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- PDB-2dbn: Crystal Structure of a Hypothetical Protein JW0805 at High pH fro... -

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Basic information

Entry
Database: PDB / ID: 2dbn
TitleCrystal Structure of a Hypothetical Protein JW0805 at High pH 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 / MAD / Resolution: 1.7 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 at High pH 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 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein ybiU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2084
Polymers51,9201
Non-polymers2883
Water12,052669
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.688, 69.688, 174.649
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 669 / 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: 2.36 Å3/Da / Density % sol: 47.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: 1.2M NaH2PO4, 0.8M K2HPO4, 0.1M CAPS buffer pH 10.5, 0.2M Li2SO4, 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: 0.97903, 0.97940, 0.964
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 20, 2005
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979031
20.97941
30.9641
ReflectionResolution: 1.7→30 Å / Num. obs: 55165 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.9 Å2
Reflection shellResolution: 1.7→1.76 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→29.9 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3118565.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2 2776 5 %RANDOM
Rwork0.187 ---
obs0.187 54975 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.1415 Å2 / ksol: 0.371133 e/Å3
Displacement parametersBiso mean: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.36 Å20.69 Å20 Å2
2--2.36 Å20 Å2
3----4.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.7→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3212 0 15 669 3896
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.85
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.224 481 5.4 %
Rwork0.218 8498 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3so4.paramso4.top

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