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- PDB-1wd6: crystal structure of JW1657 from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 1wd6
Titlecrystal structure of JW1657 from Escherichia coli
ComponentsProtein ydhR
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Oxidoreductases / oxidoreductase activity / protein homodimerization activity / cytosol
Similarity search - Function
Putative monooxygenase YdhR / Putative mono-oxygenase ydhR / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative monooxygenase YdhR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsKato-Murayama, M. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: crystal structure of JW1657 from Escherichia coli
Authors: Kato-Murayama, M. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 12, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein ydhR
B: Protein ydhR


Theoretical massNumber of molelcules
Total (without water)27,8312
Polymers27,8312
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-16 kcal/mol
Surface area9550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.803, 85.803, 95.923
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Protein ydhR / hypothetical protein JW1657


Mass: 13915.303 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pCA24N / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACX3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.66 Å3/Da / Density % sol: 66.42 %
Crystal growTemperature: 293 K / Method: oil batch / pH: 7
Details: Ammonium Sulfate, PEG8000, pH 7.0, Oil Batch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9640, 0.97914, 0.97964
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 27, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9641
20.979141
30.979641
ReflectionResolution: 2.9→30 Å / Num. obs: 9408 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 45.8 Å2
Reflection shellResolution: 2.9→3 Å / % possible all: 98.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.9→29.37 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 782711.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.242 975 10.4 %RANDOM
Rwork0.208 ---
obs-9380 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 15.3447 Å2 / ksol: 0.341733 e/Å3
Displacement parametersBiso mean: 25 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å28.19 Å20 Å2
2---0.23 Å20 Å2
3---0.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.9→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1529 0 0 18 1547
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.9
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 151 9.9 %
Rwork0.269 1368 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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