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- PDB-7n0j: Structure of YebY from E. coli K12 -

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Basic information

Entry
Database: PDB / ID: 7n0j
TitleStructure of YebY from E. coli K12
ComponentsYebY
KeywordsUNKNOWN FUNCTION / periplasmic protein
Function / homologyProtein YebY / Protein of unknown function (DUF2511) / copper ion homeostasis / outer membrane-bounded periplasmic space / Uncharacterized protein YebY
Function and homology information
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.88 Å
AuthorsHadley, R.C. / Rosenzweig, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: The copper-linked Escherichia coli AZY operon: Structure, metal binding, and a possible physiological role in copper delivery.
Authors: Hadley, R.C. / Zhitnitsky, D. / Livnat-Levanon, N. / Masrati, G. / Vigonsky, E. / Rose, J. / Ben-Tal, N. / Rosenzweig, A.C. / Lewinson, O.
History
DepositionMay 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YebY
C: YebY
D: YebY
E: YebY
F: YebY
H: YebY
I: YebY
J: YebY
B: YebY
G: YebY
K: YebY
L: YebY


Theoretical massNumber of molelcules
Total (without water)137,55212
Polymers137,55212
Non-polymers00
Water6,503361
1
A: YebY


Theoretical massNumber of molelcules
Total (without water)11,4631
Polymers11,4631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: YebY


Theoretical massNumber of molelcules
Total (without water)11,4631
Polymers11,4631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
D: YebY


Theoretical massNumber of molelcules
Total (without water)11,4631
Polymers11,4631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
E: YebY


Theoretical massNumber of molelcules
Total (without water)11,4631
Polymers11,4631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
F: YebY


Theoretical massNumber of molelcules
Total (without water)11,4631
Polymers11,4631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
H: YebY


Theoretical massNumber of molelcules
Total (without water)11,4631
Polymers11,4631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
I: YebY


Theoretical massNumber of molelcules
Total (without water)11,4631
Polymers11,4631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
J: YebY


Theoretical massNumber of molelcules
Total (without water)11,4631
Polymers11,4631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
B: YebY


Theoretical massNumber of molelcules
Total (without water)11,4631
Polymers11,4631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
G: YebY


Theoretical massNumber of molelcules
Total (without water)11,4631
Polymers11,4631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: YebY


Theoretical massNumber of molelcules
Total (without water)11,4631
Polymers11,4631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: YebY


Theoretical massNumber of molelcules
Total (without water)11,4631
Polymers11,4631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.145, 53.199, 132.363
Angle α, β, γ (deg.)90.000, 102.250, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
YebY


Mass: 11462.674 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: yebY, b1839, JW1828 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P64506
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 48.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 M Bis-Tris-HCl (pH 6.5), and 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 30, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.88→34.67 Å / Num. obs: 188643 / % possible obs: 89.8 % / Redundancy: 3.423 % / Biso Wilson estimate: 34.91 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.119 / Χ2: 1.378 / Net I/σ(I): 6.97 / Num. measured all: 645748 / Scaling rejects: 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.88-1.922.5751.6950.44197021561876520.2612.16849
1.92-1.982.7051.260.63257631515395230.4261.59262.8
1.98-2.032.8691.0130.873112714828108500.591.25973.2
2.03-2.13.0990.8821.113789314178122290.6681.07186.3
2.1-2.173.5440.781.464861513788137180.7820.92199.5
2.17-2.243.6820.6231.934956213518134590.8570.73299.6
2.24-2.333.6690.4782.474732612932128990.9080.56299.7
2.33-2.423.6440.3982.994511612440123800.9190.46899.5
2.42-2.533.6140.3263.644286611929118610.9420.38499.4
2.53-2.653.5660.2544.584030111394113010.960.399.2
2.65-2.83.5070.1915.913736910819106550.9740.22698.5
2.8-2.973.2740.1437.39318831029997390.9810.17194.6
2.97-3.173.5460.10810.2633360961694070.9880.12797.8
3.17-3.433.640.07913.5832455894089150.9930.09399.7
3.43-3.753.6290.0617.5429876825582330.9950.07199.7
3.75-4.23.6420.0520.2826967746174050.9960.05999.2
4.2-4.843.5890.04422.923476662865420.9970.05198.7
4.84-5.933.2450.04620.9117116553752750.9960.05695.3
5.93-8.393.8290.04423.4716377428442770.9970.05199.8
8.39-34.673.7010.03427.728598235123230.9980.0498.8

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.88→34.67 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 37.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2821 1997 2.05 %
Rwork0.2353 95391 -
obs0.2362 97388 90.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.62 Å2 / Biso mean: 42.4048 Å2 / Biso min: 21.11 Å2
Refinement stepCycle: final / Resolution: 1.88→34.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8663 0 0 361 9024
Biso mean---42.29 -
Num. residues----1112
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.88-1.920.5649770.47713705378249
1.92-1.970.4353990.42314695479463
1.97-2.030.36441140.38245460557473
2.03-2.10.33961360.34436495663187
2.1-2.170.38231570.311474377594100
2.17-2.260.37271550.284674707625100
2.26-2.360.36361560.273574777633100
2.36-2.490.32971570.268774977654100
2.49-2.640.32821570.272774997656100
2.64-2.850.31551560.26897467762399
2.85-3.130.31851540.25527380753497
3.13-3.590.24461600.223675687728100
3.59-4.520.22731570.17967557771499
4.52-34.670.22911620.18587684784698

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