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- PDB-1ur3: Crystal structure of the apo form of the E.coli ydhF protein -

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Basic information

Entry
Database: PDB / ID: 1ur3
TitleCrystal structure of the apo form of the E.coli ydhF protein
ComponentsHYPOTHETICAL OXIDOREDUCTASE YDHF
KeywordsOXIDOREDUCTASE / NADP BINDING / ALDO-KETO REDUCTASE
Function / homology
Function and homology information


Oxidoreductases / oxidoreductase activity / cytosol
Similarity search - Function
NADP-dependent oxidoreductase domain / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.57 Å
AuthorsJeudy, S. / Claverie, J.M. / Abergel, C.
CitationJournal: To be Published
Title: Crystal Structure of Ydhf the E.Coli Aldo-Keto Reductase Ydhf
Authors: Jeudy, S. / Claverie, J.M. / Abergel, C.
History
DepositionOct 24, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "MB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "MB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
M: HYPOTHETICAL OXIDOREDUCTASE YDHF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6742
Polymers36,5781
Non-polymers961
Water1,27971
1
M: HYPOTHETICAL OXIDOREDUCTASE YDHF
hetero molecules

M: HYPOTHETICAL OXIDOREDUCTASE YDHF
hetero molecules

M: HYPOTHETICAL OXIDOREDUCTASE YDHF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,0216
Polymers109,7333
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)87.722, 87.722, 66.168
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein HYPOTHETICAL OXIDOREDUCTASE YDHF


Mass: 36577.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P76187, Oxidoreductases
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Compound detailsBELONGS TO THE ALDO/KETO REDUCTASE 2 FAMILY.
Sequence detailsFIRST METHIONINE WAS REPLACED WITH A LEUCINE ADDITION OF 21 N-TER RESIDUES CORRESPONDING TO THE ...FIRST METHIONINE WAS REPLACED WITH A LEUCINE ADDITION OF 21 N-TER RESIDUES CORRESPONDING TO THE GATEWAY SEQUENCE TAG

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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: 2.05 Å3/Da / Density % sol: 39.8 %
Crystal growpH: 7
Details: PEG 4000 17.5%, IMIDAZOLE/MALATE 0.2M PH 7.0, AMMONIUM SULFATE 0.1M, GLYCEROL 2.5%, SPERMIDINE 0.1M

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97917,0.98735,0.96
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 15, 2002 / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979171
20.987351
30.961
ReflectionResolution: 2.57→16 Å / Num. obs: 9276 / % possible obs: 98.7 % / Redundancy: 5.4 % / Biso Wilson estimate: 57.1 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 6.3
Reflection shellResolution: 2.57→2.66 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 1.7 / % possible all: 98.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.57→16.08 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2164594.45 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 969 10.5 %RANDOM
Rwork0.2 ---
obs0.2 9239 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.8829 Å2 / ksol: 0.368591 e/Å3
Displacement parametersBiso mean: 38.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å22.76 Å20 Å2
2---0.43 Å20 Å2
3---0.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.57→16.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 5 71 2438
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it2.232
X-RAY DIFFRACTIONc_scbond_it1.822
X-RAY DIFFRACTIONc_scangle_it2.742.5
LS refinement shellResolution: 2.57→2.73 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.331 149 10 %
Rwork0.275 1342 -
obs--96.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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