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- PDB-3f1l: The 0.95 A structure of an oxidoreductase, yciK from E.coli -

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Basic information

Entry
Database: PDB / ID: 3f1l
TitleThe 0.95 A structure of an oxidoreductase, yciK from E.coli
ComponentsUncharacterized oxidoreductase yciK
KeywordsOXIDOREDUCTASE / yciK / E. coli / NADP+
Function / homology
Function and homology information


Oxidoreductases / oxidoreductase activity
Similarity search - Function
: / short chain dehydrogenase / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized oxidoreductase YciK
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.95 Å
AuthorsVijayalakshmi, J. / Woodard, R.W.
CitationJournal: to be published
Title: Structure of an oxidoreductase, yciK from E. coli, in two crystal forms - NADP+ unbound structure at 0.95 A resolution
Authors: Vijayalakshmi, J. / Meredith, T.C. / Woodard, R.W.
History
DepositionOct 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized oxidoreductase yciK
B: Uncharacterized oxidoreductase yciK


Theoretical massNumber of molelcules
Total (without water)55,9222
Polymers55,9222
Non-polymers00
Water13,745763
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-23 kcal/mol
Surface area20290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.871, 66.803, 65.053
Angle α, β, γ (deg.)90.000, 109.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized oxidoreductase yciK


Mass: 27960.889 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Strain: K-12 MG1655 / Gene: b1271, JW1263, yciK / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / References: UniProt: P31808, Oxidoreductases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 763 / 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: 1.98 Å3/Da / Density % sol: 37.84 % / Mosaicity: 1.932 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 0.1M sodium nitrate, 16 % w/v polyethylene glycol 8000, vapor diffusion, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9184 Å
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: Apr 26, 2007 / Details: Si(III) Monochromator
RadiationMonochromator: Si(III) Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 0.95→45.24 Å / Num. obs: 236813 / % possible obs: 86.7 % / Redundancy: 4.44 % / Biso Wilson estimate: 8.3 Å2 / Rmerge(I) obs: 0.062 / Χ2: 0.77 / Net I/σ(I): 8.9 / Scaling rejects: 29778
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
0.95-0.984.540.3852.8105870220490.7480.9
0.98-1.024.770.3533.3122626244600.8189.9
1.02-1.074.740.3083.7121014245900.8190.2
1.07-1.134.630.2444.6116610244670.8189.8
1.13-1.24.520.1955.5111973242910.7889.1
1.2-1.294.370.1626.6106549239470.7887.8
1.29-1.424.240.137.9101357235930.7586.3
1.42-1.624.140.09310.496536230750.7384.5
1.62-2.054.060.05416.393324227340.6883
2.05-45.244.330.03531.1104905236070.8385.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREK9.3Ddata processing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F1K, ycik structure at 2.6A resolution, solved by MAD and SAD phasing

3f1k


Resolution: 0.95→34.136 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.14 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1830 0.77 %RANDOM
Rwork0.171 ---
obs0.171 236747 86.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.342 Å2 / ksol: 0.47 e/Å3
Displacement parametersBiso max: 113.6 Å2 / Biso mean: 18.207 Å2 / Biso min: 0.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.568 Å2-0 Å20.425 Å2
2---0.205 Å2-0 Å2
3---0.772 Å2
Refinement stepCycle: LAST / Resolution: 0.95→34.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7611 0 0 763 8374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057681
X-RAY DIFFRACTIONf_angle_d0.91513848
X-RAY DIFFRACTIONf_chiral_restr0.073595
X-RAY DIFFRACTIONf_plane_restr0.0051223
X-RAY DIFFRACTIONf_dihedral_angle_d12.721982
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.95-0.9760.381270.37162291635678
0.976-1.0040.3571450.328186661881190
1.004-1.0370.2871470.286187811892890
1.037-1.0740.2641450.239187111885690
1.074-1.1170.2061460.198187041885090
1.117-1.1680.1841440.168185511869589
1.168-1.2290.1631430.153184361857988
1.229-1.3060.1821420.139182401838288
1.306-1.4070.1561410.133179581809986
1.407-1.5490.1541380.127176521779085
1.549-1.7730.1551350.125174591759484
1.773-2.2340.1511340.129171531728782
2.234-34.1580.1911430.172183771852087

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