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- PDB-1pqw: Putative enoyl reductase domain of polyketide synthase -

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Basic information

Entry
Database: PDB / ID: 1pqw
TitlePutative enoyl reductase domain of polyketide synthase
Componentspolyketide synthase
KeywordsOXIDOREDUCTASE / Rossmann fold / Dimer / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


(phenol)carboxyphthiodiolenone synthase / phthiocerol biosynthetic process / phenolic phthiocerol biosynthetic process / polyketide synthase complex / Actinobacterium-type cell wall biogenesis / DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process ...(phenol)carboxyphthiodiolenone synthase / phthiocerol biosynthetic process / phenolic phthiocerol biosynthetic process / polyketide synthase complex / Actinobacterium-type cell wall biogenesis / 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 / cytosol / cytoplasm
Similarity search - Function
Zinc-binding dehydrogenase / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / : / : / Polyketide synthase dehydratase domain / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain ...Zinc-binding dehydrogenase / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / : / : / Polyketide synthase dehydratase domain / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / PKS_KR / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / Ketosynthase family 3 (KS3) domain profile. / 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 / GroES-like superfamily / Phosphopantetheine attachment site / Thiolase-like / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phenolphthiocerol/phthiocerol polyketide synthase subunit C
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.66 Å
AuthorsGogos, A. / Mu, H. / Shapiro, L. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Putative enoyl reductase domain of polyketide synthase
Authors: Gogos, A. / Mu, H. / Shapiro, L.
History
DepositionJun 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn ...audit_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_conn.ptnr1_auth_comp_id ..._audit_author.identifier_ORCID / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: polyketide synthase
B: polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0123
Polymers41,9722
Non-polymers401
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-18 kcal/mol
Surface area15760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.830, 78.391, 81.604
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein polyketide synthase /


Mass: 20985.963 Da / Num. of mol.: 2 / Fragment: PUTATIVE ENOYL REDUCTASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: CDC1551 / Plasmid: pSMT3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P96202
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.66 Å3/Da / Density % sol: 53.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, isopropanol calcium chloride, Tris, NADPH , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97917, 0.97942, 0.96864
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 1, 2003
RadiationMonochromator: SI / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979171
20.979421
30.968641
ReflectionResolution: 2.66→17.97 Å / Num. all: 24404 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 27.7 Å2 / Limit h max: 26 / Limit h min: 0 / Limit k max: 29 / Limit k min: 0 / Limit l max: 30 / Limit l min: -30 / Observed criterion F max: 1143178.44 / Observed criterion F min: 4 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 25.8
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 6 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 15 / Rsym value: 0.16 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.66→17.97 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1204 4.9 %random
Rwork0.197 ---
obs-24404 97.9 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 24.7164 Å2 / ksol: 0.348675 e/Å3
Displacement parametersBiso max: 67.52 Å2 / Biso mean: 27.68 Å2 / Biso min: 6.58 Å2
Baniso -1Baniso -2Baniso -3
1-3.8 Å20 Å20 Å2
2---1.57 Å20 Å2
3----2.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.25 Å
Luzzati d res high-2.66
Refinement stepCycle: LAST / Resolution: 2.66→17.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2633 0 1 141 2775
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg22.7
X-RAY DIFFRACTIONx_torsion_impr_deg0.81
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.66-2.780.2531404.50.22229440.0213133308498.4
2.78-2.920.3121705.50.23229180.0243131308898.6
2.92-3.10.31315350.22628910.0253090304498.5
3.1-3.340.2681474.80.21429250.0223131307298.1
3.34-3.680.1831294.20.19729320.0163124306198
3.68-4.20.1891665.50.17228740.0153109304097.8
4.2-5.270.1931615.30.16628690.0153115303097.3
5.27-17.970.2271384.60.20328470.0193116298595.8
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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