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- PDB-7m59: Crystal structure of N2, a member of 4-oxalocrotonate tautomerase... -

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Basic information

Entry
Database: PDB / ID: 7m59
TitleCrystal structure of N2, a member of 4-oxalocrotonate tautomerase (4-OT) family
ComponentsTautomerase domain-containing protein
KeywordsISOMERASE
Function / homology4-oxalocrotonate tautomerase / Tautomerase enzyme / Tautomerase/MIF superfamily / isomerase activity / 4-oxalocrotonate tautomerase-like domain-containing protein
Function and homology information
Biological speciesGammaproteobacteria bacterium SG8_31 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMedellin, B.P. / Moreno, R.Y. / Zhang, Y.J.
Funding support4items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM-129331
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM-104896
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM125882
Robert A. Welch FoundationF-1778
CitationJournal: Biochemistry / Year: 2021
Title: Kinetic and Structural Analysis of Two Linkers in the Tautomerase Superfamily: Analysis and Implications.
Authors: Baas, B.J. / Medellin, B.P. / LeVieux, J.A. / Erwin, K. / Lancaster, E.B. / Johnson Jr., W.H. / Kaoud, T.S. / Moreno, R.Y. / de Ruijter, M. / Babbitt, P.C. / Zhang, Y.J. / Whitman, C.P.
History
DepositionMar 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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: Tautomerase domain-containing protein
B: Tautomerase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)14,0502
Polymers14,0502
Non-polymers00
Water1,63991
1
A: Tautomerase domain-containing protein
B: Tautomerase domain-containing protein

A: Tautomerase domain-containing protein
B: Tautomerase domain-containing protein

A: Tautomerase domain-containing protein
B: Tautomerase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)42,1506
Polymers42,1506
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area14180 Å2
ΔGint-70 kcal/mol
Surface area14570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.839, 78.839, 182.952
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-137-

HOH

21A-147-

HOH

31B-131-

HOH

41B-142-

HOH

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Components

#1: Protein Tautomerase domain-containing protein


Mass: 7024.948 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gammaproteobacteria bacterium SG8_31 (bacteria)
Gene: AMJ59_12120
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0S8FF56
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.89 Å3/Da / Density % sol: 68.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 40% 2-methyl-2,4-pentanediol, 4% PEG 8000, 1% sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 26628 / % possible obs: 99.7 % / Redundancy: 10.9 % / Biso Wilson estimate: 23.89 Å2 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.018 / Rrim(I) all: 0.06 / Χ2: 1.174 / Net I/σ(I): 11.7 / Num. measured all: 289310
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.65-1.685.30.61612700.7670.290.6830.56897
1.68-1.716.10.52912930.8350.2290.5780.59398.2
1.71-1.7470.48412910.8550.1950.5230.60999.1
1.74-1.7880.41513310.9120.1550.4430.64699.8
1.78-1.829.80.35513150.9580.1190.3750.681100
1.82-1.8611.40.28713380.9770.0890.30.707100
1.86-1.912.30.21813100.9880.0650.2280.784100
1.9-1.9612.30.17113210.9920.0510.1790.837100
1.96-2.0112.30.15413230.9920.0460.1610.869100
2.01-2.0812.30.12613170.9950.0370.1320.912100
2.08-2.1512.30.10413190.9970.0310.1081.011100
2.15-2.2412.30.08713640.9970.0260.0911.034100
2.24-2.3412.30.07512980.9980.0220.0781.087100
2.34-2.4612.30.06513510.9980.0190.0681.145100
2.46-2.6212.30.05713440.9990.0170.0591.201100
2.62-2.8212.20.05213430.9990.0160.0541.195100
2.82-3.1112.20.05513310.9980.0160.0571.808100
3.11-3.5511.60.05713610.9980.0180.062.798100
3.55-4.4811.40.05213720.9980.0160.0552.887100
4.48-5011.30.02814360.9990.0090.0290.90699.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RY0

3ry0


Resolution: 1.65→38 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 18.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1869 2018 7.58 %
Rwork0.1752 24608 -
obs0.1761 26626 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.35 Å2 / Biso mean: 26.1264 Å2 / Biso min: 10.85 Å2
Refinement stepCycle: final / Resolution: 1.65→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms984 0 0 91 1075
Biso mean---34.36 -
Num. residues----128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061002
X-RAY DIFFRACTIONf_angle_d0.7321358
X-RAY DIFFRACTIONf_chiral_restr0.052154
X-RAY DIFFRACTIONf_plane_restr0.004178
X-RAY DIFFRACTIONf_dihedral_angle_d7.661608
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.65-1.69110.28231350.2484167996
1.6911-1.73680.24311400.2249169899
1.7368-1.78790.21941510.21941729100
1.7879-1.84560.21991440.18931758100
1.8456-1.91150.19931390.17771735100
1.9115-1.98810.20141540.17911753100
1.9881-2.07860.22731320.18311756100
2.0786-2.18810.19521480.18731750100
2.1881-2.32520.21151410.17761768100
2.3252-2.50470.1891450.17341756100
2.5047-2.75670.19921480.16961762100
2.7567-3.15540.17681430.17081791100
3.1554-3.97480.17871450.17031799100
3.9748-380.15651530.15651874100

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