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- PDB-6wf4: Crystal Structure of TerC Co-crystallized with Polyporic Acid -

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Basic information

Entry
Database: PDB / ID: 6wf4
TitleCrystal Structure of TerC Co-crystallized with Polyporic Acid
ComponentsTerfestatin Biosyntheis Enzyme C
KeywordsBIOSYNTHETIC PROTEIN / natural products / jellyroll / Structural Genomics / PSI-Biology / Enzyme Discovery for Natural Product Biosynthesis / NatPro
Function / homologySnoaL-like domain / SnoaL-like domain / NTF2-like domain superfamily / ISOPROPYL ALCOHOL / Chem-U07 / TerC
Function and homology information
Biological speciesStreptomyces sp. RM-5-8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.97 Å
AuthorsClinger, J.A. / Miller, M.D. / Hall, R.E. / Zhang, Y. / Elshahawi, S.I. / Thorson, J.S. / Van Lanen, S.G. / Phillips Jr., G.N. / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To be published
Title: Structural and functional characterization of two cooperative enzymes responsible for the stability of p-terphenyls.
Authors: Clinger, J.A. / Zhang, Y. / Liu, Y. / Miller, M.D. / Hall, R.E. / Van Lanen, S.G. / Phillips Jr., G.N. / Thorson, J.S. / Elshahawri, S.I.
History
DepositionApr 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
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: Terfestatin Biosyntheis Enzyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3083
Polymers19,9531
Non-polymers3542
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.176, 97.176, 29.393
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-372-

HOH

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Components

#1: Protein Terfestatin Biosyntheis Enzyme C


Mass: 19953.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. RM-5-8 (bacteria) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A3B6UEU1
#2: Chemical ChemComp-U07 / (2~5~S)-2~3~,2~5~,2~6~-trihydroxy[1~1~,2~1~:2~4~,3~1~-terphenyl]-2~2~(2~5~H)-one


Mass: 294.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H14O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.01 Å3/Da / Density % sol: 38.74 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6 / Details: 20% v/v 2-Propanol, 0.1M MES, 20%w/v PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.96→48.59 Å / Num. obs: 11538 / % possible obs: 99.2 % / Redundancy: 14.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.026 / Rrim(I) all: 0.106 / Net I/σ(I): 15.2 / Num. measured all: 171889 / Scaling rejects: 111
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.96-2.014.50.79532277120.460.3580.881.588.4
8.77-48.5915.30.047235115410.0120.04846.699.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.16 Å48.59 Å
Translation4.16 Å48.59 Å

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHASER2.8.2phasing
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
DIALS2.1.2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D34

6d34


Resolution: 1.97→31.81 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.27
RfactorNum. reflection% reflection
Rfree0.2362 508 4.57 %
Rwork0.2009 --
obs0.2024 11107 96.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 169.72 Å2 / Biso mean: 50.5429 Å2 / Biso min: 16.98 Å2
Refinement stepCycle: final / Resolution: 1.97→31.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1005 0 34 74 1113
Biso mean--55.02 43.48 -
Num. residues----130
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.97-2.170.39561110.32412434254590
2.17-2.480.28421260.27032667279397
2.48-3.120.2221380.22092680281899
3.13-31.810.2051330.157928182951100

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