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- PDB-1vi7: Crystal structure of an hypothetical protein -

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Basic information

Entry
Database: PDB / ID: 1vi7
TitleCrystal structure of an hypothetical protein
ComponentsHypothetical protein yigZ
KeywordsStructural genomics / unknown function
Function / homology
Function and homology information


anion binding / guanyl ribonucleotide binding / regulation of translational initiation / ribonucleoside triphosphate phosphatase activity / cytoplasm
Similarity search - Function
Impact family, bacterial/archaeal / Uncharacterised domain UPF0029, Impact, C-terminal / Domain of unknown function (DUF1949) / Impact, N-terminal domain / Impact, N-terminal / Uncharacterised protein family UPF0029, Impact, conserved site / Impact family / Impact, N-terminal domain superfamily / Impact N-terminal domain / Uncharacterized protein family UPF0029 signature. ...Impact family, bacterial/archaeal / Uncharacterised domain UPF0029, Impact, C-terminal / Domain of unknown function (DUF1949) / Impact, N-terminal domain / Impact, N-terminal / Uncharacterised protein family UPF0029, Impact, conserved site / Impact family / Impact, N-terminal domain superfamily / Impact N-terminal domain / Uncharacterized protein family UPF0029 signature. / Alpha-Beta Plaits - #240 / Ribosomal Protein S5; domain 2 / EF-G domain III/V-like / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IMPACT family member YigZ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Se-Met MAD phasing / Resolution: 2.8 Å
AuthorsStructural GenomiX
Citation
Journal: Proteins / Year: 2004
Title: Crystal structure of YIGZ, a conserved hypothetical protein from Escherichia coli k12 with a novel fold
Authors: Park, F. / Gajiwala, K. / Eroshkina, G. / Furlong, E. / He, D. / Batiyenko, Y. / Romero, R. / Christopher, J. / Badger, J. / Hendle, J. / Lin, J. / Peat, T. / Buchanan, S.
#1: Journal: 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: 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 yigZ


Theoretical massNumber of molelcules
Total (without water)23,2691
Polymers23,2691
Non-polymers00
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.749, 148.749, 35.602
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Hypothetical protein yigZ


Mass: 23269.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YIGZ, B3848 / Production host: Escherichia coli (E. coli) / References: UniProt: P27862
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.26 Å3/Da / Density % sol: 62.24 %
Crystal grow
*PLUS
Temperature: 9 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15 mg/mlprotein1drop
21.0 mMbeta-mercaptoethanol1drop
3150 mM1dropNaCl
410 mMHEPES1droppH7.5
510 mMmethionine1drop
610 %glycerol1drop
7150 mMMES1reservoirpH6.5
8150 mMammonium sulfate1reservoir
930 %PEG5000 MME1reservoir
1028.4 mMbeta-mercaptoethanol1reservoir

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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 / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.56→37.19 Å / Num. all: 9455 / Num. obs: 9455 / % possible obs: 100 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 14.8
Reflection shellResolution: 2.56→2.7 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.952 / Mean I/σ(I) obs: 4.7 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 7231 / Num. measured all: 81478 / Rmerge(I) obs: 0.104
Reflection shell
*PLUS
% possible obs: 100 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 8.4

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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: 2.8→37.19 Å / σ(F): 0
RfactorNum. reflection
Rfree0.332 334
Rwork0.261 -
obs-7231
Solvent computationSolvent model: Babinet bulk solvent correction / Bsol: 482.947 Å2 / ksol: 0.932 e/Å3
Displacement parametersBiso mean: 42.773 Å2
Baniso -1Baniso -2Baniso -3
1--0.474 Å2-0.237 Å20 Å2
2---0.474 Å20 Å2
3---0.711 Å2
Refine Biso Class: all / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 2.8→37.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1529 0 0 91 1620
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d2.412
X-RAY DIFFRACTIONp_planar_tor3.026
X-RAY DIFFRACTIONp_chiral_restr0.162
X-RAY DIFFRACTIONp_plane_restr0.019
X-RAY DIFFRACTIONp_mcbond_it1.766
X-RAY DIFFRACTIONp_mcangle_it3.188
X-RAY DIFFRACTIONp_scbond_it2.713
X-RAY DIFFRACTIONp_scangle_it4.148
Software
*PLUS
Version: 4 / Classification: refinement
Refinement
*PLUS
Num. reflection Rfree: 274 / Rfactor obs: 0.2591 / Rfactor Rfree: 0.316 / Rfactor Rwork: 0.247
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.4

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