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- PDB-1k77: Crystal Structure of EC1530, a Putative Oxygenase from Escherichi... -

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Basic information

Entry
Database: PDB / ID: 1k77
TitleCrystal Structure of EC1530, a Putative Oxygenase from Escherichia coli
ComponentsHypothetical protein ygbMHypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / TIM Barrel / Hypothetical Protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


2-dehydrotetronate isomerase / hydroxypyruvate isomerase activity / glyoxylate metabolic process / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Hydroxypyruvate isomerase-like / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / 2-oxo-tetronate isomerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.63 Å
AuthorsKim, Y. / Skarina, T. / Beasley, S. / Laskowski, R. / Arrowsmith, C.H. / Joachimiak, A. / Edwards, A.M. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proteins / Year: 2002
Title: Crystal structure of Escherichia coli EC1530, a glyoxylate induced protein YgbM.
Authors: Kim, Y. / Skarina, T. / Beasley, S. / Laskowski, R. / Arrowsmith, C.H. / Joachimiak, A. / Edwards, A.M. / Savchenko, A.
History
DepositionOct 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein ygbM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8596
Polymers29,5811
Non-polymers2795
Water4,900272
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.907, 74.368, 39.376
Angle α, β, γ (deg.)90.00, 98.81, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-301-

MG

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Components

#1: Protein Hypothetical protein ygbM / Hypothesis / EC1530


Mass: 29580.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: Q46891
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.56 Å3/Da / Density % sol: 52.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: magnesium formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19 mg/mlprotein1drop
20.1 MHEPES1reservoirpH7.
35 %PEG80001reservoir
45 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97946, 0.97957, 0.93927
DetectorType: SBC-2 / Detector: CCD / Date: May 18, 2001 / Details: mirror
RadiationMonochromator: double crystal monochromater Si-111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979461
20.979571
30.939271
ReflectionResolution: 1.63→39 Å / Num. all: 35621 / Num. obs: 35621 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 7.1
Reflection shellResolution: 1.63→1.69 Å / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 2.7 / % possible all: 70.8
Reflection
*PLUS
Lowest resolution: 39 Å

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Processing

Software
NameClassification
d*treck/HKL2000data collection
HKL-2000data reduction
CNSrefinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.63→38.91 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 432306.02 / 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
Rfree0.214 3439 9.8 %RANDOM
Rwork0.194 ---
all0.1957 35189 --
obs0.1957 35189 94.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.5044 Å2 / ksol: 0.388004 e/Å3
Displacement parametersBiso mean: 18.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.85 Å20 Å2-0.8 Å2
2---1.21 Å20 Å2
3---3.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.63→38.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2081 0 17 272 2370
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_mcangle_it1.842
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it2.722.5
LS refinement shellResolution: 1.63→1.73 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.268 409 9.2 %
Rwork0.263 4024 -
obs--71.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2GOL.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMGOL.TOP
X-RAY DIFFRACTION4ION.PARAMFOM.TOP
Refinement
*PLUS
Lowest resolution: 39 Å / σ(F): 0 / Num. reflection Rfree: 4024 / % reflection Rfree: 9.8 % / Rfactor obs: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_mcangle_it1.842
X-RAY DIFFRACTIONc_scangle_it2.722.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.268 / % reflection Rfree: 9.2 % / Rfactor Rwork: 0.263

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