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- PDB-3t89: Crystal structure of Escherichia coli MenB, the 1,4-dihydroxy-2-n... -

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Basic information

Entry
Database: PDB / ID: 3t89
TitleCrystal structure of Escherichia coli MenB, the 1,4-dihydroxy-2-naphthoyl-CoA synthase in vitamin K2 biosynthesis
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 / bicarbonate binding / menaquinone biosynthetic process / 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, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 ...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, conserved site / Enoyl-CoA hydratase/isomerase signature. / 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
MALONATE ION / 1,4-dihydroxy-2-naphthoyl-CoA synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.949 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
D: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
E: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
F: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,94921
Polymers192,5076
Non-polymers1,44115
Water8,089449
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37110 Å2
ΔGint-132 kcal/mol
Surface area45530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.509, 133.997, 153.357
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 32084.572 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: b2262 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0ABU0, 1,4-dihydroxy-2-naphthoyl-CoA synthase
#2: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 2.04 Å3/Da / Density % sol: 39.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG3350, 200 mM sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING 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: Mar 16, 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: 1.949→50 Å / Num. obs: 113570 / % possible obs: 98.2 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.101 / Χ2: 0.96 / Net I/σ(I): 8.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-1.986.50.53754540.693195.8
1.98-2.026.50.45455490.739196.3
2.02-2.066.60.39155270.796196.8
2.06-2.16.60.3455250.854197.1
2.1-2.156.60.2955840.928197.6
2.15-2.26.60.24956240.961197.6
2.2-2.256.70.22855660.946197.9
2.25-2.316.70.21456460.937198
2.31-2.386.80.18756420.979198.3
2.38-2.466.90.17556290.924198.4
2.46-2.5470.1656621.03198.5
2.54-2.6570.13856761.062198.5
2.65-2.777.10.12156921.023198.8
2.77-2.917.10.11156951.125198.6
2.91-3.17.10.09857301.005199.1
3.1-3.337.10.08857611.119199.1
3.33-3.677.10.07857671.116199.2
3.67-4.26.90.0758071.101199.3
4.2-5.296.80.06858950.954199.6
5.29-506.90.06561390.817199.5

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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 3H02

3h02


Resolution: 1.949→42.884 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.45 / σ(F): 1.34 / Phase error: 22.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2186 5691 5.01 %
Rwork0.1856 --
obs0.1873 113502 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.341 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso max: 68.9 Å2 / Biso mean: 27.1458 Å2 / Biso min: 11.92 Å2
Baniso -1Baniso -2Baniso -3
1-10.7064 Å2-0 Å2-0 Å2
2---3.9913 Å2-0 Å2
3----6.7151 Å2
Refinement stepCycle: LAST / Resolution: 1.949→42.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11750 0 96 449 12295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512074
X-RAY DIFFRACTIONf_angle_d0.83616300
X-RAY DIFFRACTIONf_chiral_restr0.0581771
X-RAY DIFFRACTIONf_plane_restr0.0032154
X-RAY DIFFRACTIONf_dihedral_angle_d15.3994295
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9485-1.97070.30371670.22243395356293
1.9707-1.99390.29872010.22523482368397
1.9939-2.01820.27081920.2193498369096
2.0182-2.04370.26071680.21133481364997
2.0437-2.07060.27141960.20753522371897
2.0706-2.0990.2482040.20493469367397
2.099-2.1290.25971770.20383567374497
2.129-2.16070.26581850.19113540372598
2.1607-2.19450.24882150.18423545376098
2.1945-2.23050.22972050.18323500370598
2.2305-2.26890.21411630.18633578374198
2.2689-2.31020.25461810.1933576375798
2.3102-2.35460.24111610.18893586374798
2.3546-2.40270.23661850.19333597378298
2.4027-2.45490.25011840.19553577376198
2.4549-2.5120.24631800.19483589376998
2.512-2.57480.23212080.19423577378598
2.5748-2.64450.22761930.18593593378699
2.6445-2.72230.2441980.18163584378299
2.7223-2.81010.24231770.18983614379199
2.8101-2.91050.2291890.19473624381399
2.9105-3.0270.24362000.1933622382299
3.027-3.16480.22372040.18363608381299
3.1648-3.33150.21292000.18313650385099
3.3315-3.54020.20981900.18823645383599
3.5402-3.81340.1931820.17483709389199
3.8134-4.19680.16031770.15673683386099
4.1968-4.80340.16672060.153137233929100
4.8034-6.04910.17641840.180237683952100
6.0491-42.89420.212190.19563909412899

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