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- PDB-4ln9: Crystal structure of the dehydratase domain from the terminal mod... -

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Basic information

Entry
Database: PDB / ID: 4ln9
TitleCrystal structure of the dehydratase domain from the terminal module of the rifamycin polyketide synthase
ComponentsRifamycin polyketide synthase
KeywordsLYASE / DOUBLE HOTDOG FOLD / DEHYDRATION OF POLYKETIDE INTERMEDIATE / MODULE 10 OF RIFAMYCIN POLYKETIDE SYNTHASE
Function / homology
Function and homology information


phosphopantetheine binding / antibiotic biosynthetic process / transferase activity
Similarity search - Function
Polyketide synthase dehydratase / : / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain ...Polyketide synthase dehydratase / : / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Thiol Ester Dehydrase; Chain A / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / 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 / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesAmycolatopsis mediterranei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsGay, D.C. / You, Y.-O. / Cane, D. / Keatinge-Clay, A.T.
CitationJournal: Biochemistry / Year: 2013
Title: Structure and stereospecificity of the dehydratase domain from the terminal module of the rifamycin polyketide synthase.
Authors: Gay, D. / You, Y.O. / Keatinge-Clay, A. / Cane, D.E.
History
DepositionJul 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2Sep 20, 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 / 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: Rifamycin polyketide synthase
B: Rifamycin polyketide synthase


Theoretical massNumber of molelcules
Total (without water)68,2962
Polymers68,2962
Non-polymers00
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-13 kcal/mol
Surface area24340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.180, 77.180, 97.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Rifamycin polyketide synthase / RifE / Rifamycin polyketide synthase / type 1


Mass: 34148.172 Da / Num. of mol.: 2 / Fragment: DEHYDRATASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis mediterranei (bacteria) / Gene: rifE / Plasmid: pET28-a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O54593, 6-deoxyerythronolide-B synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.47 Å3/Da / Density % sol: 50.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 1.1 M sodium citrate, 0.1 M HEPES pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.2131 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 29, 2011
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2131 Å / Relative weight: 1
ReflectionResolution: 1.82→39.5 Å / Num. all: 58168 / Num. obs: 58168 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rsym value: 0.075 / Net I/σ(I): 10.6
Reflection shellResolution: 1.82→1.92 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2 / Rsym value: 0.807 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EL6

3el6


Resolution: 1.82→39.5 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.566 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25361 2931 5.1 %RANDOM
Rwork0.21144 ---
obs0.21353 55103 99.14 %-
all-58168 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.12 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.82→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4134 0 0 310 4444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0194225
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7591.9695778
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8955553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58922.045176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29715601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.91547
X-RAY DIFFRACTIONr_chiral_restr0.0660.2668
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0213279
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
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: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 205 -
Rwork0.382 4134 -
obs--99.7 %

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