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- PDB-2dbi: Crystal Structure of a Hypothetical Protein JW0805 from Escherich... -

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Basic information

Entry
Database: PDB / ID: 2dbi
TitleCrystal Structure of a Hypothetical Protein JW0805 from Escherichia coli
ComponentsHypothetical protein ybiU
KeywordsStructural genomics / unknown function / alpha/beta structure / hypothetical protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyGig2-like / Gig2-like / B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Isopenicillin N synthase-like superfamily / Jelly Rolls / Sandwich / Mainly Beta / Uncharacterized protein YbiU
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsIhsanawati / Murayama, K. / Bessho, Y. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be published
Title: Crystal Structure of a Hypothetical Protein JW0805 from Escherichia coli
Authors: Ihsanawati / Murayama, K. / Bessho, Y. / Shirouzu, M. / Yokoyama, S.
History
DepositionDec 15, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein ybiU


Theoretical massNumber of molelcules
Total (without water)51,9201
Polymers51,9201
Non-polymers00
Water11,115617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.973, 69.973, 174.804
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Hypothetical protein ybiU / Hypothetical Protein JW0805


Mass: 51920.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Description: Cell-free protein synthesis / Plasmid: PX050510-04 / Production host: Cell free synthesis / References: UniProt: P75791
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 617 / 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: 2.38 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M bis-tris pH5.5, 25% PEG 3350, 0.2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 20, 2005
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 32097 / % possible obs: 93.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 6.2 Å2
Reflection shellResolution: 2→2.07 Å / % possible all: 36.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DBN

2dbn


Resolution: 2.05→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3570523.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1585 5 %RANDOM
Rwork0.18 ---
obs0.18 31991 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.7085 Å2 / ksol: 0.362091 e/Å3
Displacement parametersBiso mean: 17.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å20.12 Å20 Å2
2--1.65 Å20 Å2
3----3.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3166 0 0 617 3783
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 2.07→2.13 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.223 165 5.1 %
Rwork0.17 3082 -
obs--57.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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