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- PDB-3m21: Crystal structure of DmpI from Helicobacter pylori Determined to ... -

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Basic information

Entry
Database: PDB / ID: 3m21
TitleCrystal structure of DmpI from Helicobacter pylori Determined to 1.9 Angstroms resolution
ComponentsProbable tautomerase HP_0924
KeywordsISOMERASE / 4-oxalocrotonate tautomerase / catalytic proline / hexamer / beta-alpha-beta
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: 1.9 Å
AuthorsHackert, M.L. / Whitman, C.P. / Almrud, J.J. / Dasgupta, R. / Kern, A.D. / Czerwinski, R.M.
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
DepositionMar 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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: Probable tautomerase HP_0924
B: Probable tautomerase HP_0924
C: Probable tautomerase HP_0924
D: Probable tautomerase HP_0924
E: Probable tautomerase HP_0924
F: Probable tautomerase HP_0924


Theoretical massNumber of molelcules
Total (without water)44,3366
Polymers44,3366
Non-polymers00
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12750 Å2
ΔGint-80 kcal/mol
Surface area16230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.040, 53.040, 130.877
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Probable tautomerase HP_0924


Mass: 7389.381 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: 899453, HP_0924 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.04 Å3/Da / Density % sol: 39.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Crystals were grown using a well solution of 25% t-butanol, 0.1M Na Citrate, pH 5.5. Protein was 20 mg/ml in 50 mM NaH2PO4, pH 7.3. 5 microliters of well solution was mixed with 5 ...Details: Crystals were grown using a well solution of 25% t-butanol, 0.1M Na Citrate, pH 5.5. Protein was 20 mg/ml in 50 mM NaH2PO4, pH 7.3. 5 microliters of well solution was mixed with 5 microliters of protein and vapor equilibrated using sitting drop, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 10, 2000 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 27541 / % possible obs: 89.3 % / Observed criterion σ(I): 3 / Redundancy: 5.4 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.044 / Χ2: 0.944 / Net I/σ(I): 22.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.85-1.9240.32124880.57179.9
1.92-1.990.21830400.58999.7
1.99-2.080.14130930.581100
2.08-2.190.10530610.656100
2.19-2.330.08615870.78651.9
2.33-2.510.06130880.82100
2.51-2.760.05230771.05399.6
2.76-3.160.04630441.36799.5
3.16-3.980.04120871.75167.4
3.98-300.02829761.42594.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BJP

1bjp


Resolution: 1.9→30 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 63 / Stereochemistry target values: mlf
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1284 5 %random
Rwork0.236 ---
all-27541 --
obs-25134 88.5 %-
Solvent computationBsol: 59.282 Å2
Displacement parametersBiso max: 72.59 Å2 / Biso mean: 33.18 Å2 / Biso min: 13.31 Å2
Baniso -1Baniso -2Baniso -3
1-2.676 Å20 Å20 Å2
2--2.676 Å20 Å2
3----5.351 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2913 0 0 273 3186
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d0.983
X-RAY DIFFRACTIONc_mcbond_it1.5131.5
X-RAY DIFFRACTIONc_scbond_it1.9762
X-RAY DIFFRACTIONc_mcangle_it2.3232
X-RAY DIFFRACTIONc_scangle_it2.762.5
LS refinement shellResolution: 1.9→1.94 Å / Rfactor Rfree: 0.335 / Rfactor Rwork: 0.281
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4cis_peptide.param

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