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- PDB-4rpm: Crystal structure of the SAT domain from the non-reducing fungal ... -

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Basic information

Entry
Database: PDB / ID: 4rpm
TitleCrystal structure of the SAT domain from the non-reducing fungal polyketide synthase CazM with bound hexanoyl
ComponentsSAT domain from CazM
KeywordsTRANSFERASE
Function / homology
Function and homology information


secondary metabolite biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process
Similarity search - Function
Methyltransferase, fungal type, helix-turn-helix domain / Methyltransferase, Helix-turn-helix domain / Fatty acyl-coenzyme A reductase, NAD-binding domain / Male sterility protein / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. ...Methyltransferase, fungal type, helix-turn-helix domain / Methyltransferase, Helix-turn-helix domain / Fatty acyl-coenzyme A reductase, NAD-binding domain / Male sterility protein / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, dehydratase domain superfamily / 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. / 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 / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
HEXANOIC ACID / HEXANOYL-COENZYME A / Iterative polyketide synthase CazM
Similarity search - Component
Biological speciesChaetomium globosum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY STARTING FROM 4RO5 / Resolution: 1.4 Å
AuthorsWinter, J.M. / Cascio, D. / Sawaya, M.R. / Tang, Y.
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Biochemical and Structural Basis for Controlling Chemical Modularity in Fungal Polyketide Biosynthesis.
Authors: Winter, J.M. / Cascio, D. / Dietrich, D. / Sato, M. / Watanabe, K. / Sawaya, M.R. / Vederas, J.C. / Tang, Y.
History
DepositionOct 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SAT domain from CazM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5583
Polymers44,5761
Non-polymers9822
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.670, 52.360, 168.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SAT domain from CazM


Mass: 44576.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium globosum (fungus) / Strain: CBS 148.51 / Gene: cazM, CHGG_07645 / Plasmid: pHis8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2GWK9
#2: Chemical ChemComp-6NA / HEXANOIC ACID


Mass: 116.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O2
#3: Chemical ChemComp-HXC / HEXANOYL-COENZYME A


Mass: 865.677 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46N7O17P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAS PER THE AUTH THE SEQUENCE REPRESENTED BY UNP Q2GWK9 IS INCORRECT IN THIS REGION. THE AUTHORS ...AS PER THE AUTH THE SEQUENCE REPRESENTED BY UNP Q2GWK9 IS INCORRECT IN THIS REGION. THE AUTHORS RESEQUENCED THIS REGION AND FOUND AN EXTRA BASE CAUSING A DISCREPANCY BETWEEN THE AUTHORS SEQUENCE AND UNIPROT SEQ. THIS DISCREPANCY CAUSES THE ARTIFICIAL OCCURRENCE OF AN EXTRA INTRON IN THAT REGION. THIS ENTIRE REGION WAS RE-SEQUENCED BY THE AUTHORS USING CDNA AND THEY HAVE AN ACTIVE ENZYME AND THEIR SEQUENCE MATCHES TO THE 4RO5 CRYSTAL STRUCTURE AT 1.6A RESOLUTION. THE AUTHORS WILL DEPOSIT THE CORRECTED SEQUENCE SOON

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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: 2.25 Å3/Da / Density % sol: 45.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Tris HCl pH 7, 20% PEG 8000 and 1.4 mM hexanoyl-CoA, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.4→84.01 Å / Num. all: 79353 / Num. obs: 79353 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3.57 % / Biso Wilson estimate: 16.21 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Χ2: 1.069 / Net I/σ(I): 12.79
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.4-1.440.5392.01201775680196.6
1.44-1.470.422.72209485680198.6
1.47-1.520.3123.65199775489198.8
1.52-1.560.2554.41189575334198.5
1.56-1.620.2025.41184945214199.1
1.62-1.670.1736.69188985042199.2
1.67-1.740.1448.01182314901199.1
1.74-1.810.1159.81170424662198.7
1.81-1.890.09211.8151484476198.4
1.89-1.980.07914.94161244357199.2
1.98-2.090.06417.88150894126199.4
2.09-2.210.05420.42140703899199.4
2.21-2.370.04821.79122893632197.4
2.37-2.550.04523118233413198.5
2.55-2.80.04325.45113653170199
2.8-3.130.0426.69101082877198.6
3.13-3.610.03427.5882052500196.9
3.61-4.420.03229.6879072216198.8
4.42-6.260.03328.5455641692196.9
6.26-84.010.03927.983056993195.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: RIGID BODY STARTING FROM 4RO5
Starting model: PDB entry 4RO5

4ro5


Resolution: 1.4→84.01 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2044 7935 10 %RANDOM
Rwork0.1871 ---
obs0.1889 79350 98.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.7 Å2 / Biso mean: 22.6185 Å2 / Biso min: 10.57 Å2
Refinement stepCycle: LAST / Resolution: 1.4→84.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3013 0 16 185 3214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063136
X-RAY DIFFRACTIONf_angle_d1.0184272
X-RAY DIFFRACTIONf_chiral_restr0.068486
X-RAY DIFFRACTIONf_plane_restr0.005562
X-RAY DIFFRACTIONf_dihedral_angle_d11.3931156
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.41510.27332510.25862259251094
1.4151-1.43170.29732600.24682338259899
1.4317-1.44920.24012620.23642355261798
1.4492-1.46750.25312610.22462348260999
1.4675-1.48690.23632620.21762359262199
1.4869-1.50720.24372590.20442332259198
1.5072-1.52880.22772640.20262376264099
1.5288-1.55160.23122580.19762322258098
1.5516-1.57580.21852680.19952408267699
1.5758-1.60170.21582550.18752307256298
1.6017-1.62930.20582690.17932416268599
1.6293-1.65890.20432600.18012343260399
1.6589-1.69080.21462680.18632417268599
1.6908-1.72530.22822610.183523472608100
1.7253-1.76290.20832650.18462380264599
1.7629-1.80390.21952620.18492362262499
1.8039-1.8490.18432620.1812353261598
1.849-1.8990.21112640.17932380264499
1.899-1.95490.20672650.19022388265399
1.9549-2.0180.20212670.185924002667100
2.018-2.09010.19882670.18342401266899
2.0901-2.17380.1982690.18382423269299
2.1738-2.27270.21022650.17922381264699
2.2727-2.39260.17992600.18442348260896
2.3926-2.54250.2232660.19992391265799
2.5425-2.73880.21712680.18972414268299
2.7388-3.01440.23692720.19932443271599
3.0144-3.45060.20982660.20032401266797
3.4506-4.34740.18262750.17152475275099
4.3474-84.010.16872840.16912548283297
Refinement TLS params.Method: refined / Origin x: 27.5665 Å / Origin y: 29.6235 Å / Origin z: 19.9478 Å
111213212223313233
T0.0905 Å2-0.0118 Å2-0.0034 Å2-0.1114 Å20.0058 Å2--0.0942 Å2
L0.8679 °2-0.3121 °2-0.0671 °2-1.1032 °2-0.2976 °2--1.3556 °2
S-0.0094 Å °-0.0636 Å °-0.0444 Å °0.0367 Å °0.0058 Å °-0.0038 Å °-0.0041 Å °0.0493 Å °0.0006 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 395
2X-RAY DIFFRACTION1allA1 - 572
3X-RAY DIFFRACTION1allA179 - 685
4X-RAY DIFFRACTION1allA1 - 401
5X-RAY DIFFRACTION1allA1 - 402

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