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- PDB-3t8b: Crystal structure of Mycobacterium tuberculosis MenB with altered... -

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Basic information

Entry
Database: PDB / ID: 3t8b
TitleCrystal structure of Mycobacterium tuberculosis MenB with altered hexameric assembly
Components1,4-Dihydroxy-2-naphthoyl-CoA synthase
KeywordsLYASE / crotonase superfamily
Function / homology
Function and homology information


1,4-dihydroxy-2-naphthoyl-CoA synthase / 1,4-dihydroxy-2-naphthoyl-CoA synthase activity / menaquinone biosynthetic process / protein hexamerization / plasma membrane
Similarity search - Function
1,4-Dihydroxy-2-naphthoyl-CoA synthase, MenB / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
1,4-dihydroxy-2-naphthoyl-CoA synthase / 1,4-dihydroxy-2-naphthoyl-CoA synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.649 Å
AuthorsLi, H.-J. / Li, X. / Liu, N. / Zhang, H. / Truglio, J. / Mishra, S. / Kisker, C. / Garcia-Diaz, M. / Tonge, P.
CitationJournal: Biochemistry / Year: 2011
Title: Mechanism of the Intramolecular Claisen Condensation Reaction Catalyzed by MenB, a Crotonase Superfamily Member.
Authors: Li, H.J. / Li, X. / Liu, N. / Zhang, H. / Truglio, J.J. / Mishra, S. / Kisker, C. / Garcia-Diaz, M. / Tonge, P.J.
History
DepositionAug 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 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 / 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_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

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Assembly

Deposited unit
A: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
B: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8993
Polymers73,8072
Non-polymers921
Water5,044280
1
A: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
B: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
hetero molecules

A: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
B: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
hetero molecules

A: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
B: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,6969
Polymers221,4206
Non-polymers2763
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area17640 Å2
ΔGint-60 kcal/mol
Surface area44920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.233, 132.233, 71.139
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein 1,4-Dihydroxy-2-naphthoyl-CoA synthase / MenB / DHNA-CoA synthase


Mass: 36903.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv0548c / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): CodonPlus
References: UniProt: O06414, UniProt: P9WNP5*PLUS, 1,4-dihydroxy-2-naphthoyl-CoA synthase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 1.621723 Å3/Da / Density % sol: 24.154737 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 19% PEG3350, 200 mM lithium sulfate, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 6, 2010
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.649→50 Å / Num. obs: 55893 / % possible obs: 100 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.083 / Χ2: 1.012 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.65-1.685.60.68127790.7791100
1.68-1.715.60.61128250.7881100
1.71-1.745.60.5228230.7811100
1.74-1.785.60.43927730.8041100
1.78-1.825.60.38528170.8581100
1.82-1.865.60.31327650.9081100
1.86-1.95.60.2728160.9391100
1.9-1.965.60.2127810.9981100
1.96-2.015.70.18227651.0171100
2.01-2.085.70.16527911.0781100
2.08-2.155.70.13327991.0491100
2.15-2.245.70.11428101.0741100
2.24-2.345.70.10328051.0971100
2.34-2.465.70.09427781.1651100
2.46-2.625.70.08527781.2111100
2.62-2.825.70.08128261.3951100
2.82-3.115.70.07127841.311100
3.11-3.555.60.06127751.0541100
3.55-4.485.50.05128070.9561100
4.48-505.80.05227960.9561100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q51

1q51


Resolution: 1.649→36.977 Å / Occupancy max: 1 / Occupancy min: 0.23 / SU ML: 1.69 / σ(F): 0.14 / Phase error: 17.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1871 2741 5.13 %
Rwork0.141 --
obs0.1434 53381 95.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.737 Å2 / ksol: 0.399 e/Å3
Displacement parametersBiso max: 64.45 Å2 / Biso mean: 21.9176 Å2 / Biso min: 9.43 Å2
Baniso -1Baniso -2Baniso -3
1--3.0006 Å20 Å20 Å2
2---3.0006 Å20 Å2
3---6.0012 Å2
Refinement stepCycle: LAST / Resolution: 1.649→36.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3371 0 6 280 3657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043508
X-RAY DIFFRACTIONf_angle_d0.834765
X-RAY DIFFRACTIONf_chiral_restr0.062519
X-RAY DIFFRACTIONf_plane_restr0.003627
X-RAY DIFFRACTIONf_dihedral_angle_d15.8181230
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6494-1.67780.26521170.17492305242287
1.6778-1.70830.27921260.15272331245787
1.7083-1.74120.2151340.14142385251989
1.7412-1.77670.19161240.13192397252191
1.7767-1.81540.18461390.12922435257492
1.8154-1.85760.19881440.11912435257993
1.8576-1.9040.20441410.11362469261093
1.904-1.95550.16151460.1062518266496
1.9555-2.01310.18881350.10762523265896
2.0131-2.0780.17161260.11172586271297
2.078-2.15230.17441180.10872607272597
2.1523-2.23840.19241240.11722647277199
2.2384-2.34030.19351720.11922598277099
2.3403-2.46370.18291320.13082602273499
2.4637-2.6180.20261360.14012609274599
2.618-2.82010.17331390.15362655279499
2.8201-3.10370.19731560.15032616277299
3.1037-3.55250.20281500.149426132763100
3.5525-4.47460.15441320.13926692801100
4.4746-36.98620.15831500.169626402790100

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