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- PDB-2hiq: Crystal structure of JW1657 from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 2hiq
TitleCrystal structure of JW1657 from Escherichia coli
ComponentsHypothetical protein ydhR
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / HYPOTHETICAL PROTEIN JW1657 / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
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 / Putative monooxygenase YdhR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsChen, L.Q. / Chen, L.R. / Liu, Z.-J. / Temple, W. / Lee, D. / Chang, S.-H. / Rose, J.P. / Ebihara, A. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be Published
Title: Crystal structure of JW1657 from Escherichia coli at 2.0A resolution
Authors: Chen, L.Q. / Chen, L.R. / Liu, Z.-J. / Temple, W. / Lee, D. / Chang, S.-H. / Rose, J.P. / Ebihara, A. / Wang, B.-C.
History
DepositionJun 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 ydhR
B: Hypothetical protein ydhR


Theoretical massNumber of molelcules
Total (without water)25,0262
Polymers25,0262
Non-polymers00
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-15 kcal/mol
Surface area9490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.960, 84.960, 95.940
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 Hypothetical protein ydhR / HYPOTHETICAL PROTEIN JW1657


Mass: 12513.216 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ydhR / Plasmid: PCA24N / Production host: Escherichia coli (E. coli) / References: UniProt: Q2MB61, UniProt: P0ACX3*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 3.99 Å3/Da / Density % sol: 69.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.6
Details: 100 mM Sodium Cacodylate, 2.5 M Ammonium Sulfate, pH 6.6, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9724 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 2, 2006 / Details: Rosenbaum
RadiationMonochromator: SI220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 27533 / Num. obs: 27533 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 17.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 7.2 / Num. unique all: 2721 / Rsym value: 0.476 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SCA2STRUCTUREphasing
RefinementMethod to determine structure: SAD / Resolution: 2→19.96 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 251092.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1307 4.9 %RANDOM
Rwork0.249 ---
all0.255 26848 --
obs0.249 26848 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.8365 Å2 / ksol: 0.360105 e/Å3
Displacement parametersBiso mean: 30.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å21.88 Å20 Å2
2--1.03 Å20 Å2
3----2.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1524 0 0 101 1625
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.12
X-RAY DIFFRACTIONc_scbond_it2.472
X-RAY DIFFRACTIONc_scangle_it3.772.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 207 4.7 %
Rwork0.281 4200 -
obs--97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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