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- PDB-5kp8: Crystal Structure of the Curacin Biosynthetic Pathway HMG Synthas... -

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Basic information

Entry
Database: PDB / ID: 5kp8
TitleCrystal Structure of the Curacin Biosynthetic Pathway HMG Synthase in Complex with Acetyl 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 / ergosterol biosynthetic 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
Chem-6VG / 4'-PHOSPHOPANTETHEINE / CurD / CurB
Similarity search - Component
Biological speciesMoorea producens 3L (bacteria)
Lyngbya majuscula (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 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)61,4364
Polymers60,6782
Non-polymers7592
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-15 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.892, 100.892, 104.461
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein CurD / Hydroxymethylglutaryl-CoA synthase


Mass: 49225.617 Da / Num. of mol.: 1 / Fragment: unp residues 17-76 / Mutation: C114S, K368A, Q369A, Q371A
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: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS
#4: Chemical ChemComp-6VG / ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] ethanethioate


Mass: 400.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H25N2O8PS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.77 Å3/Da / Density % sol: 55.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 6% PEG 8000, 100 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: 1.9→87.38 Å / Num. obs: 48869 / % possible obs: 100 % / Redundancy: 19.5 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 16.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5KP5, 5KP6

5kp5

5kp6


Resolution: 1.9→87.38 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.968 / SU B: 5.387 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.182 2374 4.9 %RANDOM
Rwork0.157 ---
obs0.158 48869 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.12 Å20 Å2
2--0.25 Å20 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.9→87.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3805 0 45 219 4069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193943
X-RAY DIFFRACTIONr_bond_other_d0.0010.023763
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.9835318
X-RAY DIFFRACTIONr_angle_other_deg0.76738663
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5585491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.22923.898177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62615689
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5221528
X-RAY DIFFRACTIONr_chiral_restr0.080.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024468
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02896
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4052.3891958
X-RAY DIFFRACTIONr_mcbond_other1.4032.3881957
X-RAY DIFFRACTIONr_mcangle_it2.1763.5722445
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 153 -
Rwork0.24 3396 -
obs--100 %
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)
10.3910.202-0.4230.3317-0.27440.57860.0357-0.0943-0.01480.01190.0334-0.055-0.00210.1964-0.06910.10.0566-0.0230.2331-0.06260.149440.521832.893613.5174
20.62490.57520.21871.49310.77270.82910.05770.0181-0.0932-0.02420.0009-0.0150.09760.0477-0.05850.15050.0665-0.02760.1194-0.02130.127730.569320.5217-5.2378
30.1875-0.08840.08550.0767-0.05950.41310.0458-0.0032-0.03390.00960.04370.02360.04190.0568-0.08940.12760.0338-0.00980.1415-0.00760.122325.874330.78933.2657
40.0228-0.01840.07230.27640.11820.9323-0.0346-0.0547-0.01290.09740.11410.04380.0555-0.012-0.07950.15260.08250.01310.19650.05040.117221.19927.232923.7422
52.5758-0.8618-0.33611.92950.66191.5966-0.0192-0.186-0.04970.19580.0680.11440.2493-0.0331-0.04870.18120.09490.03190.17990.08990.058424.298822.346133.9036
60.18940.0813-0.10440.2173-0.03820.53160.0024-0.0486-0.03120.06080.06870.0070.08870.1226-0.0710.12740.0682-0.01640.15470.00740.116635.320625.993113.0744
70.8276-0.15050.18510.90390.06810.62060.01030.1317-0.0555-0.03520.0508-0.04940.02720.2091-0.06110.07410.03040.02670.2189-0.03750.109645.848937.205-5.579
85.4373-3.05561.40682.3378-1.18510.88530.046-0.38720.04650.1214-0.01540.06670.00190.0462-0.03070.16940.03080.02020.2001-0.05190.021221.852545.426644.1164
93.1479-0.66043.55916.3681-0.70954.03140.0327-0.1052-0.00720.2079-0.01970.06840.0363-0.0818-0.0130.09770.04020.02720.2346-0.02380.048533.874346.092845.1168
103.48130.3185-0.24818.64294.70672.6168-0.1609-0.020.23190.04550.315-0.22150.04390.1592-0.15410.1380.064-0.02150.1702-0.02010.069531.465646.886434.3537
116.68381.1967-2.99691.9909-0.87242.8751-0.0154-0.1850.10830.29230.1104-0.14880.1198-0.1914-0.09510.20460.04820.00960.2450.00450.038520.424639.094236.3152
123.18850.65481.27721.87311.34941.1982-0.094-0.32730.2643-0.11630.02080.0123-0.1032-0.10880.07320.16040.10050.03880.2508-0.01610.099117.548746.505832.4782
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 57
2X-RAY DIFFRACTION2A58 - 82
3X-RAY DIFFRACTION3A83 - 211
4X-RAY DIFFRACTION4A212 - 263
5X-RAY DIFFRACTION5A264 - 282
6X-RAY DIFFRACTION6A283 - 380
7X-RAY DIFFRACTION7A381 - 419
8X-RAY DIFFRACTION8B1 - 17
9X-RAY DIFFRACTION9B18 - 27
10X-RAY DIFFRACTION10B28 - 41
11X-RAY DIFFRACTION11B42 - 55
12X-RAY DIFFRACTION12B56 - 78

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