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- PDB-1o65: Crystal structure of an hypothetical protein -

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Basic information

Entry
Database: PDB / ID: 1o65
TitleCrystal structure of an hypothetical protein
ComponentsHypothetical protein yiiM
KeywordsStructural genomics / unknown function
Function / homology
Function and homology information


toxin catabolic process / oxidoreductase activity, acting on other nitrogenous compounds as donors / molybdenum ion binding / response to toxic substance / pyridoxal phosphate binding / oxidoreductase activity / protein homodimerization activity / cytosol
Similarity search - Function
YiiM-like, 3-alpha helix domain / : / YiiM-like, 3-alpha helix domain / PK beta-barrel domain-like / Molybdenum cofactor sulfurase, C-terminal / MOSC domain / MOSC domain profile. / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase-like, insert domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Se-Met MAD phasing / Resolution: 2.33 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
DepositionOct 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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

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Assembly

Deposited unit
A: Hypothetical protein yiiM
B: Hypothetical protein yiiM
C: Hypothetical protein yiiM


Theoretical massNumber of molelcules
Total (without water)83,8613
Polymers83,8613
Non-polymers00
Water3,297183
1
A: Hypothetical protein yiiM


Theoretical massNumber of molelcules
Total (without water)27,9541
Polymers27,9541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein yiiM


Theoretical massNumber of molelcules
Total (without water)27,9541
Polymers27,9541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hypothetical protein yiiM


Theoretical massNumber of molelcules
Total (without water)27,9541
Polymers27,9541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.116, 97.878, 98.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Hypothetical protein yiiM


Mass: 27953.566 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YIIM, B3910 / Production host: Escherichia coli (E. coli) / References: UniProt: P32157
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.08 Å3/Da / Density % sol: 40.76 %
Crystal growTemperature: 277 K / Method: hanging drop vapor diffusion / pH: 7.5
Components of the solutions
IDConc.NameCrystal-IDSol-ID
116mg/ml protein11
2150mM NaCl12
310mM Hepes12
41mM beta-mercaptoethanol12
510mM methionine12
Crystal grow
*PLUS
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: 0.9795 , 0.9795
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: MAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. all: 30106 / Num. obs: 30106 / % possible obs: 98.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 23.3
Reflection shellResolution: 2.33→2.46 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 13.7 / % possible all: 98.9
Reflection
*PLUS
Highest resolution: 2.33 Å
Reflection shell
*PLUS
% possible obs: 98.9 %

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Processing

Software
NameVersionClassification
REFMAC4refinement
MOSFLMdata reduction
CCP4(SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: Se-Met MAD phasing / Resolution: 2.33→50 Å / σ(F): 0
RfactorNum. reflection
Rfree0.308 1526
Rwork0.231 -
obs-30106
Solvent computationSolvent model: Babinet bulk solvent correction / Bsol: 228.942 Å2 / ksol: 0.95 e/Å3
Displacement parametersBiso mean: 32.945 Å2
Baniso -1Baniso -2Baniso -3
1-1.226 Å20 Å20 Å2
2---0.75 Å20 Å2
3----0.476 Å2
Refine Biso Class: all / Treatment: isotropic
Refinement stepCycle: 1 / Resolution: 2.33→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5177 0 0 183 5360
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d2.098
X-RAY DIFFRACTIONp__planar_tor2.891
X-RAY DIFFRACTIONp_chiral_restr0.123
X-RAY DIFFRACTIONp_plane_restr0.013
X-RAY DIFFRACTIONp_mcbond_it1.634
X-RAY DIFFRACTIONp_mcangle_it2.844
X-RAY DIFFRACTIONp_scbond_it2.643
X-RAY DIFFRACTIONp_scangle_it3.791
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.1

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