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- PDB-2orm: Crystal Structure of the 4-Oxalocrotonate Tautomerase Homologue D... -

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Basic information

Entry
Database: PDB / ID: 2orm
TitleCrystal Structure of the 4-Oxalocrotonate Tautomerase Homologue DmpI from Helicobacter pylori.
ComponentsProbable tautomerase HP0924
KeywordsISOMERASE / homohexamer / 4-OT / 4-Oxalocrotonate Tautomerase Homologue
Function / homology
Function and homology information


Isomerases; Intramolecular oxidoreductases; Interconverting keto- and enol-groups / isomerase activity
Similarity search - Function
4-oxalocrotonate tautomerase, Pseudomonas-type / 4-oxalocrotonate tautomerase / Tautomerase enzyme / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable tautomerase HP_0924
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHackert, M.L. / Whitman, C.P. / Almrud, J.J. / Dasgupta, R. / Czerwinski, R.M. / Kern, A.D.
CitationJournal: Bioorg.Chem. / Year: 2010
Title: Kinetic and structural characterization of DmpI from Helicobacter pylori and Archaeoglobus fulgidus, two 4-oxalocrotonate tautomerase family members.
Authors: Almrud, J.J. / Dasgupta, R. / Czerwinski, R.M. / Kern, A.D. / Hackert, M.L. / Whitman, C.P.
History
DepositionFeb 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 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: Probable tautomerase HP0924
B: Probable tautomerase HP0924
C: Probable tautomerase HP0924
D: Probable tautomerase HP0924
E: Probable tautomerase HP0924
F: Probable tautomerase HP0924


Theoretical massNumber of molelcules
Total (without water)44,3366
Polymers44,3366
Non-polymers00
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12870 Å2
ΔGint-77 kcal/mol
Surface area16340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)41.830, 50.770, 89.310
Angle α, β, γ (deg.)90.00, 99.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Probable tautomerase HP0924


Mass: 7389.381 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: J99 / Gene: dmpi (GI 7449587) / Plasmid: pET 24a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: O25581, Isomerases; Intramolecular oxidoreductases; Interconverting keto- and enol-groups
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.11 Å3/Da / Density % sol: 41.73 %
Crystal growTemperature: 277 K / pH: 7.5
Details: 2 uL of protein (20 mg/mL) in 20mM phosphate buffer (pH 7.4) were mixed with 2 uL of 0.2M CaCl2, 0.1M Hepes (pH 7.5), and 28% PEG 400. This combined volume was equilibrated at 4 degrees ...Details: 2 uL of protein (20 mg/mL) in 20mM phosphate buffer (pH 7.4) were mixed with 2 uL of 0.2M CaCl2, 0.1M Hepes (pH 7.5), and 28% PEG 400. This combined volume was equilibrated at 4 degrees Celcius against 50 uL of 0.2M CaCl2, 0.1M Hepes (pH 7.5), and 28% PEG 400 , VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 7.50

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 10, 2000
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→24.5 Å / Num. obs: 20368 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 5.94 % / Biso Wilson estimate: 19.2 Å2 / Rsym value: 0.096 / Net I/σ(I): 13.5
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 4 / Rsym value: 0.476 / % possible all: 90

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Processing

Software
NameClassification
HKL-2000data collection
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BJP

1bjp


Resolution: 2.1→24.5 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: RANDOM / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1044 -THROUGHOUT
Rwork0.217 ---
obs0.217 20368 92.1 %-
all-21823 --
Displacement parametersBiso mean: 31 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å20 Å20.85 Å2
2---2.06 Å20 Å2
3---0.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→24.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2932 0 0 126 3058
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.1→2.2 Å / Rfactor Rfree error: 0.026
RfactorNum. reflection% reflection
Rfree0.289 120 -
Rwork0.257 --
obs--89 %

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