0.1003-0.35130.8755-0.21843.53720.24160.54980.0783-0.27890.00030.1601-0.14470.0973-0.14690.3450.1466-0.1340.3714-0.13870.2578-36.005810.6043-50.1647
41.9248-0.95460.14385.37151.9081.3077-0.20830.1047-0.13140.11070.1307-0.18140.1086-0.06670.01130.47980.1568-0.02250.6478-0.16070.2897-26.2957-4.5864-65.3119
53.8913-0.0926-1.26072.68491.00262.26140.0196-0.1014-0.43140.15690.07170.33130.155-0.3419-0.08330.2183-0.0613-0.11510.15790.06310.4856-53.5895-4.7188-16.6887
61.7123-0.15880.4160.78842.28663.5104-0.2189-0.27220.31771.01650.33870.73391.0428-0.1647-0.08770.9269-0.09270.13370.6690.21231.1296-54.3956-15.52714.014
71.0749-0.5358-0.07053.21880.72392.8153-0.00860.2779-0.03480.06140.15280.13070.15590.001-0.15710.13450.0235-0.04470.29410.09720.2985-21.221615.98740.9621
83.63310.3128-0.95691.5481-0.64521.750.0082-0.720.05520.06310.06240.1850.1071-0.1105-0.08690.13440.0410.03880.37390.08230.2417-34.899218.669919.1996
92.53720.8178-0.59560.9045-0.63220.40880.19250.0516-0.73270.09050.05930.01510.54190.1627-0.23550.69540.0721-0.22090.3678-0.12410.6754-26.4363-17.9853-21.3981
100.7701-0.17481.18032.0451.50144.7919-0.08720.3984-0.645-0.01920.3028-0.47320.082-0.4222-0.18021.0018-0.0859-0.34520.5289-0.03341.0205-37.2866-33.057-36.2393
112.13531.396-0.35251.82850.3431.4874-0.0030.5375-0.0419-0.34120.1629-0.1357-0.311.0367-0.15920.35090.0459-0.01660.8372-0.1420.2518-8.199514.5616-37.9348
121.1693-0.82660.16474.52920.1983-0.07320.0010.35480.3238-0.9611-0.2665-0.1333-0.39430.46440.21060.7195-0.13370.16611.21490.03640.5446-5.794534.4395-48.5339
132.41651.6253-1.04843.2980.75870.18820.32430.28610.87710.0216-0.20410.9622-0.0258-0.0984-0.16510.16950.1365-0.05830.33190.29110.474-40.957847.1642-18.5237
140.91720.6028-1.47390.5671-0.46492.6988-0.16910.45-0.0958-0.3328-0.0070.4981-0.6644-0.30280.15630.33050.1854-0.38050.5869-0.15550.3024-39.2575.923-65.1769
150.64591.6162-0.13922.12010.0133.2274-0.3970.3234-0.0653-0.21020.09480.64210.4116-0.56320.24940.18230.23580.13650.2388-0.05550.898-58.5755-5.86-11.0171
160.32310.26960.76851.20120.93424.47890.047-0.0839-0.17320.1249-0.0420.14060.08570.44710.00340.13490.0076-0.05250.38230.13610.3338-18.419814.67515.9971
170.81570.7865-1.04913.2856-0.16641.8788-0.39070.0243-0.2873-0.2140.3778-0.2557-0.01710.5181-0.03810.47830.3261-0.17620.4511-0.20590.7744-24.8778-25.6564-26.3548
181.7181.3519-1.12353.45290.41872.5954-0.41530.9657-0.2602-0.24950.4213-0.8613-0.21490.36050.00520.2513-0.073-0.19510.99730.02030.56070.547823.8416-40.7665
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H
9X-RAY DIFFRACTION9chain I
10X-RAY DIFFRACTION10chain J
11X-RAY DIFFRACTION11chain K
12X-RAY DIFFRACTION12chain L
13X-RAY DIFFRACTION13chain T
14X-RAY DIFFRACTION14chain U
15X-RAY DIFFRACTION15chain V
16X-RAY DIFFRACTION16chain W
17X-RAY DIFFRACTION17chain X
18X-RAY DIFFRACTION18chain Y

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