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- PDB-5kp5: Crystal Structure of the Curacin Biosynthetic Pathway HMG Synthase -

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Basic information

Entry
Database: PDB / ID: 5kp5
TitleCrystal Structure of the Curacin Biosynthetic Pathway HMG Synthase
ComponentsCurD
KeywordsTRANSFERASE / HMG Synthase
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 / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMoorea producens 3L (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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

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Assembly

Deposited unit
A: CurD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3382
Polymers49,2421
Non-polymers961
Water2,810156
1
A: CurD
hetero molecules

A: CurD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6754
Polymers98,4832
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6380 Å2
ΔGint-62 kcal/mol
Surface area27230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.162, 101.162, 106.234
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 3.36 Å3/Da / Density % sol: 63.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 6% PEG 8000, 20 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: 2.1→87.61 Å / Num. obs: 37159 / % possible obs: 100 % / Redundancy: 19.5 % / Biso Wilson estimate: 51.1 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.112 / Net I/σ(I): 15.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YSL

1ysl


Resolution: 2.1→87.61 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.962 / SU B: 8.454 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.124
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1899 1826 4.9 %RANDOM
Rwork0.1585 ---
obs0.1601 35297 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 135.03 Å2 / Biso mean: 58.407 Å2 / Biso min: 35.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20.42 Å20 Å2
2--0.85 Å2-0 Å2
3----2.75 Å2
Refinement stepCycle: final / Resolution: 2.1→87.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3133 0 5 156 3294
Biso mean--117.34 63.99 -
Num. residues----403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193205
X-RAY DIFFRACTIONr_bond_other_d0.0010.023011
X-RAY DIFFRACTIONr_angle_refined_deg1.3621.9644327
X-RAY DIFFRACTIONr_angle_other_deg0.76336919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8225403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.38423.581148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48815545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6071524
X-RAY DIFFRACTIONr_chiral_restr0.080.2467
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023682
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02758
X-RAY DIFFRACTIONr_mcbond_it2.5544.2041615
X-RAY DIFFRACTIONr_mcbond_other2.554.2031614
X-RAY DIFFRACTIONr_mcangle_it3.5896.2882017
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 131 -
Rwork0.3 2586 -
all-2717 -
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)
11.14441.76720.73323.0070.63391.63690.29960.0375-0.14380.5545-0.0971-0.07980.11140.4105-0.20240.15210.02180.02370.1566-0.00440.180240.671131.960215.6323
20.3167-0.04950.35770.4929-0.33190.59790.11490.0546-0.0898-0.012-0.01290.02840.08220.1024-0.10190.10850.0454-0.01230.1343-0.03160.155930.063328.3846-0.3171
30.88291.20040.70371.88890.54631.3536-0.02480.07560.0037-0.0640.06940.10430.05350.2261-0.04460.09770.0766-0.01090.1260.00020.174231.01929.163.6886
40.6785-0.30220.22910.5957-0.28061.2968-0.0019-0.2508-0.09960.08110.13130.1498-0.0410.0145-0.12940.06820.01320.03550.13040.07630.100919.535929.525517.1572
50.2476-0.0047-0.02780.0953-0.06321.02270.0431-0.1013-0.08690.09380.08190.03410.04790.1198-0.12510.11510.07920.00040.14020.06730.135432.672525.92118.1075
61.35291.13020.18531.9108-0.38880.3556-0.05320.3099-0.1941-0.24740.0955-0.22590.0910.17-0.04230.06810.03270.06740.2536-0.07080.148146.261336.9663-5.8286
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 33
2X-RAY DIFFRACTION2A34 - 132
3X-RAY DIFFRACTION3A133 - 177
4X-RAY DIFFRACTION4A178 - 242
5X-RAY DIFFRACTION5A243 - 381
6X-RAY DIFFRACTION6A382 - 419

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