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- PDB-5kp6: Crystal Structure of the Curacin Biosynthetic Pathway HMG Synthas... -

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Basic information

Entry
Database: PDB / ID: 5kp6
TitleCrystal Structure of the Curacin Biosynthetic Pathway HMG Synthase in Complex with Apo Donor-ACP
Components
  • CurB
  • CurD
KeywordsTRANSFERASE / HMG synthase / enzyme-ACP complex
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA synthase / hydroxymethylglutaryl-CoA synthase activity / farnesyl diphosphate biosynthetic process, mevalonate pathway / 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 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / 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 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / 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
Biological speciesMoorea producens 3L (bacteria)
Lyngbya majuscula (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: CurD
B: CurB


Theoretical massNumber of molelcules
Total (without water)60,6942
Polymers60,6942
Non-polymers00
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-18 kcal/mol
Surface area19820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.312, 101.312, 104.593
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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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: 11452.133 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.8 Å3/Da / Density % sol: 56.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 6% PEG 8000, 60 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: 2.05→87.74 Å / Num. obs: 39403 / % possible obs: 100 % / Redundancy: 19.5 % / Biso Wilson estimate: 37 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.117 / Net I/σ(I): 19.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KP5

5kp5


Resolution: 2.05→87.74 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 6.995 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.131
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1932 1926 4.9 %RANDOM
Rwork0.1553 ---
obs0.1572 37444 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 120.56 Å2 / Biso mean: 49.469 Å2 / Biso min: 27.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20.24 Å20 Å2
2--0.47 Å2-0 Å2
3----1.54 Å2
Refinement stepCycle: final / Resolution: 2.05→87.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3747 0 0 214 3961
Biso mean---55.86 -
Num. residues----482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193813
X-RAY DIFFRACTIONr_bond_other_d0.0010.023656
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.9755141
X-RAY DIFFRACTIONr_angle_other_deg0.77638416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.655479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.28723.977171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33915677
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5991527
X-RAY DIFFRACTIONr_chiral_restr0.0840.2566
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024328
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02859
X-RAY DIFFRACTIONr_mcbond_it2.1083.4851925
X-RAY DIFFRACTIONr_mcbond_other2.0983.4831924
X-RAY DIFFRACTIONr_mcangle_it2.9965.2112401
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 159 -
Rwork0.278 2706 -
all-2865 -
obs--99.83 %
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)
13.52493.03361.58983.20761.26861.74450.3437-0.2609-0.0090.5392-0.26450.00640.1430.1218-0.07920.1799-0.0065-0.02360.15240.01850.094240.825431.8915.4941
20.78070.09630.13360.7196-0.30980.98490.08430.0547-0.1841-0.0471-0.0066-0.02510.10170.0871-0.07780.05140.0322-0.0150.0576-0.01250.057129.667328.0166-0.5285
30.8624-0.29320.28750.8952-0.09440.8021-0.0077-0.1527-0.14250.11820.09360.04720.0782-0.0092-0.08590.08390.03210.00260.08320.04530.041226.101926.114918.6211
42.03510.84-0.63973.2633-1.51662.82350.0316-0.0446-0.14680.2416-0.0815-0.3591-0.16280.3940.04990.05160.0129-0.01060.1892-0.01370.054547.544935.32128.4127
53.01420.28960.31591.7462-0.04450.94470.03970.0436-0.0914-0.0132-0.0237-0.19490.06030.1398-0.0160.04130.00470.02230.1531-0.01690.042745.524537.7798-5.5978
67.9959-3.6229-0.76872.0840.50823.07280.1197-0.81590.10330.01650.0974-0.0449-0.16150.0639-0.21710.18380.011-0.00580.3023-0.03950.028119.96646.436744.482
76.11-3.0055.47526.7971.11557.79410.2836-0.25580.66630.0681-0.4917-0.78120.4508-0.31540.2080.48340.0931-0.04080.8555-0.07470.276332.751444.43844.6141
82.3483-2.59531.8558.14252.83046.0034-0.0103-0.1146-0.0351-0.30360.2008-0.0881-0.2583-0.0034-0.19050.16860.0203-0.01220.0849-0.04260.158929.182951.441836.2867
97.55873.03661.634610.18775.36457.8382-0.2181-0.37760.19050.01190.1955-0.5196-0.2090.22380.02270.10240.0698-0.04420.1469-0.0440.066531.834143.98232.8928
1011.286-3.5924-3.60589.0871.23231.31520.0695-0.7961-0.1290.5141-0.0930.05290.1174-0.00050.02350.3392-0.09430.0150.56470.05530.013319.240138.579837.3627
118.55432.2076-0.60768.170.52585.66040.021-0.50950.1960.2924-0.06250.311-0.312-0.53820.04150.10240.07090.02650.1634-0.01260.019615.926441.906729.1633
1211.1539-0.13810.87712.64541.43660.86710.1119-0.33880.51080.1131-0.17360.06060.0426-0.12660.06170.19450.07230.05350.1433-0.06750.090418.969150.198635.2545
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 33
2X-RAY DIFFRACTION2A34 - 145
3X-RAY DIFFRACTION3A146 - 348
4X-RAY DIFFRACTION4A349 - 377
5X-RAY DIFFRACTION5A378 - 419
6X-RAY DIFFRACTION6B1 - 14
7X-RAY DIFFRACTION7B15 - 27
8X-RAY DIFFRACTION8B28 - 33
9X-RAY DIFFRACTION9B34 - 43
10X-RAY DIFFRACTION10B44 - 55
11X-RAY DIFFRACTION11B56 - 65
12X-RAY DIFFRACTION12B66 - 78

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