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- PDB-7vo4: Pimaricin type I PKS thioesterase domain (apo Pim TE) -

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Basic information

Entry
Database: PDB / ID: 7vo4
TitlePimaricin type I PKS thioesterase domain (apo Pim TE)
ComponentsScnS4
KeywordsBIOSYNTHETIC PROTEIN / thioesterase / type I thioesterase / pimaricin / polyketide synthase thioesterase domain
Function / homology
Function and homology information


toxin biosynthetic process / macrolide biosynthetic process / DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
Polyketide synthase extender module SpnB, Rossmann fold domain / Polyketide synthase, thioesterase domain / Thioesterase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Thioesterase / Thioesterase domain / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain ...Polyketide synthase extender module SpnB, Rossmann fold domain / Polyketide synthase, thioesterase domain / Thioesterase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Thioesterase / Thioesterase domain / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / 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 / 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. / PKS_KR / 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 / 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 hydrolase fold / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Biological speciesStreptomyces chattanoogensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBai, L. / Zhou, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: Acs Catalysis / Year: 2022
Title: Structural and Mechanistic Insights into Chain Release of the Polyene PKS Thioesterase Domain
Authors: Zhou, Y. / Tao, W. / Qi, Z. / Wei, J. / Shi, T. / Kang, Q. / Zheng, J. / Zhao, Y. / Bai, L.
History
DepositionOct 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ScnS4
B: ScnS4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8943
Polymers61,7982
Non-polymers961
Water1,11762
1
A: ScnS4
hetero molecules

B: ScnS4


Theoretical massNumber of molelcules
Total (without water)61,8943
Polymers61,7982
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y+1/2,-z1
Buried area1700 Å2
ΔGint-32 kcal/mol
Surface area20830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.946, 58.867, 85.043
Angle α, β, γ (deg.)90.000, 101.070, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ScnS4


Mass: 30898.953 Da / Num. of mol.: 2 / Fragment: pimaricin type I PKS thioesterase domain (Pim TE)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces chattanoogensis (bacteria)
Gene: scnS4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F1CLA7
#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.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.06 Å3/Da / Density % sol: 40.43 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M HEPES pH 7.5, 18%-25% w/v Polyethylene glycol 6000, 5% v/v (+/-)-2-Methyl-2,4-pentanediol
PH range: 7.5-9.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.1→83.46 Å / Num. obs: 29474 / % possible obs: 99.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.043 / Rrim(I) all: 0.08 / Χ2: 0.998 / Net I/σ(I): 6.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.142.90.460.77114260.7710.3090.5570.98195.8
2.14-2.183.10.46114470.7680.3080.5571.05397.6
2.18-2.223.10.39814360.8150.2640.4791.04699.2
2.22-2.263.20.38114900.8330.2520.4591.04999.4
2.26-2.313.10.31614550.880.2150.3841.02499.2
2.31-2.373.40.31214840.8760.1990.3721.03699.7
2.37-2.423.50.26314400.9280.1640.3111.04799.9
2.42-2.493.50.22714820.9380.1420.2681.08199.5
2.49-2.563.50.18814700.9580.1170.2221.01599.6
2.56-2.653.40.16614790.9610.1050.1961.05999.8
2.65-2.743.30.14114780.9710.0910.1691.02399.7
2.74-2.853.10.11214740.980.0750.1351.00399.6
2.85-2.983.50.10114530.9870.0630.1190.99399.7
2.98-3.143.50.08115010.9910.050.0961.00899.7
3.14-3.333.50.06414610.9930.040.0750.96799.6
3.33-3.593.30.05114830.9950.0330.0610.96299.5
3.59-3.953.40.04315000.9960.0270.0510.9799.3
3.95-4.523.50.03714820.9970.0230.0440.94499.6
4.52-5.73.20.03615020.9970.0230.0430.88399.3
5.7-9.93.30.03215310.9970.0210.0390.82998.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2h7x

2h7x


Resolution: 2.1→83.46 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.905 / SU B: 5.661 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2503 1465 4.9 %RANDOM
Rwork0.2042 ---
obs0.2064 28306 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.51 Å2 / Biso mean: 30.106 Å2 / Biso min: 12.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å2-0 Å20.63 Å2
2---0.53 Å20 Å2
3---0.15 Å2
Refinement stepCycle: final / Resolution: 2.1→83.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3597 0 5 62 3664
Biso mean--32.5 27.03 -
Num. residues----492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193664
X-RAY DIFFRACTIONr_bond_other_d0.0020.023486
X-RAY DIFFRACTIONr_angle_refined_deg1.871.9734992
X-RAY DIFFRACTIONr_angle_other_deg1.13237953
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9085483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.59622.117137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.65315540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2961536
X-RAY DIFFRACTIONr_chiral_restr0.1210.2600
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214132
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02796
LS refinement shellResolution: 2.1→2.151 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.368 104 -
Rwork0.32 2083 -
obs--99.91 %

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