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- PDB-1viv: Crystal structure of a hypothetical protein -

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Basic information

Entry
Database: PDB / ID: 1viv
TitleCrystal structure of a hypothetical protein
ComponentsHypothetical protein yckF
KeywordsStructural genomics / unknown function
Function / homology
Function and homology information


6-phospho-3-hexuloisomerase / hexulose-6-phosphate isomerase activity / formaldehyde assimilation via ribulose monophosphate cycle / carbohydrate derivative metabolic process / carbohydrate derivative binding / response to toxic substance
Similarity search - Function
3-hexulose-6-phosphate isomerase / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-hexulose-6-phosphate isomerase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Se-Met MAD phasing / Resolution: 2.6 Å
AuthorsStructural GenomiX
CitationJournal: Proteins / Year: 2005
Title: Structural analysis of a set of proteins resulting from a bacterial genomics project
Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / ...Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / Feil, I. / Furlong, E.B. / Gajiwala, K.S. / Gao, X. / He, D. / Hendle, J. / Huber, A. / Hoda, K. / Kearins, P. / Kissinger, C. / Laubert, B. / Lewis, H.A. / Lin, J. / Loomis, K. / Lorimer, D. / Louie, G. / Maletic, M. / Marsh, C.D. / Miller, I. / Molinari, J. / Muller-Dieckmann, H.J. / Newman, J.M. / Noland, B.W. / Pagarigan, B. / Park, F. / Peat, T.S. / Post, K.W. / Radojicic, S. / Ramos, A. / Romero, R. / Rutter, M.E. / Sanderson, W.E. / Schwinn, K.D. / Tresser, J. / Winhoven, J. / Wright, T.A. / Wu, L. / Xu, J. / Harris, T.J.
History
DepositionDec 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein yckF
B: Hypothetical protein yckF


Theoretical massNumber of molelcules
Total (without water)42,6912
Polymers42,6912
Non-polymers00
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-28 kcal/mol
Surface area15130 Å2
MethodPISA, PQS
2
A: Hypothetical protein yckF
B: Hypothetical protein yckF

A: Hypothetical protein yckF
B: Hypothetical protein yckF


Theoretical massNumber of molelcules
Total (without water)85,3814
Polymers85,3814
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_855-x+y+3,y,-z+1/21
Buried area12040 Å2
ΔGint-90 kcal/mol
Surface area26550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.363, 71.363, 245.452
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-223-

HOH

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Components

#1: Protein Hypothetical protein yckF


Mass: 21345.311 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: YCKF, BSU03450 / Production host: Escherichia coli (E. coli) / References: UniProt: P42404
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.11 Å3/Da / Density % sol: 41.79 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES1droppH7.5
2150 mM1dropNaCl
310 mMmethionine1drop
410 %glycerol1drop
55 mMdithiothreitol1drop
610 mg/mlprotein1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9794, 0.9794
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: MAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.32→35.68 Å / Num. all: 16522 / Num. obs: 16522 / % possible obs: 98.2 % / Redundancy: 14.4 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 24.7
Reflection shellResolution: 2.32→2.45 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 6.2 / % possible all: 88.4
Reflection shell
*PLUS
% possible obs: 88.4 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
REFMAC4refinement
CCP4(SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: Se-Met MAD phasing / Resolution: 2.6→35.68 Å / σ(F): 0
RfactorNum. reflection
Rfree0.331 584
Rwork0.277 -
obs-12161
Solvent computationSolvent model: Babinet bulk solvent correction / Bsol: 490 Å2 / ksol: 0.999 e/Å3
Displacement parametersBiso mean: 49.65 Å2
Baniso -1Baniso -2Baniso -3
1-2.458 Å21.229 Å20 Å2
2--2.458 Å20 Å2
3----3.687 Å2
Refine Biso Class: all / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 2.6→35.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2660 0 0 94 2754
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d1.204
X-RAY DIFFRACTIONp_planar_tor5.329
X-RAY DIFFRACTIONp_chiral_restr0.075
X-RAY DIFFRACTIONp_plane_restr0.004
X-RAY DIFFRACTIONp_mcbond_it0.957
X-RAY DIFFRACTIONp_mcangle_it1.77
X-RAY DIFFRACTIONp_scbond_it1.858
X-RAY DIFFRACTIONp_scangle_it2.969
Software
*PLUS
Version: 4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.2

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