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- PDB-2q1k: Cyrstal Structure of AscE from Aeromonas hydrophilla -

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Basic information

Entry
Database: PDB / ID: 2q1k
TitleCyrstal Structure of AscE from Aeromonas hydrophilla
ComponentsAscE
KeywordsCHAPERONE / helix-turn-helix / TTSS
Function / homologyType III secretion system, secretion protein E / Type III secretion system, cytoplasmic E component of needle / Immunoglobulin FC, subunit C / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha / AscE
Function and homology information
Biological speciesAeromonas hydrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsTan, Y.W. / Yu, H.B. / Leung, K.Y. / Sivaraman, J. / Mok, Y.K.
CitationJournal: Protein Sci. / Year: 2008
Title: Structure of AscE and induced burial regions in AscE and AscG upon formation of the chaperone needle-subunit complex of type III secretion system in Aeromonas hydrophila.
Authors: Tan, Y.W. / Yu, H.B. / Leung, K.Y. / Sivaraman, J. / Mok, Y.K.
History
DepositionMay 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: AscE
B: AscE
C: AscE
D: AscE


Theoretical massNumber of molelcules
Total (without water)31,1854
Polymers31,1854
Non-polymers00
Water0
1
A: AscE
B: AscE


Theoretical massNumber of molelcules
Total (without water)15,5922
Polymers15,5922
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: AscE
D: AscE


Theoretical massNumber of molelcules
Total (without water)15,5922
Polymers15,5922
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.039, 69.039, 105.043
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
AscE


Mass: 7796.232 Da / Num. of mol.: 4 / Mutation: L9M, L58M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Strain: AH-1 / Gene: ascE / Plasmid: Modified Pet-32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1EHA4

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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: 2.01 Å3/Da / Density % sol: 38.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG 4000, 1.4M NaCl, 13mM TCEP hydrochloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9790, 0.9792, 0.9600
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 26, 2006
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97921
30.961
Reflection

D res low: 50 Å

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2D res high (Å)Num. obs% possible obs
6.917.71298550.0960.892.41884799.4
7.227.4860580.1020.862.81202599.9
6.737.71119020.0910.832.51660398.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.175099.810.0461.0957.5
4.15.1710010.0741.1437.4
3.584.199.910.0951.2326.9
3.263.5810010.1061.1257.6
3.023.2610010.1241.0187.6
2.853.0210010.1780.7027.6
2.72.8510010.2360.5747.3
2.592.799.810.3190.6276.6
2.492.5997.910.2950.5455.6
2.42.4996.210.3510.5414.7
6.035099.820.030.6487.7
4.796.0310020.0650.8457.2
4.184.7910020.0780.9897.5
3.84.1810020.1111.1817.5
3.533.810020.171.2917.1
3.323.5310020.1820.9477.5
3.153.3210020.2010.7797.5
3.023.1510020.2670.6957.2
2.93.0210020.3460.5926.5
2.82.999.320.4370.5395.9
5.385099.830.0330.7717.4
4.275.3810030.0631.2127.4
3.734.2710030.0861.167.5
3.393.7310030.1221.1097.2
3.153.3910030.1260.8017.6
2.963.1510030.1810.6567.5
2.822.9610030.2550.5617.1
2.692.8299.630.350.5216.2
2.592.6996.230.4230.6135
2.52.5990.330.3860.5494.1
ReflectionResolution: 2.7→50 Å / Num. obs: 11024 / % possible obs: 99.4 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.096 / Χ2: 0.887 / Net I/σ(I): 7.7
Reflection shellResolution: 2.7→2.79 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.351 / Num. unique all: 1841 / Rsym value: 0.236 / Χ2: 0.541 / % possible all: 96.2

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Phasing

PhasingMethod: MAD
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.39-80.8540.6321139
4.52-5.390.9450.8471142
4.03-4.520.9690.9231133
3.7-4.030.9610.9161103
3.46-3.70.9390.8771072
3.27-3.460.9370.8781099
3.12-3.270.9430.8731056
2.99-3.120.9240.8651025
2.88-2.990.9020.8471011
2.78-2.880.9340.899934
2.7-2.780.8830.831838

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
CNSrefinement
PDB_EXTRACT2data extraction
CBASSdata collection
HKL-2000data reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→8 Å / FOM work R set: 0.759 / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.288 549 4.3 %
Rwork0.243 --
obs-11024 86 %
Solvent computationBsol: 68.259 Å2
Displacement parametersBiso mean: 45.412 Å2
Baniso -1Baniso -2Baniso -3
1--2.81 Å20 Å20 Å2
2---2.81 Å20 Å2
3---5.62 Å2
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1684 0 0 0 1684
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.301
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.7-2.790.334550.301738793
2.79-2.90.366430.284870913
2.9-3.020.241530.219981051
3.02-3.170.368560.26110131069
3.17-3.360.393530.27810911144
3.36-3.60.276460.24811151161
3.6-3.920.296740.23910751149
3.92-4.40.256510.20411931244
4.4-5.270.228760.21511781254
5.27-80.27420.27412041246
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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