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- PDB-4tm8: Crystal structure of 6-phosphogluconolactonase from Mycobacterium... -

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Basic information

Entry
Database: PDB / ID: 4tm8
TitleCrystal structure of 6-phosphogluconolactonase from Mycobacterium smegmatis N131D mutant
Components6-phosphogluconolactonase
KeywordsHYDROLASE / Rossmann fold
Function / homology
Function and homology information


6-phosphogluconolactonase / 6-phosphogluconolactonase activity / pentose-phosphate shunt / carbohydrate metabolic process / metal ion binding
Similarity search - Function
6-Phosphogluconolactonase / 6-phosphogluconolactonase, DevB-type / Glucosamine/galactosamine-6-phosphate isomerase / Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase / Rossmann fold - #1360 / NagB/RpiA transferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-phosphogluconolactonase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.81 Å
AuthorsFujieda, N. / Stuttfeld, E. / Maier, T.
CitationJournal: Chem Sci / Year: 2015
Title: Enzyme repurposing of a hydrolase as an emergent peroxidase upon metal binding.
Authors: Fujieda, N. / Schatti, J. / Stuttfeld, E. / Ohkubo, K. / Maier, T. / Fukuzumi, S. / Ward, T.R.
History
DepositionMay 31, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Derived calculations ...Database references / Derived calculations / Experimental preparation / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / exptl_crystal_grow / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _entity_src_gen.pdbx_alt_source_flag / _exptl_crystal_grow.temp / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-phosphogluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0402
Polymers26,9441
Non-polymers961
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-7 kcal/mol
Surface area10200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.310, 176.310, 38.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-425-

HOH

21A-429-

HOH

31A-432-

HOH

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Components

#1: Protein 6-phosphogluconolactonase / / 6-phosphogluconolactonase DevB


Mass: 26943.912 Da / Num. of mol.: 1 / Mutation: N131D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: pgl, MSMEG_3099, MSMEI_3021 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QWX6, 6-phosphogluconolactonase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.76 Å3/Da / Density % sol: 55.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% polyethylene glycol 1000, 0.2 M Li2SO4, 0.1M phosphate/citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→55.754 Å / Num. obs: 27962 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 11.4 % / Biso Wilson estimate: 34.59 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.05 / Χ2: 1.018 / Net I/σ(I): 26.93 / Num. measured all: 318419
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.81-1.920.930.612449417445443990.64198.8
1.92-2.050.9830.3137.7548572417341730.327100
2.05-2.210.9950.1614.6446645392239220.167100
2.21-2.420.9970.09622.4340593361636160.101100
2.42-2.710.9990.06233.6539348329332930.064100
2.71-3.130.9990.04743.0732474291029100.049100
3.13-3.830.9990.03756.2928702251625150.039100
3.83-5.40.9990.03659.9820807195719570.037100
5.40.9980.045911861118011770.04299.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: dev_1394)refinement
RefinementResolution: 1.81→55.754 Å / FOM work R set: 0.8563 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2014 1375 4.93 %
Rwork0.175 26529 -
obs0.1763 27904 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.03 Å2 / Biso mean: 47.34 Å2 / Biso min: 24.26 Å2
Refinement stepCycle: final / Resolution: 1.81→55.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 0 5 102 1903
Biso mean--48.16 52.31 -
Num. residues----245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111900
X-RAY DIFFRACTIONf_angle_d1.2872598
X-RAY DIFFRACTIONf_chiral_restr0.094293
X-RAY DIFFRACTIONf_plane_restr0.007354
X-RAY DIFFRACTIONf_dihedral_angle_d12.869686
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.81-1.87470.31411470.274325702717
1.8747-1.94980.27731320.2326122744
1.9498-2.03850.21941250.201626262751
2.0385-2.1460.21921320.189426332765
2.146-2.28040.19981360.179526082744
2.2804-2.45650.23151300.192326442774
2.4565-2.70370.2241450.18326392784
2.7037-3.09490.20091420.192826582800
3.0949-3.89910.20551450.163326992844
3.8991-55.78060.17081410.155528402981
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.3821-3.43853.56875.3473-4.17163.68850.4496-0.5895-0.1957-0.03070.23440.4679-0.5754-0.4118-0.49790.3955-0.1929-0.01310.55130.00310.4189-13.022810.1553.8117
24.7742-1.71463.47086.8211-4.43139.53610.5168-0.92581.3550.3264-0.07840.2401-0.577-0.5437-0.29870.372-0.04520.20270.4084-0.07690.4757-25.82212.97179.1319
37.5159-1.3067-2.0085.6898-0.01556.05580.304-0.68770.43530.4531-0.16480.1974-0.4017-0.1863-0.11870.2372-0.06140.09120.4609-0.09060.3256-29.44157.187212.3235
45.39011.2994-0.72127.2346-0.51942.51410.2091-0.4084-0.51770.3229-0.14660.80520.0073-0.5311-0.06090.1967-0.08140.05440.55920.00940.3158-35.0508-2.61929.5365
59.5479-2.0033-0.49422.64611.11722.26220.0067-0.56340.02420.13330.0478-0.0743-0.0588-0.2395-0.08790.2816-0.08190.05290.6897-0.01880.3359-36.79870.632914.5306
64.12141.7473-0.06547.6313-0.36313.6442-0.1448-0.0566-1.5963-0.2710.01260.45131.088-1.00350.04430.3657-0.29140.0270.7455-0.05760.7096-40.3045-11.41785.0178
76.93753.7649-1.56865.82010.70775.4399-0.17051.14380.2899-1.0549-0.19421.7518-0.27-1.83210.10880.3678-0.008-0.17690.8686-0.09250.5265-38.463-4.5259-4.835
85.49530.3849-1.95725.7220.45532.8648-0.0380.3153-0.4308-0.2011-0.07270.15120.0725-0.42320.11320.2522-0.07010.01530.4074-0.04040.3365-23.0271-3.01950.2769
97.75990.39020.14443.06340.68371.87750.08460.7318-1.5304-0.39590.00520.31070.5196-0.2028-0.0330.3574-0.09480.02450.429-0.18320.6217-26.1751-13.371-3.1649
106.48891.1738-1.31252.79840.30122.90460.00050.2061-0.1341-0.1699-0.08080.035-0.0699-0.2010.05660.1966-0.03350.00080.2827-0.0060.2125-18.7872-0.5293-1.0091
117.5309-2.91552.84046.6582-3.3838.95260.0297-0.99680.28440.2126-0.0856-0.5636-0.1978-0.01410.06790.2145-0.08240.01720.4012-0.04810.2993-11.0365.04165.7009
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resid 0 through 11 )A0 - 11
2X-RAY DIFFRACTION2chain A and (resid 12 through 34 )A12 - 34
3X-RAY DIFFRACTION3chain A and (resid 35 through 60 )A35 - 60
4X-RAY DIFFRACTION4chain A and (resid 61 through 83 )A61 - 83
5X-RAY DIFFRACTION5chain A and (resid 84 through 102 )A84 - 102
6X-RAY DIFFRACTION6chain A and (resid 103 through 116 )A103 - 116
7X-RAY DIFFRACTION7chain A and (resid 117 through 134 )A117 - 134
8X-RAY DIFFRACTION8chain A and (resid 135 through 159 )A135 - 159
9X-RAY DIFFRACTION9chain A and (resid 160 through 181 )A160 - 181
10X-RAY DIFFRACTION10chain A and (resid 182 through 230 )A182 - 230
11X-RAY DIFFRACTION11chain A and (resid 231 through 244 )A231 - 244

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