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- PDB-4myy: Structure of a class 2 docking domain complex from modules CurG a... -

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Basic information

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


DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / oxidoreductase activity / plasma membrane / cytoplasm
Similarity search - Function
: / Class 2 C-terminal docking domain / : / Beta-ketoacyl synthase-like, N-terminal / CurL-like, PKS C-terminal / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH ...: / Class 2 C-terminal docking domain / : / Beta-ketoacyl synthase-like, N-terminal / CurL-like, PKS C-terminal / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, enoylreductase domain / Enoylreductase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / GroES-like superfamily / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Biological speciesMoorea producens 3L (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CurG, CurH fusion protein
B: CurG, CurH fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9495
Polymers18,6612
Non-polymers2883
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-64 kcal/mol
Surface area10400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.752, 36.752, 187.257
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 CurG, CurH fusion protein / Polyketide synthase module / Zn-dependent oxidoreductase/polyketide synthase module


Mass: 9330.586 Da / Num. of mol.: 2
Fragment: CurG, C-terminal docking domain, UNP residues 1554-1583, CurH N-terminal docking domain, UNP residues 1-44
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moorea producens 3L (bacteria) / Gene: LYNGBM3L_74500,LYNGBM3L_74480 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F4Y429, UniProt: F4Y428
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 122 / 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: 1.96 Å3/Da / Density % sol: 37.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 3M Ammonium Sulfate and 8% Glycerol, pH 7.5, 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: Aug 22, 2011
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: 1.68→50 Å / Num. all: 17279 / Num. obs: 17279 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Rsym value: 0.061
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 11 % / Num. unique all: 1640 / Rsym value: 0.72 / % possible all: 96.1

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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: 1.68→31.85 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.45 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24802 882 5.1 %RANDOM
Rwork0.1948 ---
all0.1974 17705 --
obs0.1974 16316 97.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.572 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.22 Å20 Å2
2--0.22 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.68→31.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1265 0 15 122 1402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191288
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2262.0171720
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7295163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9728.51954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37715287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.279152
X-RAY DIFFRACTIONr_chiral_restr0.0720.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02884
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.1312.979655
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.0984.715814
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7363.801633
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.7077.0442039
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: 1.681→1.725 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 71 -
Rwork0.232 1112 -
obs--94.87 %
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)
17.6722-5.4899-3.623217.69524.17154.8351-0.02130.0168-0.2691-0.0017-0.12870.867-0.087-0.31760.15010.0458-0.03670.01110.0818-0.00640.1099-14.8372.426-8.345
24.2520.9081-0.19668.8293-3.78392.60730.00660.27720.1164-0.1751-0.03620.2880.05930.01970.02960.0703-0.03880.00290.0655-0.03920.1329-3.4132.935-20.915
30.6553-0.22050.26747.0069-8.1879.5684-0.03550.23070.0534-0.3023-0.1246-0.12680.35730.16450.16010.1080.02380.02040.18160.02470.11396.73413.447-31.293
46.5253-6.48450.15819.05030.00332.2345-0.0906-0.01430.32480.09190.0348-0.3082-0.1913-0.10470.05580.04270.0050.0030.0444-0.02220.1199-1.36615.165-16.271
54.39561.216-0.273812.6459-5.31535.48040.19880.1378-0.0858-0.1874-0.11410.4045-0.10520.1902-0.08470.0503-0.03150.00010.0561-0.01630.128311.42614.701-18.158
613.5342-7.2434-4.33795.32661.71441.9060.0736-0.2862-0.15030.0255-0.08620.0616-0.11770.15840.01260.19490.0018-0.02430.0969-0.03250.09310.04510.452-3.949
712.1782-8.343-7.49078.37285.98754.8915-0.17580.01580.04360.18490.14530.0730.15830.02650.03050.1236-0.05220.05750.11030.00760.1007-15.7158.4264.522
82.0971-3.55961.00137.1646-3.77074.43210.05990.0434-0.0799-0.09470.06990.1379-0.0871-0.1644-0.12980.1088-0.09180.00420.11350.01280.1717-9.5510.369-13.751
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 12
2X-RAY DIFFRACTION2A13 - 31
3X-RAY DIFFRACTION3A39 - 59
4X-RAY DIFFRACTION4A60 - 82
5X-RAY DIFFRACTION5B-2 - 12
6X-RAY DIFFRACTION6B13 - 31
7X-RAY DIFFRACTION7B39 - 59
8X-RAY DIFFRACTION8B60 - 81

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