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- PDB-5kp7: Crystal Structure of the Curacin Biosynthetic Pathway HMG Synthas... -

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Basic information

Entry
Database: PDB / ID: 5kp7
TitleCrystal Structure of the Curacin Biosynthetic Pathway HMG Synthase in Complex with Holo Donor-ACP
Components
  • CurB
  • CurD
KeywordsTRANSFERASE / HMG Synthase / Acyl Carrier Protein / enzyme-ACP complex
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA synthase / hydroxymethylglutaryl-CoA synthase activity / acetyl-CoA metabolic process
Similarity search - Function
Hydroxymethylglutaryl-coenzyme A synthase, N-terminal / Hydroxymethylglutaryl-coenzyme A synthase, C-terminal domain / Hydroxymethylglutaryl-coenzyme A synthase N terminal / Hydroxymethylglutaryl-coenzyme A synthase C terminal / ACP-like / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Thiolase-like / Phosphopantetheine attachment site ...Hydroxymethylglutaryl-coenzyme A synthase, N-terminal / Hydroxymethylglutaryl-coenzyme A synthase, C-terminal domain / Hydroxymethylglutaryl-coenzyme A synthase N terminal / Hydroxymethylglutaryl-coenzyme A synthase C terminal / ACP-like / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
4'-PHOSPHOPANTETHEINE / CurD / CurB
Similarity search - Component
Biological speciesMoorea producens 3L (bacteria)
Lyngbya majuscula (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMaloney, F.P. / Smith, J.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01-DK042303 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01-CA108874 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Anatomy of the beta-branching enzyme of polyketide biosynthesis and its interaction with an acyl-ACP substrate.
Authors: Maloney, F.P. / Gerwick, L. / Gerwick, W.H. / Sherman, D.H. / Smith, J.L.
History
DepositionJul 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Sep 21, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CurD
B: CurB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3575
Polymers60,8072
Non-polymers5503
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-39 kcal/mol
Surface area19810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.117, 101.117, 104.595
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-872-

HOH

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Components

#1: Protein CurD / Hydroxymethylglutaryl-CoA synthase


Mass: 49241.680 Da / Num. of mol.: 1 / Mutation: K344A, Q345A, Q347A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moorea producens 3L (bacteria) / Gene: LYNGBM3L_74540 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: F4Y432, hydroxymethylglutaryl-CoA synthase
#2: Protein CurB


Mass: 11565.290 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lyngbya majuscula (bacteria) / Gene: curB / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6DNF1
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.78 Å3/Da / Density % sol: 55.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 10% PEG 8000, 120 mM (NH4)2SO4, 1X MMT pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 6, 2014
RadiationMonochromator: crystal monochromator and K-B pair of biomorph mirrors
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.6→87.57 Å / Num. obs: 81779 / % possible obs: 100 % / Redundancy: 19.8 % / Biso Wilson estimate: 23.9 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.116 / Net I/σ(I): 16.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KP5 and 5KP6

5kp5

5kp6


Resolution: 1.6→87.57 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.974 / SU B: 2.859 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.063
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1668 4031 4.9 %RANDOM
Rwork0.1511 ---
obs0.1518 77704 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 96.42 Å2 / Biso mean: 34.237 Å2 / Biso min: 17.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.1 Å20 Å2
2--0.21 Å2-0 Å2
3----0.67 Å2
Refinement stepCycle: final / Resolution: 1.6→87.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3813 0 31 341 4185
Biso mean--57.77 44.19 -
Num. residues----489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193953
X-RAY DIFFRACTIONr_bond_other_d0.0020.023772
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.9795339
X-RAY DIFFRACTIONr_angle_other_deg0.96438684
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7185496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.94423.876178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64115694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3241528
X-RAY DIFFRACTIONr_chiral_restr0.1590.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024486
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02902
X-RAY DIFFRACTIONr_mcbond_it0.8481.6261969
X-RAY DIFFRACTIONr_mcbond_other0.8461.6231968
X-RAY DIFFRACTIONr_mcangle_it1.4592.4282461
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 313 -
Rwork0.293 5678 -
all-5991 -
obs--99.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.79741.38150.44432.38480.32561.61470.2702-0.2836-0.11650.4693-0.1958-0.1577-0.05550.2237-0.07440.2255-0.0083-0.03570.22240.01220.12340.62331.89215.85
20.5553-0.0510.1060.6371-0.21980.88690.06270.001-0.1549-0.0165-0.0005-0.00640.09230.0685-0.06220.12180.037-0.01280.1386-0.00510.134429.6428.4262.078
30.3868-0.3370.3090.8094-0.28750.981-0.0457-0.1992-0.12160.16940.12280.06390.0327-0.0713-0.07710.16430.04450.02170.20780.06040.125722.82729.0824.346
40.5290.1288-0.07810.5831-0.24820.87970.0244-0.0841-0.17610.05070.0212-0.07950.09540.1363-0.04560.14550.0466-0.01970.16910.01510.151535.71726.44112.68
51.86150.7330.06231.8991-0.18161.40830.03370.0539-0.1792-0.0044-0.0163-0.23660.06170.2646-0.01750.1020.01670.03940.2212-0.01990.136346.0337.358-5.465
614.0775-5.4692.56526.1754-2.09442.2290.1767-0.95960.16070.4883-0.17650.0940.0794-0.1048-0.00020.33520.060.01770.3908-0.08360.023324.72144.98644.451
710.3993-1.1473-0.84043.5937-0.44382.199-0.168-0.58090.6460.16190.1792-0.4644-0.1850.2385-0.01120.21070.0981-0.05140.139-0.11930.238131.09851.44338.814
812.11311.6775-2.35773.48790.04082.7255-0.0105-0.55380.08650.33610.07050.00180.1811-0.2063-0.060.21050.03180.01990.24750.00280.004922.8739.55135.319
95.82252.0342.99145.79484.65725.2301-0.0999-0.47220.660.0492-0.04730.2272-0.3087-0.52550.14720.20340.11620.07160.2256-0.0330.141217.80547.25132.45
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 33
2X-RAY DIFFRACTION2A34 - 193
3X-RAY DIFFRACTION3A194 - 286
4X-RAY DIFFRACTION4A287 - 379
5X-RAY DIFFRACTION5A380 - 419
6X-RAY DIFFRACTION6B1 - 23
7X-RAY DIFFRACTION7B24 - 35
8X-RAY DIFFRACTION8B36 - 56
9X-RAY DIFFRACTION9B57 - 78

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