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- PDB-1q52: Crystal Structure of Mycobacterium tuberculosis MenB, a Key Enzym... -

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Basic information

Entry
Database: PDB / ID: 1q52
TitleCrystal Structure of Mycobacterium tuberculosis MenB, a Key Enzyme in Vitamin K2 Biosynthesis
ComponentsmenB
KeywordsLYASE / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
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 / 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
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: 1.8 Å
AuthorsTruglio, J.J. / Theis, K. / Feng, Y. / Gajda, R. / Machutta, C. / Tonge, P.J. / Kisker, C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal structure of Mycobacterium tuberculosis MenB, a key enzyme in vitamin K2 biosynthesis.
Authors: Truglio, J.J. / Theis, K. / Feng, Y. / Gajda, R. / Machutta, C. / Tonge, P.J. / Kisker, C.
History
DepositionAug 5, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: menB
B: menB
C: menB
D: menB
E: menB
F: menB
G: menB
H: menB
I: menB
J: menB
K: menB
L: menB


Theoretical massNumber of molelcules
Total (without water)416,78312
Polymers416,78312
Non-polymers00
Water53,7572984
1
A: menB
B: menB
C: menB
D: menB
E: menB
F: menB


Theoretical massNumber of molelcules
Total (without water)208,3926
Polymers208,3926
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34740 Å2
ΔGint-179 kcal/mol
Surface area50460 Å2
MethodPISA
2
G: menB
H: menB
I: menB
J: menB
K: menB
L: menB


Theoretical massNumber of molelcules
Total (without water)208,3926
Polymers208,3926
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33820 Å2
ΔGint-171 kcal/mol
Surface area50610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.375, 139.432, 142.027
Angle α, β, γ (deg.)90.00, 97.29, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains 2 biologically active hexamers

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Components

#1: Protein
menB


Mass: 34731.938 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: O06414, UniProt: P9WNP5*PLUS, 1,4-dihydroxy-2-naphthoyl-CoA synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2984 / 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: 42.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: dioxane, ammonium sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.5-2 %dioxane1reservoir
21.2-1.3 Mammonium sulfate1reservoir
30.1 MMES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 10, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 312176
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 50 Å / % possible obs: 97.9 % / Num. measured all: 1210072 / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
BEASTphasing
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.114 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21861 15654 5 %RANDOM
Rwork0.19538 ---
all0.19749 ---
obs0.19749 312176 97.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.313 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2--0.06 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25503 0 0 2984 28487
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02126151
X-RAY DIFFRACTIONr_angle_refined_deg1.7941.92635458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.94353216
X-RAY DIFFRACTIONr_chiral_restr0.1350.23723
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0220694
X-RAY DIFFRACTIONr_nbd_refined0.2130.213426
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.22788
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2360.265
X-RAY DIFFRACTIONr_mcbond_it1.1941.516019
X-RAY DIFFRACTIONr_mcangle_it1.981225534
X-RAY DIFFRACTIONr_scbond_it3.098310132
X-RAY DIFFRACTIONr_scangle_it4.8044.59924
LS refinement shellResolution: 1.803→1.849 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.322 1031
Rwork0.286 19920
Refinement
*PLUS
Lowest resolution: 50 Å / Rfactor Rfree: 0.218 / Rfactor Rwork: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.6

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