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- PDB-4myz: Structure of a class 2 docking domain complex from modules CurK a... -

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Basic information

Entry
Database: PDB / ID: 4myz
TitleStructure of a class 2 docking domain complex from modules CurK and CurL of the curacin A polyketide synthase
ComponentsCurK, CurL fusion protein
KeywordsPROTEIN BINDING / Protein-protein interaction / fusion protein
Function / homology
Function and homology information


: / S-adenosylmethionine-dependent methyltransferase activity / acyltransferase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / oxidoreductase activity / metal ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3430 / : / Beta-ketoacyl synthase-like, N-terminal / Polyketide synthase, methyltransferase domain / Methyltransferase in polyketide synthase (PKS) enzymes. / Zinc-binding dehydrogenase / : / Methyltransferase type 12 / Methyltransferase domain / : ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3430 / : / Beta-ketoacyl synthase-like, N-terminal / Polyketide synthase, methyltransferase domain / Methyltransferase in polyketide synthase (PKS) enzymes. / Zinc-binding dehydrogenase / : / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / PKS_KR / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / GroES-like superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Phosphopantetheine attachment site / Thiolase-like / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Helix non-globular / Special / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Biological speciesMoorea producens 3L (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWhicher, J.R. / Smaga, S.S. / Smith, J.L.
CitationJournal: Chem.Biol. / Year: 2013
Title: Cyanobacterial polyketide synthase docking domains: a tool for engineering natural product biosynthesis.
Authors: Whicher, J.R. / Smaga, S.S. / Hansen, D.A. / Brown, W.C. / Gerwick, W.H. / Sherman, D.H. / Smith, J.L.
History
DepositionSep 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Aug 9, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CurK, CurL fusion protein
B: CurK, CurL fusion protein
C: CurK, CurL fusion protein


Theoretical massNumber of molelcules
Total (without water)25,6363
Polymers25,6363
Non-polymers00
Water2,882160
1
A: CurK, CurL fusion protein
B: CurK, CurL fusion protein


Theoretical massNumber of molelcules
Total (without water)17,0912
Polymers17,0912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-34 kcal/mol
Surface area6560 Å2
MethodPISA
2
C: CurK, CurL fusion protein

C: CurK, CurL fusion protein


Theoretical massNumber of molelcules
Total (without water)17,0912
Polymers17,0912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2750 Å2
ΔGint-33 kcal/mol
Surface area7150 Å2
MethodPISA
3
A: CurK, CurL fusion protein
B: CurK, CurL fusion protein
C: CurK, CurL fusion protein

A: CurK, CurL fusion protein
B: CurK, CurL fusion protein
C: CurK, CurL fusion protein


Theoretical massNumber of molelcules
Total (without water)51,2736
Polymers51,2736
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12610 Å2
ΔGint-109 kcal/mol
Surface area16670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.889, 59.532, 52.867
Angle α, β, γ (deg.)90.00, 124.87, 90.00
Int Tables number5
Space group name H-MC121
DetailsChains A and B form a dimer within the asymmetric unit. Chain C forms a dimer across the crystallographic 2-fold with Chain C in the adjacent asymmetric unit.

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Components

#1: Protein CurK, CurL fusion protein / Polyketide synthase module


Mass: 8545.486 Da / Num. of mol.: 3
Fragment: CurK C-terminal docking domain, UNP residues 2203-2232, CurL N-terminal docking domain, UNP residues 1-38
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moorea producens 3L (bacteria) / Gene: LYNGBM3L_74450, LYNGBM3L_74440 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F4Y425, UniProt: F4Y424
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 3.4M Ammonium sulfate and 0.1M Bis-Tris propane pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 7, 2012
RadiationMonochromator: double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 35689 / Num. obs: 35689 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.045
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.65 / % possible all: 98.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→26.45 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.106 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20276 1768 5 %RANDOM
Rwork0.17767 ---
obs0.179 33881 96.58 %-
all-36890 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.172 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å20.18 Å2
2--0.53 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.5→26.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1193 0 0 160 1353
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191209
X-RAY DIFFRACTIONr_bond_other_d0.0010.021270
X-RAY DIFFRACTIONr_angle_refined_deg1.1942.0441619
X-RAY DIFFRACTIONr_angle_other_deg0.70332947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7585151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.57727.11552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.68415273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.206156
X-RAY DIFFRACTIONr_chiral_restr0.0680.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021278
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02200
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_it1.641.878604
X-RAY DIFFRACTIONr_mcbond_other1.6331.874603
X-RAY DIFFRACTIONr_mcangle_it2.7952.778746
X-RAY DIFFRACTIONr_mcangle_other2.4073.04744
X-RAY DIFFRACTIONr_scbond_it2.4272.305605
X-RAY DIFFRACTIONr_scbond_other2.5152.478606
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8593.579871
X-RAY DIFFRACTIONr_long_range_B_refined8.70319.0361526
X-RAY DIFFRACTIONr_long_range_B_other8.42517.7061457
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.503→1.542 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 131 -
Rwork0.261 2462 -
obs--95.93 %
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)
12.96682.68440.36434.91571.91114.87660.0641-0.2799-0.07180.0249-0.0473-0.25710.00960.3566-0.01690.0536-0.0149-0.02670.20890.00190.035616.98517.39-5.745
212.00853.70442.23082.8908-0.03861.3122-0.0406-0.34480.48150.2057-0.11550.1205-0.2002-0.03850.15610.1057-0.0151-0.02710.1588-0.05480.078817.61830.376-6.648
34.13991.59120.69212.29040.22064.09730.013-0.06640.38160.13690.0127-0.0477-0.51410.025-0.02570.1067-0.0075-0.01580.1265-0.02740.069116.11530.213-15.212
42.04881.47541.78461.63720.9382.97570.1797-0.0537-0.01090.1186-0.1206-0.15240.04040.0846-0.05910.1063-0.0254-0.02520.206-0.02410.083323.78721.693-9.345
52.0151-0.3891-0.80236.74022.7023.26720.0846-0.269-0.01120.0881-0.02830.03410.0370.2162-0.05630.04550.0019-0.02990.16920.00730.02948.09112.7561.067
62.27091.9253-0.81525.3556-2.31131.74980.04480.276-0.1716-0.1892-0.0837-0.15280.153-0.01690.03890.07530.012-0.02890.1915-0.01520.0316-1.5538.613-6.056
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 30
2X-RAY DIFFRACTION2A50 - 72
3X-RAY DIFFRACTION3B6 - 30
4X-RAY DIFFRACTION4B48 - 73
5X-RAY DIFFRACTION5C6 - 31
6X-RAY DIFFRACTION6C48 - 71

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