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- PDB-1zw0: Crystal structure of the Yersinia Type III Secretion protein YscE -

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Basic information

Entry
Database: PDB / ID: 1zw0
TitleCrystal structure of the Yersinia Type III Secretion protein YscE
Componentstype III secretion proteinType three secretion system
KeywordsCHAPERONE / Type III secretion / Yersinia / translocation / export
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 / cytoplasm / Type 3 secretion system chaperone YscE / Type 3 secretion system chaperone YscE
Function and homology information
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsPhan, J. / Austin, B.P. / Waugh, D.S.
CitationJournal: Protein Sci. / Year: 2005
Title: Crystal structure of the Yersinia type III secretion protein YscE
Authors: Phan, J. / Austin, B.P. / Waugh, D.S.
History
DepositionJun 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: type III secretion protein
B: type III secretion protein
C: type III secretion protein
D: type III secretion protein
E: type III secretion protein
F: type III secretion protein
G: type III secretion protein
H: type III secretion protein


Theoretical massNumber of molelcules
Total (without water)60,9358
Polymers60,9358
Non-polymers00
Water6,017334
1
A: type III secretion protein
B: type III secretion protein


Theoretical massNumber of molelcules
Total (without water)15,2342
Polymers15,2342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-20 kcal/mol
Surface area8290 Å2
MethodPISA
2
C: type III secretion protein
D: type III secretion protein


Theoretical massNumber of molelcules
Total (without water)15,2342
Polymers15,2342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-21 kcal/mol
Surface area7630 Å2
MethodPISA
3
E: type III secretion protein
F: type III secretion protein


Theoretical massNumber of molelcules
Total (without water)15,2342
Polymers15,2342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-20 kcal/mol
Surface area7410 Å2
MethodPISA
4
G: type III secretion protein
H: type III secretion protein


Theoretical massNumber of molelcules
Total (without water)15,2342
Polymers15,2342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-22 kcal/mol
Surface area8260 Å2
MethodPISA
5
A: type III secretion protein
B: type III secretion protein

A: type III secretion protein
B: type III secretion protein

C: type III secretion protein
D: type III secretion protein
E: type III secretion protein
F: type III secretion protein
G: type III secretion protein
H: type III secretion protein

C: type III secretion protein
D: type III secretion protein
E: type III secretion protein
F: type III secretion protein
G: type III secretion protein
H: type III secretion protein


Theoretical massNumber of molelcules
Total (without water)121,87016
Polymers121,87016
Non-polymers00
Water28816
TypeNameSymmetry operationNumber
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_754-x+2,-y,z-11
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area30780 Å2
ΔGint-277 kcal/mol
Surface area49870 Å2
MethodPISA
6
A: type III secretion protein
B: type III secretion protein
C: type III secretion protein
D: type III secretion protein

A: type III secretion protein
B: type III secretion protein
C: type III secretion protein
D: type III secretion protein

E: type III secretion protein
F: type III secretion protein
G: type III secretion protein
H: type III secretion protein

E: type III secretion protein
F: type III secretion protein
G: type III secretion protein
H: type III secretion protein


Theoretical massNumber of molelcules
Total (without water)121,87016
Polymers121,87016
Non-polymers00
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation2_756-x+2,-y,z+11
Buried area28990 Å2
ΔGint-270 kcal/mol
Surface area51650 Å2
MethodPISA
7
G: type III secretion protein
H: type III secretion protein

E: type III secretion protein
F: type III secretion protein

A: type III secretion protein
B: type III secretion protein
C: type III secretion protein
D: type III secretion protein


Theoretical massNumber of molelcules
Total (without water)60,9358
Polymers60,9358
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation3_647-x+3/2,y-1/2,-z+21
identity operation1_555x,y,z1
Buried area13880 Å2
ΔGint-126 kcal/mol
Surface area26450 Å2
MethodPISA
8
A: type III secretion protein
B: type III secretion protein

E: type III secretion protein
F: type III secretion protein

C: type III secretion protein
D: type III secretion protein
G: type III secretion protein
H: type III secretion protein


Theoretical massNumber of molelcules
Total (without water)60,9358
Polymers60,9358
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation3_645-x+3/2,y-1/2,-z1
identity operation1_555x,y,z1
Buried area13650 Å2
ΔGint-122 kcal/mol
Surface area26670 Å2
MethodPISA
9
G: type III secretion protein
H: type III secretion protein

E: type III secretion protein
F: type III secretion protein

A: type III secretion protein
B: type III secretion protein
C: type III secretion protein
D: type III secretion protein


Theoretical massNumber of molelcules
Total (without water)60,9358
Polymers60,9358
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation3_646-x+3/2,y-1/2,-z+11
identity operation1_555x,y,z1
Buried area12800 Å2
ΔGint-119 kcal/mol
Surface area27520 Å2
MethodPISA
10
G: type III secretion protein
H: type III secretion protein

A: type III secretion protein
B: type III secretion protein
C: type III secretion protein
D: type III secretion protein


Theoretical massNumber of molelcules
Total (without water)45,7016
Polymers45,7016
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation1_556x,y,z+11
identity operation1_555x,y,z1
Buried area9180 Å2
ΔGint-87 kcal/mol
Surface area21440 Å2
MethodPISA
11
A: type III secretion protein
B: type III secretion protein

C: type III secretion protein
D: type III secretion protein
G: type III secretion protein
H: type III secretion protein


Theoretical massNumber of molelcules
Total (without water)45,7016
Polymers45,7016
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation1_554x,y,z-11
identity operation1_555x,y,z1
Buried area10030 Å2
ΔGint-91 kcal/mol
Surface area20590 Å2
MethodPISA
12
A: type III secretion protein
B: type III secretion protein

G: type III secretion protein
H: type III secretion protein

E: type III secretion protein
F: type III secretion protein


Theoretical massNumber of molelcules
Total (without water)45,7016
Polymers45,7016
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation3_647-x+3/2,y-1/2,-z+21
Buried area9290 Å2
ΔGint-85 kcal/mol
Surface area21280 Å2
MethodPISA
13
A: type III secretion protein
B: type III secretion protein

G: type III secretion protein
H: type III secretion protein

E: type III secretion protein
F: type III secretion protein


Theoretical massNumber of molelcules
Total (without water)45,7016
Polymers45,7016
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation3_646-x+3/2,y-1/2,-z+11
Buried area9100 Å2
ΔGint-87 kcal/mol
Surface area21460 Å2
MethodPISA
14
A: type III secretion protein
B: type III secretion protein

G: type III secretion protein
H: type III secretion protein


Theoretical massNumber of molelcules
Total (without water)30,4674
Polymers30,4674
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area5490 Å2
ΔGint-56 kcal/mol
Surface area15380 Å2
MethodPISA
15
E: type III secretion protein
F: type III secretion protein

C: type III secretion protein
D: type III secretion protein


Theoretical massNumber of molelcules
Total (without water)30,4674
Polymers30,4674
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_657-x+3/2,y+1/2,-z+21
Buried area5300 Å2
ΔGint-51 kcal/mol
Surface area14150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.969, 84.622, 81.799
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-81-

HOH

21E-102-

HOH

31E-141-

HOH

DetailsThe biological assembly is a putative tetramer. The selected putative tetramer comes from two asymmetric units.

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Components

#1: Protein
type III secretion protein / Type three secretion system


Mass: 7616.855 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Plasmid: pBA1493 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus-RIL / References: UniProt: Q7ARI1, UniProt: O68692*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.4 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG 3350, sodium acetate, glycerol, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 12, 2004
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 54088 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3.3 / Redundancy: 7.3 % / Biso Wilson estimate: 28.581 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 20
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.3 / Num. unique all: 5329 / % possible all: 88

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.333 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25912 2740 5.1 %RANDOM
Rwork0.22545 ---
obs0.22715 51152 99.77 %-
all-54088 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.284 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å20 Å20 Å2
2--0.93 Å20 Å2
3----2.12 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3770 0 0 334 4104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0223798
X-RAY DIFFRACTIONr_bond_other_d0.0020.023641
X-RAY DIFFRACTIONr_angle_refined_deg1.991.9695096
X-RAY DIFFRACTIONr_angle_other_deg2.02938504
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2755467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.68526.226159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.80515796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4851515
X-RAY DIFFRACTIONr_chiral_restr0.1270.2620
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024050
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02623
X-RAY DIFFRACTIONr_nbd_refined0.2420.21113
X-RAY DIFFRACTIONr_nbd_other0.2020.23787
X-RAY DIFFRACTIONr_nbtor_refined0.190.21921
X-RAY DIFFRACTIONr_nbtor_other0.10.22242
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.250.2278
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0850.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2580.2121
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2570.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0131.53114
X-RAY DIFFRACTIONr_mcbond_other0.4581.5990
X-RAY DIFFRACTIONr_mcangle_it2.0623816
X-RAY DIFFRACTIONr_scbond_it3.64131562
X-RAY DIFFRACTIONr_scangle_it5.3614.51280
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 210 -
Rwork0.268 3708 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 61.9939 Å / Origin y: 4.5164 Å / Origin z: 60.4374 Å
111213212223313233
T-0.1562 Å20.0012 Å20.0086 Å2--0.1461 Å20.0139 Å2---0.0781 Å2
L0.5033 °2-0.1091 °20.1894 °2-0.348 °2-0.1663 °2--2.2522 °2
S0.0036 Å °-0.2071 Å °-0.0128 Å °-0.037 Å °0.0486 Å °0.0338 Å °-0.0927 Å °-0.1243 Å °-0.0522 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 651 - 65
2X-RAY DIFFRACTION1BB1 - 661 - 66
3X-RAY DIFFRACTION1CC1 - 581 - 58
4X-RAY DIFFRACTION1DD1 - 661 - 66
5X-RAY DIFFRACTION1EE1 - 651 - 65
6X-RAY DIFFRACTION1FF1 - 661 - 66
7X-RAY DIFFRACTION1GG2 - 652 - 65
8X-RAY DIFFRACTION1HH1 - 661 - 66

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