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- PDB-5tnv: Crystal Structure of a Xylose isomerase-like TIM barrel Protein f... -

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Basic information

Entry
Database: PDB / ID: 5tnv
TitleCrystal Structure of a Xylose isomerase-like TIM barrel Protein from Mycobacterium smegmatis in Complex with Magnesium
ComponentsAP endonuclease, family protein 2
KeywordsISOMERASE / Xylose isomerase-like TIM barrel
Function / homology
Function and homology information


endonuclease activity / metal ion binding
Similarity search - Function
: / 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
AP endonuclease, family protein 2
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.04 Å
AuthorsCook, W.J. / Fedorov, A.A. / Fedorov, E.V. / Huang, H. / Bonanno, J.B. / Gerlt, J.A. / Almo, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Crystal Structure of a Xylose isomerase-like TIM barrel Protein from Mycobacterium smegmatis in Complex with Magnesium
Authors: Cook, W.J. / Fedorov, A.A. / Fedorov, E.V. / Huang, H. / Bonanno, J.B. / Gerlt, J.A. / Almo, S.C.
History
DepositionOct 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references / Structure summary
Revision 1.2May 3, 2017Group: Database references / Structure summary
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: AP endonuclease, family protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2742
Polymers36,2501
Non-polymers241
Water7,782432
1
A: AP endonuclease, family protein 2
hetero molecules

A: AP endonuclease, family protein 2
hetero molecules

A: AP endonuclease, family protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,8226
Polymers108,7493
Non-polymers733
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area6100 Å2
ΔGint-46 kcal/mol
Surface area33000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.869, 82.869, 125.218
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-601-

HOH

21A-760-

HOH

31A-894-

HOH

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Components

#1: Protein AP endonuclease, family protein 2 / Xylose isomerase-like TIM barrel


Mass: 36249.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_6790, MSMEI_6607 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0R760
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M lithium sulfate; 25% PEG-3350, 0.1 M HEPES; 5 mM Mg

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 17, 2016 / Details: Diamond
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.04→29.41 Å / Num. obs: 150741 / % possible obs: 98.5 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.05 / Net I/av σ(I): 9.4 / Net I/σ(I): 15.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.04-1.13.50.3152.5196.1
1.1-1.175.30.2113.71100
1.17-1.255.40.15551100
1.25-1.355.50.1196.41100
1.35-1.475.60.098.41100
1.47-1.655.60.06511.31100
1.65-1.95.70.0513.6199.9
1.9-2.335.60.03916188.8
2.33-3.35.80.03218.31100
3.3-29.415.50.02722.4198.4

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Processing

Software
NameVersionClassification
SHELXL2016/4refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXCD3.3.22phasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.04→29.41 Å / Num. parameters: 25767 / Num. restraintsaints: 31527 / Cross valid method: THROUGHOUT / σ(F): 0
Details: STRUCTURE DETERMINATION WAS BY SIRAS USING THE SHELXC/D/E SUITE OF PROGRAMS. THE THREE MERCURY SITES WERE LOCATED WITH SHELXD. PHASING, DENSITY MODIFICATION AND INITIAL CHAIN TRACING WERE DONE WITH SHELXE
RfactorNum. reflection% reflectionSelection details
Rfree0.137 7456 5 %RANDOM
obs0.116 -98.4 %-
all-143142 --
Refine analyzeOccupancy sum hydrogen: 2313 / Occupancy sum non hydrogen: 2828.9
Refinement stepCycle: 1 / Resolution: 1.04→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2399 0 1 432 2832
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.375
X-RAY DIFFRACTIONs_zero_chiral_vol0.083
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.092
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.036
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.036
X-RAY DIFFRACTIONs_approx_iso_adps0.118

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