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- PDB-2qo3: Crystal Structure of [KS3][AT3] didomain from module 3 of 6-deoxy... -

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Basic information

Entry
Database: PDB / ID: 2qo3
TitleCrystal Structure of [KS3][AT3] didomain from module 3 of 6-deoxyerthronolide B synthase
ComponentsEryAII Erythromycin polyketide synthase modules 3 and 4
KeywordsTRANSFERASE / ketosynthase / acyltransferase / Phosphopantetheine
Function / homology
Function and homology information


erythronolide synthase activity / 6-deoxyerythronolide-B synthase / macrolide biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / oxidoreductase activity
Similarity search - Function
Alpha-Beta Plaits - #3290 / Erythronolide synthase, docking / Erythronolide synthase, docking domain superfamily / Erythronolide synthase, docking / : / : / Polyketide synthase extender module SpnB, Rossmann fold domain / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Polyketide synthase, docking domain ...Alpha-Beta Plaits - #3290 / Erythronolide synthase, docking / Erythronolide synthase, docking domain superfamily / Erythronolide synthase, docking / : / : / Polyketide synthase extender module SpnB, Rossmann fold domain / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / PKS_PP_betabranch / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / 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 / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, enoylreductase domain / Enoylreductase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / 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 / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-CER / 6-deoxyerythronolide-B synthase / Erythronolide synthase EryA2
Similarity search - Component
Biological speciesSaccharopolyspora erythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsKhosla, C. / Cane, E.D. / Tang, Y. / Chen, Y.A. / Kim, C.Y.
Citation
Journal: Chem.Biol. / Year: 2007
Title: Structural and mechanistic analysis of protein interactions in module 3 of the 6-deoxyerythronolide B synthase
Authors: Tang, Y. / Chen, Y.A. / Kim, C.Y. / Cane, E.D. / Khosla, C.
#1: Journal: Chem.Biol. / Year: 2007
Title: Structure-based dissociation of a type I polyketide synthase module
Authors: Chen, Y.A. / Cane, E.D. / Khosla, C.
#2: Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: The 2.7-Angstrom crystal structure of a 194-kDa homodimeric fragment of the 6-deoxyerythronolide B synthase
Authors: Tang, Y. / Kim, C.Y. / Mathews, I.I. / Cane, E.D. / Khosla, C.
#3: Journal: Biochemistry / Year: 2004
Title: Reconstituting modular activity from separated domains of 6-deoxyerythronolide B synthase
Authors: Kim, C.Y. / Alekseyev, V.Y. / Chen, Y.A. / Tang, Y. / Cane, E.D. / Khosla, C.
History
DepositionJul 19, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EryAII Erythromycin polyketide synthase modules 3 and 4
B: EryAII Erythromycin polyketide synthase modules 3 and 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,0188
Polymers193,3782
Non-polymers6406
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.203, 139.005, 102.342
Angle α, β, γ (deg.)90.00, 106.14, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 5 / Auth seq-ID: 30 - 900 / Label seq-ID: 5 - 875

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein EryAII Erythromycin polyketide synthase modules 3 and 4 / 6 Deoxyerythronolide B Synthase


Mass: 96689.180 Da / Num. of mol.: 2
Fragment: ketosynthase-acyltransferase didomain of didomain module 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Gene: eryAII / Plasmid: PAYC09 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: A4F7P0, UniProt: Q03132*PLUS, 6-deoxyerythronolide-B synthase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CER / (2S, 3R)-3-HYDROXY-4-OXO-7,10-TRANS,TRANS-DODECADIENAMIDE / CERULENIN


Mass: 225.284 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19NO3 / Comment: antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES pH7.0, 0.2M Li2SO4, 25% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 9, 2005 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 228717 / Num. obs: 228471 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 8.4
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 3.09 / Num. unique all: 6207 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→41.52 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.877 / SU B: 23.423 / SU ML: 0.243 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.817 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26806 3145 5.1 %RANDOM
Rwork0.21401 ---
obs0.21679 58910 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.862 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20.19 Å2
2---0.21 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.59→41.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12928 0 26 194 13148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02113198
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9421.95917941
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.67951732
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09422.796583
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.235151979
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.38815141
X-RAY DIFFRACTIONr_chiral_restr0.1330.22020
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210253
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2670.26436
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.28892
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2574
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.290.288
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3150.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9061.58789
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.497213685
X-RAY DIFFRACTIONr_scbond_it2.34734898
X-RAY DIFFRACTIONr_scangle_it3.934.54256
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
3440medium positional0.50.5
2925loose positional0.85
3440medium thermal0.772
2925loose thermal1.8510
LS refinement shellResolution: 2.595→2.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 204 -
Rwork0.225 4092 -
obs--95.21 %
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)
10.13090.0433-0.0551.3079-0.27290.30480.02180.0225-0.03660.0395-0.1008-0.1805-0.06410.0260.079-0.16360.0005-0.0336-0.05160.0057-0.103122.40526.33226.745
20.0344-0.1899-0.02131.44590.20990.10350.01040.0066-0.0020.0028-0.06790.19930.0573-0.00370.0575-0.1101-0.01770.0198-0.0546-0.0141-0.0783-12.642-26.67526.618
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA29 - 9084 - 883
2X-RAY DIFFRACTION2BB29 - 9084 - 883

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