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- PDB-3m20: Crystal structure of DmpI from Archaeoglobus fulgidus determined ... -

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Basic information

Entry
Database: PDB / ID: 3m20
TitleCrystal structure of DmpI from Archaeoglobus fulgidus determined to 2.37 Angstroms resolution
Components4-oxalocrotonate tautomerase, putative
KeywordsISOMERASE / 4-oxalocrotonate tautomerase / Archaeoglobus fulgidus / DmpI / thermophile / beta-alpha-beta / catalytic proline
Function / homology
Function and homology information


: / 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
4-oxalocrotonate tautomerase, putative
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsHackert, M.L. / Whitman, C.P. / Almrud, J.J. / Dasgupta, R. / 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
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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: 4-oxalocrotonate tautomerase, putative
B: 4-oxalocrotonate tautomerase, putative
C: 4-oxalocrotonate tautomerase, putative


Theoretical massNumber of molelcules
Total (without water)20,4843
Polymers20,4843
Non-polymers00
Water36020
1
A: 4-oxalocrotonate tautomerase, putative
B: 4-oxalocrotonate tautomerase, putative
C: 4-oxalocrotonate tautomerase, putative

A: 4-oxalocrotonate tautomerase, putative
B: 4-oxalocrotonate tautomerase, putative
C: 4-oxalocrotonate tautomerase, putative


Theoretical massNumber of molelcules
Total (without water)40,9676
Polymers40,9676
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area13060 Å2
ΔGint-84 kcal/mol
Surface area13450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.070, 49.070, 118.747
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein 4-oxalocrotonate tautomerase, putative /


Mass: 6827.901 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: AF_0669, dmpi / Plasmid: pET24a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: O29588, EC: 5.3.2.2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 37.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 28 % PEG400, 200mM CaCl2, 0.1M HEPES (pH 7.5), vapor diffusion, sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 10, 2000 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.29→24.53 Å / Num. all: 7771 / Num. obs: 8623 / % possible obs: 96.4 % / Observed criterion σ(F): 2 / Biso Wilson estimate: 33.6 Å2 / Limit h max: 18 / Limit h min: 0 / Limit k max: 18 / Limit k min: 0 / Limit l max: 51 / Limit l min: 0 / Observed criterion F max: 1289650.3 / Observed criterion F min: 7.3 / Rmerge(I) obs: 0.064 / Χ2: 1.03 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
2.29-2.370.4758580.8197.4
2.37-2.480.3188640.74999.1
2.48-2.610.2248490.78198
2.61-2.770.1798620.82998
2.77-2.990.1328670.85598.5
2.99-3.290.088940.96998.6
3.29-3.760.068001.28789.4
3.76-4.730.0439161.4299.5
4.73-300.0329821.41299.4

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Processing

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

1bjp


Resolution: 2.37→24.53 Å / Rfactor Rfree error: 0.018 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.316 317 4.7 %random
Rwork0.296 ---
all-7175 --
obs-6674 93 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 56.0354 Å2 / ksol: 0.332806 e/Å3
Displacement parametersBiso max: 82.86 Å2 / Biso mean: 46.78 Å2 / Biso min: 20.61 Å2
Baniso -1Baniso -2Baniso -3
1--11.41 Å2-6.48 Å20 Å2
2---11.41 Å20 Å2
3---22.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.7 Å0.51 Å
Luzzati d res high-2.37
Refinement stepCycle: LAST / Resolution: 2.37→24.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1267 0 0 20 1287
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d27.4
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.37-2.480.443354.40.4047600.07587679590.8
2.48-2.610.455455.70.3887410.06886678690.8
2.61-2.770.476445.40.3377670.07287681192.6
2.77-2.990.3713340.3497850.06587681893.4
2.99-3.290.38323.70.3778230.06790485594.5
3.29-3.760.318435.60.2817240.04889276786
3.76-4.730.313414.60.2798490.04991589097.3
4.73-24.530.209444.60.2299080.03297395297.8

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