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- PDB-1ry9: Spa15, a Type III Secretion Chaperone from Shigella flexneri -

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Basic information

Entry
Database: PDB / ID: 1ry9
TitleSpa15, a Type III Secretion Chaperone from Shigella flexneri
ComponentsSurface presentation of antigens protein spaK
KeywordsCHAPERONE / alpha/beta fold
Function / homologySurface presentation of antigens protein SpaK / Invasion protein B family / Yope Regulator; Chain: A, - #10 / Yope Regulator; Chain: A, / 2-Layer Sandwich / Alpha Beta / Surface presentation of antigens protein SpaK
Function and homology information
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.82 Å
Authorsvan Eerde, A. / Hamiaux, C. / Perez, J. / Parsot, C. / Dijkstra, B.W.
CitationJournal: Embo Rep. / Year: 2004
Title: Structure of Spa15, a type III secretion chaperone from Shigella flexneri with broad specificity.
Authors: van Eerde, A. / Hamiaux, C. / Perez, J. / Parsot, C. / Dijkstra, B.W.
History
DepositionDec 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Surface presentation of antigens protein spaK
B: Surface presentation of antigens protein spaK
C: Surface presentation of antigens protein spaK
D: Surface presentation of antigens protein spaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,34010
Polymers66,1274
Non-polymers2136
Water4,234235
1
A: Surface presentation of antigens protein spaK
B: Surface presentation of antigens protein spaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2066
Polymers33,0642
Non-polymers1424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Surface presentation of antigens protein spaK
D: Surface presentation of antigens protein spaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1354
Polymers33,0642
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.878, 87.682, 58.703
Angle α, β, γ (deg.)90.00, 90.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Surface presentation of antigens protein spaK / Spa15 protein


Mass: 16531.850 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: SPAK, SPA15, CP0148 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P35530
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.2 %
Description: The first crystal is a native one, all data collection and refinement statistics belongs to the native crystal.
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: Ammonium Suplhate, ethylene glycol, Guanidium chloride, MES, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-210.9196
SYNCHROTRONESRF BM30A20.9794, 0.9795, 0.9760
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJun 23, 2002
MAR CCD 165 mm2CCDSep 26, 2002
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.91961
20.97941
30.97951
40.9761
ReflectionResolution: 1.82→50 Å / Num. all: 45246 / Num. obs: 45246 / % possible obs: 97.4 %
Reflection shellResolution: 1.82→1.89 Å / % possible all: 92.3

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Processing

Software
NameVersionClassification
REFMAC5.1.27refinement
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.82→43.85 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.872 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.145 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21108 2292 5.1 %RANDOM
Rwork0.18117 ---
obs0.18272 42717 97.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.01 Å2
2--0.01 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.82→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4244 0 6 235 4485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224358
X-RAY DIFFRACTIONr_bond_other_d0.0020.024024
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.9585930
X-RAY DIFFRACTIONr_angle_other_deg0.69639351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0245532
X-RAY DIFFRACTIONr_chiral_restr0.090.2714
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024783
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02817
X-RAY DIFFRACTIONr_nbd_refined0.20.3861
X-RAY DIFFRACTIONr_nbd_other0.2280.34787
X-RAY DIFFRACTIONr_nbtor_other0.0880.52723
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.5290
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.342
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2050.3139
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.537
X-RAY DIFFRACTIONr_mcbond_it2.4091.52679
X-RAY DIFFRACTIONr_mcangle_it3.96924379
X-RAY DIFFRACTIONr_scbond_it5.60231679
X-RAY DIFFRACTIONr_scangle_it8.3524.51551
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.284 163
Rwork0.252 2963
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)
11.12310.01670.01622.1919-1.08010.97760.055-0.1321-0.03730.1836-0.08010.0889-0.12560.02050.02510.0606-0.0068-0.01280.04550.00020.022428.275645.255930.0352
21.93260.36090.25061.72260.7491.1569-0.02660.2042-0.1074-0.15630.0278-0.046-0.11190.0461-0.00120.0473-0.0014-0.00750.0522-0.01580.019222.099744.94613.428
31.2517-0.0613-0.06022.18180.99931.03080.0741-0.13320.04480.1657-0.0965-0.10060.0928-0.02050.02240.0493-0.00870.00960.0460.01350.0125-4.054832.059459.3462
42.21910.4267-0.37261.8565-0.88911.2656-0.03410.26510.0937-0.14210.04460.0240.0871-0.0297-0.01050.03790.00040.01280.060.00640.00762.703432.418232.82
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 13313 - 145
2X-RAY DIFFRACTION2BB1 - 13313 - 145
3X-RAY DIFFRACTION3CC1 - 13313 - 145
4X-RAY DIFFRACTION4DD1 - 13313 - 145

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