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- PDB-5kci: Crystal Structure of HTC1 -

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Basic information

Entry
Database: PDB / ID: 5kci
TitleCrystal Structure of HTC1
ComponentsUncharacterized protein YPL067C
KeywordsUNKNOWN FUNCTION / histidine triad amyloid toxicity
Function / homologyProtein of unknown function DUF3605 / Protein of unknown function (DUF3605) / N-acetylglucosamine metabolic process / cytoplasm / Uncharacterized protein YPL067C
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.833 Å
AuthorsMartin, R.M. / Horowitz, S. / Koepnick, B. / Cooper, S. / Flatten, J. / Rogawski, D.S. / Koropatkin, N.M. / Beinlich, F.R.M. / Players, F. / Students, U.M. ...Martin, R.M. / Horowitz, S. / Koepnick, B. / Cooper, S. / Flatten, J. / Rogawski, D.S. / Koropatkin, N.M. / Beinlich, F.R.M. / Players, F. / Students, U.M. / Popovic, Z. / Baker, D. / Khatib, F. / Bardwell, J.C.A.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102829 United States
CitationJournal: Nat Commun / Year: 2016
Title: Determining crystal structures through crowdsourcing and coursework.
Authors: Horowitz, S. / Koepnick, B. / Martin, R. / Tymieniecki, A. / Winburn, A.A. / Cooper, S. / Flatten, J. / Rogawski, D.S. / Koropatkin, N.M. / Hailu, T.T. / Jain, N. / Koldewey, P. / Ahlstrom, ...Authors: Horowitz, S. / Koepnick, B. / Martin, R. / Tymieniecki, A. / Winburn, A.A. / Cooper, S. / Flatten, J. / Rogawski, D.S. / Koropatkin, N.M. / Hailu, T.T. / Jain, N. / Koldewey, P. / Ahlstrom, L.S. / Chapman, M.R. / Sikkema, A.P. / Skiba, M.A. / Maloney, F.P. / Beinlich, F.R. / Popovic, Z. / Baker, D. / Khatib, F. / Bardwell, J.C.
History
DepositionJun 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 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 YPL067C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1494
Polymers22,8951
Non-polymers2543
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.460, 62.460, 117.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsMonomer according to Analytical Ultracentrifugation

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Components

#1: Protein Uncharacterized protein YPL067C


Mass: 22894.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Has one extra N-terminal serine after His-tag cleavage
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: YPL067C / Production host: Escherichia coli (E. coli) / References: UniProt: Q02754
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 5.6-8.1% glycerol, 1.6-2.1 M ammonium sulfate, 0.1-0.2 M Tris.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97851 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97851 Å / Relative weight: 1
ReflectionResolution: 1.83→42.81 Å / Num. obs: 21161 / % possible obs: 100 % / Redundancy: 7.8 % / Net I/σ(I): 12.7
Reflection shellResolution: 1.83→1.89 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 2 / CC1/2: 0.873 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.833→42.81 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2528 1998 9.45 %
Rwork0.2011 --
obs0.2059 21145 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.833→42.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1495 0 12 138 1645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091567
X-RAY DIFFRACTIONf_angle_d0.8882127
X-RAY DIFFRACTIONf_dihedral_angle_d13.732937
X-RAY DIFFRACTIONf_chiral_restr0.052224
X-RAY DIFFRACTIONf_plane_restr0.007273
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.833-1.87880.31331390.28021340X-RAY DIFFRACTION100
1.8788-1.92960.28011390.25821324X-RAY DIFFRACTION100
1.9296-1.98640.29361380.23881330X-RAY DIFFRACTION100
1.9864-2.05050.27341410.21971350X-RAY DIFFRACTION100
2.0505-2.12380.23821400.21861342X-RAY DIFFRACTION100
2.1238-2.20890.24361400.20221341X-RAY DIFFRACTION100
2.2089-2.30940.22231410.20081350X-RAY DIFFRACTION100
2.3094-2.43110.25791400.20491346X-RAY DIFFRACTION100
2.4311-2.58340.2331430.21141371X-RAY DIFFRACTION100
2.5834-2.78290.28871430.22241361X-RAY DIFFRACTION100
2.7829-3.06280.28951440.21371377X-RAY DIFFRACTION100
3.0628-3.50590.2521460.19951394X-RAY DIFFRACTION100
3.5059-4.41630.24251470.17131413X-RAY DIFFRACTION100
4.4163-42.82120.23431570.19261508X-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)
10.91220.6379-0.12641.91061.12521.4828-0.0156-0.0035-0.04670.1484-0.07730.0180.87030.1031-0.07650.5365-0.04850.00820.2093-0.0070.2496-11.465812.9951-5.0158
21.6593-0.26260.44512.5971.05262.08520.2052-0.03310.1006-0.1919-0.21470.04240.115-0.1380.00480.30210.0070.03090.15940.00520.2617-14.350924.0131-1.9519
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 16:75)
2X-RAY DIFFRACTION2(chain A and resid 76:199)

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