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- PDB-5xb6: Crystal structure of YcjY from E. Coli -

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Basic information

Entry
Database: PDB / ID: 5xb6
TitleCrystal structure of YcjY from E. Coli
ComponentsUncharacterized protein YcjY
KeywordsHYDROLASE
Function / homology
Function and homology information


hydrolase activity / cell division
Similarity search - Function
: / Xaa-Pro dipeptidyl-peptidase-like domain / X-Pro dipeptidyl-peptidase (S15 family) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein YcjY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsChen, C.F. / Gao, Z.Q. / Liu, Q.S.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: To Be Published
Title: Crystal structure of YcjY from E. Coli
Authors: Chen, C.F. / Gao, Z.Q. / Liu, Q.S.
History
DepositionMar 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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: Uncharacterized protein YcjY
B: Uncharacterized protein YcjY
C: Uncharacterized protein YcjY
D: Uncharacterized protein YcjY
E: Uncharacterized protein YcjY
F: Uncharacterized protein YcjY
G: Uncharacterized protein YcjY
H: Uncharacterized protein YcjY
I: Uncharacterized protein YcjY
J: Uncharacterized protein YcjY
K: Uncharacterized protein YcjY
L: Uncharacterized protein YcjY


Theoretical massNumber of molelcules
Total (without water)404,26112
Polymers404,26112
Non-polymers00
Water73,8984102
1
A: Uncharacterized protein YcjY
B: Uncharacterized protein YcjY


Theoretical massNumber of molelcules
Total (without water)67,3772
Polymers67,3772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-12 kcal/mol
Surface area20740 Å2
MethodPISA
2
C: Uncharacterized protein YcjY
D: Uncharacterized protein YcjY


Theoretical massNumber of molelcules
Total (without water)67,3772
Polymers67,3772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-12 kcal/mol
Surface area20770 Å2
MethodPISA
3
E: Uncharacterized protein YcjY
F: Uncharacterized protein YcjY


Theoretical massNumber of molelcules
Total (without water)67,3772
Polymers67,3772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-14 kcal/mol
Surface area20690 Å2
MethodPISA
4
G: Uncharacterized protein YcjY
H: Uncharacterized protein YcjY


Theoretical massNumber of molelcules
Total (without water)67,3772
Polymers67,3772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-14 kcal/mol
Surface area20700 Å2
MethodPISA
5
I: Uncharacterized protein YcjY
J: Uncharacterized protein YcjY


Theoretical massNumber of molelcules
Total (without water)67,3772
Polymers67,3772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-15 kcal/mol
Surface area20550 Å2
MethodPISA
6
K: Uncharacterized protein YcjY
L: Uncharacterized protein YcjY


Theoretical massNumber of molelcules
Total (without water)67,3772
Polymers67,3772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-13 kcal/mol
Surface area20780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.584, 216.405, 258.839
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
Uncharacterized protein YcjY


Mass: 33688.402 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ycjY, b1327, JW5804 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P76049
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4102 / 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: 2.69 Å3/Da / Density % sol: 54.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 1.4 M Ammonium sulfate 0.1 M BIS-TRIS pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 284153 / % possible obs: 91.4 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.095 / Χ2: 1.175 / Net I/σ(I): 13.7
Reflection shellResolution: 1.96→1.99 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 2.25 / Num. unique obs: 13252 / Χ2: 1.175 / % possible all: 86.1

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→38.364 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.79
RfactorNum. reflection% reflection
Rfree0.219 13581 5.05 %
Rwork0.182 --
obs0.1838 268967 91.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→38.364 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28444 0 0 4102 32546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00729234
X-RAY DIFFRACTIONf_angle_d1.12939779
X-RAY DIFFRACTIONf_dihedral_angle_d13.30510633
X-RAY DIFFRACTIONf_chiral_restr0.0774309
X-RAY DIFFRACTIONf_plane_restr0.0055235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.2664150.22727951X-RAY DIFFRACTION87
2.0227-2.04650.30484640.22947936X-RAY DIFFRACTION86
2.0465-2.07150.27544410.21597917X-RAY DIFFRACTION87
2.0715-2.09770.2584450.21287938X-RAY DIFFRACTION86
2.0977-2.12530.26574310.21878012X-RAY DIFFRACTION88
2.1253-2.15440.27284560.21577909X-RAY DIFFRACTION86
2.1544-2.18520.27044070.21138061X-RAY DIFFRACTION88
2.1852-2.21780.29324190.2337976X-RAY DIFFRACTION86
2.2178-2.25240.33773790.27257802X-RAY DIFFRACTION85
2.2524-2.28940.28984100.23457845X-RAY DIFFRACTION85
2.2894-2.32880.26174230.2028059X-RAY DIFFRACTION88
2.3288-2.37120.24554380.20078101X-RAY DIFFRACTION88
2.3712-2.41680.25274250.19838141X-RAY DIFFRACTION88
2.4168-2.46610.25043990.19298164X-RAY DIFFRACTION88
2.4661-2.51970.23914320.1928236X-RAY DIFFRACTION89
2.5197-2.57830.24154300.19678325X-RAY DIFFRACTION90
2.5783-2.64280.22624720.19468405X-RAY DIFFRACTION91
2.6428-2.71420.24054640.19688453X-RAY DIFFRACTION92
2.7142-2.79410.23814580.19828669X-RAY DIFFRACTION93
2.7941-2.88420.24194550.19138834X-RAY DIFFRACTION95
2.8842-2.98730.23594740.19378907X-RAY DIFFRACTION96
2.9873-3.10680.22474900.18259006X-RAY DIFFRACTION97
3.1068-3.24820.22835280.18259088X-RAY DIFFRACTION98
3.2482-3.41930.19715150.17089143X-RAY DIFFRACTION99
3.4193-3.63340.20794390.16849096X-RAY DIFFRACTION97
3.6334-3.91370.17764840.15099325X-RAY DIFFRACTION99
3.9137-4.3070.15514770.13519406X-RAY DIFFRACTION100
4.307-4.92920.15425120.13479389X-RAY DIFFRACTION100
4.9292-6.2060.19634840.17559533X-RAY DIFFRACTION100
6.206-38.37060.19475150.189759X-RAY DIFFRACTION99

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