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- PDB-5vyv: Crystal structure of a protein of unknown function YceH/ECK1052 i... -

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Basic information

Entry
Database: PDB / ID: 5vyv
TitleCrystal structure of a protein of unknown function YceH/ECK1052 involved in membrane biogenesis from Escherichia coli
ComponentsUPF0502 protein YceH
KeywordsUNKNOWN FUNCTION / MEMBRANE BIOGENESIS / ALPHA/BETA PROTEIN / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES / NIAID
Function / homology
Function and homology information


Protein of unknown function DUF480 / Protein of unknown function, DUF480 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / UPF0502 protein YceH
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsStogios, P.J. / Skarina, T. / McChesney, C. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
CitationJournal: To Be Published
Title: Crystal structure of a protein of unknown function YceH/ECK1052 involved in membrane biogenesis from Escherichia coli
Authors: Stogios, P.J.
History
DepositionMay 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF0502 protein YceH
B: UPF0502 protein YceH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5153
Polymers48,4092
Non-polymers1061
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-1 kcal/mol
Surface area17550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.777, 74.853, 58.661
Angle α, β, γ (deg.)90.00, 100.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UPF0502 protein YceH


Mass: 24204.373 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: yceH, Z1704, ECs1445 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8X8M9
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 1.68 Å3/Da / Density % sol: 26.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 8K, 50 mM potassium dihydrogen phosphate / PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.48→30 Å / Num. obs: 11477 / % possible obs: 100 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.048 / Net I/σ(I): 21.19
Reflection shellResolution: 2.48→2.52 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 2.08 / Num. unique obs: 565 / CC1/2: 0.631 / Rpim(I) all: 0.435 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2733: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U8J

5u8j


Resolution: 2.48→28.817 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.35
RfactorNum. reflection% reflectionSelection details
Rfree0.2655 574 5.01 %RANDOM
Rwork0.2063 ---
obs0.2094 11455 99.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.48→28.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2731 0 7 105 2843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032815
X-RAY DIFFRACTIONf_angle_d0.613798
X-RAY DIFFRACTIONf_dihedral_angle_d25.7441107
X-RAY DIFFRACTIONf_chiral_restr0.04428
X-RAY DIFFRACTIONf_plane_restr0.003502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4752-2.72420.3661400.30332677X-RAY DIFFRACTION98
2.7242-3.11790.30981430.25772711X-RAY DIFFRACTION100
3.1179-3.92670.26391450.20052738X-RAY DIFFRACTION100
3.9267-28.81930.2311460.17232755X-RAY DIFFRACTION100
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)
13.0413-1.5851-1.15738.07241.76729.01110.73861.48431.0078-0.7327-0.1478-1.1399-0.40451.7444-0.62630.55580.13610.0570.77280.05970.2673-10.1473.901753.8849
25.4962-0.05121.4387.5869-0.91415.6425-0.0570.039-0.0681-0.4297-0.2310.46310.1461-0.43430.31240.24180.04040.01530.312-0.02320.2049-19.8408-4.837262.3763
32.8768-2.59530.1256.7214-2.17464.85580.419-0.052-1.073-0.2816-0.97181.20712.0613-0.08050.37830.7654-0.04620.12390.3876-0.1620.8158-19.6144-20.016860.2306
45.86981.4222-0.20177.4911-1.91524.33250.1839-0.20840.30450.6974-0.3101-0.4525-0.92670.11960.06390.45270.01660.02560.26330.01840.254-6.72847.779668.9165
53.0989-1.7055-0.36724.7061-1.44822.83430.18120.22950.09330.9433-0.8287-1.76990.0730.52770.33750.26580.0209-0.17760.4840.15960.88293.6184-18.403978.1911
64.90950.20220.05185.63363.45686.28960.13310.4393-1.0738-0.6337-0.5366-0.20861.75280.8060.3630.48180.22720.17750.46740.10420.65762.2559-26.47669.1434
74.0787-0.0887-6.05044.8394-1.07949.7176-0.44320.6221-0.69410.63880.1696-0.16810.9145-0.050.24020.410.02460.06270.4918-0.01180.4877-9.9368-19.936873.0792
84.3645-0.1806-1.40160.6734-1.84368.0381-0.4048-0.9251-0.17032.31710.35440.1213-0.64270.1456-0.00431.17660.143-0.01480.5510.0940.4098-8.9754-16.142691.7262
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:7)
2X-RAY DIFFRACTION2(chain A and resid 8:72)
3X-RAY DIFFRACTION3(chain A and resid 73:82)
4X-RAY DIFFRACTION4(chain A and resid 83:173)
5X-RAY DIFFRACTION5(chain B and resid 1:53)
6X-RAY DIFFRACTION6(chain B and resid 54:79)
7X-RAY DIFFRACTION7(chain B and resid 80:99)
8X-RAY DIFFRACTION8(chain B and resid 100:173)

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