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- PDB-3tx2: Structure of a Probable 6-phosphogluconolactonase from Mycobacter... -

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Basic information

Entry
Database: PDB / ID: 3tx2
TitleStructure of a Probable 6-phosphogluconolactonase from Mycobacterium abscessus
ComponentsProbable 6-phosphogluconolactonase
KeywordsHYDROLASE / SSGCID / Seattle Structural Genomics Center for Infectious Disease / Probable 6-phosphogluconolactonase
Function / homology
Function and homology information


6-phosphogluconolactonase / 6-phosphogluconolactonase activity / pentose-phosphate shunt / carbohydrate metabolic process
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
BENZOIC ACID / 6-phosphogluconolactonase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionSep 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable 6-phosphogluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8005
Polymers26,5401
Non-polymers2604
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)136.350, 41.180, 44.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Probable 6-phosphogluconolactonase


Mass: 26539.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Strain: ATCC 19977 / DSM 44196 / Gene: MAB_2763 / Production host: Escherichia coli (E. coli) / References: UniProt: B1MC71
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1600mM sodium citrate, Protein 51.9 mg/ml, Cryo protectant 25% ethlyene glycol, Target DB: MyabA.01244.a.A1 PS00890, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.5→68.18 Å / Num. obs: 41365 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.916 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 17.07
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.5-1.540.4484.37152523016100
1.54-1.580.3615.3914964293399.9
1.58-1.630.3016.39149052863100
1.63-1.680.2717.08149612808100
1.68-1.730.2437.98146222709100
1.73-1.790.1939.9714438263499.9
1.79-1.860.16711.5213839250799.9
1.86-1.940.15113.9612651238598.6
1.94-2.020.1116.6813143236299.9
2.02-2.120.08519.62124822233100
2.12-2.240.08220.9411496212398.7
2.24-2.370.07123.1110381199898.1
2.37-2.540.05826.2710672192199.8
2.54-2.740.0528.798221786100
2.74-30.04431.459026166399.9
3-3.350.03934.897977149199.9
3.35-3.870.03636.456970134299.3
3.87-4.740.0339.26031114499
4.74-6.710.02838.46479491899.9
6.710.02637.38249352995.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å42.71 Å
Translation2.5 Å42.71 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ICO

3ico


Resolution: 1.5→68.18 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.2035 / WRfactor Rwork: 0.1837 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8627 / SU B: 2.57 / SU ML: 0.052 / SU R Cruickshank DPI: 0.0795 / SU Rfree: 0.0768 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2106 2082 5 %RANDOM
Rwork0.1916 ---
obs0.1926 41364 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 38.17 Å2 / Biso mean: 14.4893 Å2 / Biso min: 3.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2--0.29 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.5→68.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1828 0 17 355 2200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021927
X-RAY DIFFRACTIONr_bond_other_d0.0060.021245
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.9662647
X-RAY DIFFRACTIONr_angle_other_deg0.92933062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8955262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04724.41677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.02215288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3521511
X-RAY DIFFRACTIONr_chiral_restr0.0760.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212205
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02374
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 147 -
Rwork0.222 2642 -
all-2789 -
obs--99.93 %
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)
11.38840.22140.40990.2455-0.19420.5786-0.05150.10140.1014-0.02620.0311-0.0413-0.0679-0.01180.02040.107-0.00260.00610.0840.0040.099354.58866.92411.5921
21.4674-0.1925-1.22471.3555-1.90226.15630.13690.17050.1551-0.0995-0.0093-0.038-0.194-0.0354-0.12760.09610.01550.02660.1120.00820.113444.51812.4904-3.5177
30.7690.1991-0.08981.3424-0.22090.69220.0126-0.01480.0283-0.0116-0.00480.0876-0.0061-0.0617-0.00780.07770.003-0.00670.0948-0.00030.081236.1472-0.02666.1302
41.25560.2170.16320.3468-0.11770.75680.003-0.09720.01940.0352-0.0109-0.05230.02630.00730.0080.09070.00330.00270.0912-0.00840.08852.4426-1.507615.7039
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 57
2X-RAY DIFFRACTION2A58 - 72
3X-RAY DIFFRACTION3A73 - 137
4X-RAY DIFFRACTION4A138 - 247

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