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- PDB-1o67: Crystal structure of an hypothetical protein -

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Basic information

Entry
Database: PDB / ID: 1o67
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 / MOLECULAR REPLACEMENT / Resolution: 2.54 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 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)84,8453
Polymers84,8453
Non-polymers00
Water54030
1
A: Hypothetical protein yiiM


Theoretical massNumber of molelcules
Total (without water)28,2821
Polymers28,2821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein yiiM


Theoretical massNumber of molelcules
Total (without water)28,2821
Polymers28,2821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hypothetical protein yiiM


Theoretical massNumber of molelcules
Total (without water)28,2821
Polymers28,2821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.529, 99.327, 99.406
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: 28281.832 Da / Num. of mol.: 3 / Mutation: I110(MSE)
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.: 30 / Source method: isolated from a natural source / Formula: H2O
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: 2.17 Å3/Da / Density % sol: 43.27 %
Components of the solutions
IDConc.NameCrystal-IDSol-ID
116mg/ml protein11
2150mM NaCl12
310mM Hepes12
41mM beta-mercaptoethanol12
510mM methionine12
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: 0.9795 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.56→59.63 Å / Num. all: 24697 / Num. obs: 24697 / % possible obs: 98.9 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 20.2
Reflection shellResolution: 2.54→2.68 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 5.5 / % possible all: 98.9
Reflection
*PLUS
Highest resolution: 2.54 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: MOLECULAR REPLACEMENT / Resolution: 2.54→59.63 Å / σ(F): 0
RfactorNum. reflection
Rfree0.305 1257
Rwork0.239 -
obs-24696
Solvent computationSolvent model: Babinet bulk solvent correction / Bsol: 171.654 Å2 / ksol: 0.949 e/Å3
Displacement parametersBiso mean: 39.604 Å2
Baniso -1Baniso -2Baniso -3
1-2.15 Å20 Å20 Å2
2---0.834 Å20 Å2
3----1.317 Å2
Refine Biso Class: all / Treatment: isotropic
Refinement stepCycle: 1 / Resolution: 2.54→59.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5089 0 0 30 5119
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d2.193
X-RAY DIFFRACTIONp_planar_tor2.724
X-RAY DIFFRACTIONp_chiral_restr0.125
X-RAY DIFFRACTIONp_plane_restr0.013
X-RAY DIFFRACTIONp_mcbond_it1.692
X-RAY DIFFRACTIONp_mcangle_it3.122
X-RAY DIFFRACTIONp_scbond_it2.865
X-RAY DIFFRACTIONp_scangle_it4.333
Software
*PLUS
Version: 4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.2

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