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- PDB-3ico: Crystal structure of 6-phosphogluconolactonase from Mycobacterium... -

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Basic information

Entry
Database: PDB / ID: 3ico
TitleCrystal structure of 6-phosphogluconolactonase from Mycobacterium tuberculosis
Components6-phosphogluconolactonase
KeywordsHYDROLASE / SSGCID / Infectious Disease / NIAID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


6-phosphogluconolactonase / 6-phosphogluconolactonase activity / pentose-phosphate shunt, oxidative branch / carbohydrate metabolic process / plasma membrane / cytoplasm
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 / 6-phosphogluconolactonase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 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
DepositionJul 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 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 / struct_ncs_dom_lim / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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: 6-phosphogluconolactonase
B: 6-phosphogluconolactonase
C: 6-phosphogluconolactonase
D: 6-phosphogluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,05510
Polymers112,4794
Non-polymers5766
Water8,935496
1
A: 6-phosphogluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2162
Polymers28,1201
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 6-phosphogluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2162
Polymers28,1201
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 6-phosphogluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3123
Polymers28,1201
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 6-phosphogluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3123
Polymers28,1201
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.301, 68.081, 73.542
Angle α, β, γ (deg.)108.500, 107.110, 104.950
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 5 / Auth seq-ID: 3 - 246 / Label seq-ID: 24 - 267

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
6-phosphogluconolactonase / / 6PGL


Mass: 28119.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Expressed with a hexahis tag followed by 3C protease cleavage site. The affinity tag was not removed prior to crystallization.
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: pgl, devB, Rv1445c, MT1492, MTCY493.09 / Production host: Escherichia coli (E. coli)
References: UniProt: P63338, UniProt: P9WQP5*PLUS, 6-phosphogluconolactonase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 496 / 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: 2.13 Å3/Da / Density % sol: 42.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: JCSG condition H9, 0.2 M lithium sulfate, 0.1 M BisTris pH 5.5, 25% PEG 3350, 26.9 mg/mL protein, Crystal Tracking ID 202955h9, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 48256 / % possible obs: 95.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.056 / Χ2: 1.049 / Net I/σ(I): 23.75
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 7.4 / Num. unique all: 4584 / Χ2: 1.055 / % possible all: 90.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.38 Å33.9 Å
Translation2.38 Å33.9 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VL1

1vl1


Resolution: 2.15→33.9 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.211 / WRfactor Rwork: 0.174 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.853 / SU B: 5.067 / SU ML: 0.133 / SU R Cruickshank DPI: 0.294 / SU Rfree: 0.204 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.294 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2412 5 %RANDOM
Rwork0.182 ---
obs0.184 48228 95.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 45.34 Å2 / Biso mean: 19.629 Å2 / Biso min: 4.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å21.06 Å2-0.39 Å2
2--0.41 Å20.05 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.15→33.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7208 0 30 496 7734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227458
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.97410212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9795992
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00824.23305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.203151088
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.511552
X-RAY DIFFRACTIONr_chiral_restr0.0840.21155
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0225808
X-RAY DIFFRACTIONr_mcbond_it0.5021.54938
X-RAY DIFFRACTIONr_mcangle_it0.94327872
X-RAY DIFFRACTIONr_scbond_it1.61532520
X-RAY DIFFRACTIONr_scangle_it2.7494.52340
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A952MEDIUM POSITIONAL0.270.5
B952MEDIUM POSITIONAL0.210.5
C952MEDIUM POSITIONAL0.230.5
D952MEDIUM POSITIONAL0.230.5
A778LOOSE POSITIONAL0.415
B778LOOSE POSITIONAL0.385
C778LOOSE POSITIONAL0.395
D778LOOSE POSITIONAL0.475
A952MEDIUM THERMAL0.982
B952MEDIUM THERMAL1.042
C952MEDIUM THERMAL1.022
D952MEDIUM THERMAL0.742
A778LOOSE THERMAL1.0210
B778LOOSE THERMAL1.0310
C778LOOSE THERMAL1.0310
D778LOOSE THERMAL0.910
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 182 -
Rwork0.2 3174 -
all-3356 -
obs--88.67 %

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