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- PDB-3t8a: Crystal structure of Mycobacterium tuberculosis MenB in complex w... -

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Basic information

Entry
Database: PDB / ID: 3t8a
TitleCrystal structure of Mycobacterium tuberculosis MenB in complex with substrate analogue, OSB-NCoA
Components1,4-Dihydroxy-2-naphthoyl-CoA synthase
KeywordsLYASE/LYASE INHIBITOR / crotonase superfamily / LYASE-LYASE INHIBITOR complex
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 / cytosol
Similarity search - Function
1,4-Dihydroxy-2-naphthoyl-CoA synthase, MenB / Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / 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 ...1,4-Dihydroxy-2-naphthoyl-CoA synthase, MenB / Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
o-succinylbenzoyl-N-coenzyme A / 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: 2.245 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)112,6195
Polymers110,7103
Non-polymers1,9092
Water1,928107
1
A: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
B: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
C: 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
C: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,23810
Polymers221,4206
Non-polymers3,8194
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area28080 Å2
ΔGint-145 kcal/mol
Surface area46540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.133, 87.133, 414.840
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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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.: 3
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-S0N / o-succinylbenzoyl-N-coenzyme A


Mass: 954.663 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H45N8O20P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.05 Å3/Da / Density % sol: 40.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 19% PEG6000, 300 mM sodium chloride, 100 mM HEPES, 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: Nov 6, 2009
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: 2.245→50 Å / Num. obs: 45905 / % possible obs: 99.6 % / Redundancy: 15.2 % / Rmerge(I) obs: 0.113 / Χ2: 1.071 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.25-2.299.50.54221430.839195.2
2.29-2.3310.80.53621980.84198.7
2.33-2.3811.80.50322290.842199.7
2.38-2.4212.80.46622680.8831100
2.42-2.4813.80.46622200.8881100
2.48-2.5314.30.40522440.9061100
2.53-2.614.80.35422700.9141100
2.6-2.6715.20.3222490.9841100
2.67-2.7515.40.28622781.0051100
2.75-2.8315.80.23622451.0321100
2.83-2.94160.19122691.0511100
2.94-3.0516.40.17622771.0721100
3.05-3.1916.70.13722931.1481100
3.19-3.3617.20.12223271.1371100
3.36-3.5717.50.09622771.31100
3.57-3.8517.70.08423341.2251100
3.85-4.2317.60.08323351.191100
4.23-4.8517.20.07723961.2781100
4.85-6.116.80.0724071.2971100
6.1-50160.05426461.086199.1

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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: 2.245→46.607 Å / Occupancy max: 1 / Occupancy min: 0.39 / SU ML: 2.4 / σ(F): 0.23 / Phase error: 21.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2374 2165 5.01 %
Rwork0.1943 --
obs0.1965 43244 94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.854 Å2 / ksol: 0.396 e/Å3
Displacement parametersBiso max: 89.08 Å2 / Biso mean: 37.9204 Å2 / Biso min: 17.9 Å2
Baniso -1Baniso -2Baniso -3
1-7.108 Å2-0 Å2-0 Å2
2--7.108 Å2-0 Å2
3----14.216 Å2
Refinement stepCycle: LAST / Resolution: 2.245→46.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5873 0 76 107 6056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076099
X-RAY DIFFRACTIONf_angle_d0.9518276
X-RAY DIFFRACTIONf_chiral_restr0.062869
X-RAY DIFFRACTIONf_plane_restr0.0041085
X-RAY DIFFRACTIONf_dihedral_angle_d19.7252172
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2455-2.29770.25471260.20922267239379
2.2977-2.35520.22931390.18712496263588
2.3552-2.41880.23131240.1782530265489
2.4188-2.490.23511360.17212578271491
2.49-2.57040.24951450.1832647279293
2.5704-2.66220.22681340.17262671280594
2.6622-2.76880.2451190.17272719283894
2.7688-2.89480.22061660.17582750291696
2.8948-3.04740.25581590.1882741290096
3.0474-3.23830.24141510.19532834298597
3.2383-3.48830.22911430.18882872301598
3.4883-3.83910.2331450.17992869301498
3.8391-4.39430.20041510.18162933308498
4.3943-5.53490.21631510.1962968311998
5.5349-46.61750.27131760.23413204338098

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