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- PDB-3t88: Crystal structure of Escherichia coli MenB in complex with substr... -

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Basic information

Entry
Database: PDB / ID: 3t88
TitleCrystal structure of Escherichia coli 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 / 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
TRIETHYLENE GLYCOL / o-succinylbenzoyl-N-coenzyme A / 1,4-dihydroxy-2-naphthoyl-CoA synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 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)199,90230
Polymers192,5076
Non-polymers7,39424
Water14,610811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44690 Å2
ΔGint-208 kcal/mol
Surface area46540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.493, 141.791, 89.122
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 6 molecules ABCDEF

#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

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Non-polymers , 5 types, 835 molecules

#2: Chemical
ChemComp-S0N / o-succinylbenzoyl-N-coenzyme A


Mass: 954.663 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C32H45N8O20P3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 811 / 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: 2.31 Å3/Da / Density % sol: 46.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG3350, 200 mM sodium chloride, 100 mM Bis-Tris, pH 6.5, 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: 1.998→50 Å / Num. obs: 120517 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.163 / Χ2: 2.722 / Net I/σ(I): 6.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.0360.67459010.942199.1
2.03-2.076.30.58359690.999199.4
2.07-2.116.50.52658980.993199.4
2.11-2.156.60.45559431.064199.7
2.15-2.26.70.39459371.126199.7
2.2-2.256.80.37659871.162199.8
2.25-2.316.90.34659691.236199.9
2.31-2.376.90.31559891.33199.9
2.37-2.4470.28759871.3921100
2.44-2.527.10.26660031.4691100
2.52-2.617.20.23760021.6021100
2.61-2.717.30.21160181.8671100
2.71-2.847.30.19160262.0131100
2.84-2.997.20.1760262.3641100
2.99-3.177.20.14960392.8821100
3.17-3.427.20.13560583.7391100
3.42-3.767.20.12460675.481100
3.76-4.317.10.11161166.9081100
4.31-5.436.80.10461657.0161100
5.43-507.10.09864177.3291100

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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: 1.998→44.797 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.49 / σ(F): 1.34 / Phase error: 18.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.195 6053 5.03 %
Rwork0.1554 --
obs0.1573 120444 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.485 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso max: 68.85 Å2 / Biso mean: 22.4121 Å2 / Biso min: 9.89 Å2
Baniso -1Baniso -2Baniso -3
1--4.1081 Å2-0 Å20 Å2
2---2.8576 Å20 Å2
3---6.9657 Å2
Refinement stepCycle: LAST / Resolution: 1.998→44.797 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12927 0 480 811 14218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813748
X-RAY DIFFRACTIONf_angle_d1.20618589
X-RAY DIFFRACTIONf_chiral_restr0.0691907
X-RAY DIFFRACTIONf_plane_restr0.0052436
X-RAY DIFFRACTIONf_dihedral_angle_d21.6525313
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 (%)
1.998-2.02070.28061880.20073456364491
2.0207-2.04440.26431970.19913749394699
2.0444-2.06940.24072150.18473764397999
2.0694-2.09560.23471840.17453770395499
2.0956-2.12310.21621890.17253806399599
2.1231-2.15220.22881900.16237583948100
2.1522-2.1830.21882090.163437603969100
2.183-2.21550.2221930.163938003993100
2.2155-2.25020.23812190.168637743993100
2.2502-2.2870.22882050.16437933998100
2.287-2.32650.21112030.164537873990100
2.3265-2.36880.22162150.156837713986100
2.3688-2.41430.21091970.158238274024100
2.4143-2.46360.21531880.161638033991100
2.4636-2.51720.22342100.164137793989100
2.5172-2.57570.22292090.157538104019100
2.5757-2.64010.21931920.151338224014100
2.6401-2.71150.19061780.152138334011100
2.7115-2.79130.21152080.15638164024100
2.7913-2.88140.21312070.16438424049100
2.8814-2.98430.19882040.161638094013100
2.9843-3.10380.20121820.155838384020100
3.1038-3.2450.21062090.156938314040100
3.245-3.4160.2121970.159638664063100
3.416-3.630.15532090.149938414050100
3.63-3.91010.15081940.13738824076100
3.9101-4.30330.15632070.125138754082100
4.3033-4.92530.14712220.118838904112100
4.9253-6.20280.15522180.153939274145100
6.2028-44.80790.18122150.162641124327100

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