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- PDB-6nd7: The crystal structure of TerB co-crystallized with polyporic acid -

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Basic information

Entry
Database: PDB / ID: 6nd7
TitleThe crystal structure of TerB co-crystallized with polyporic acid
ComponentsTerB Oxidoreductase
KeywordsOXIDOREDUCTASE / NADPH reductase / natural products
Function / homologyNAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily / ISOPROPYL ALCOHOL / Chem-KJG / Chem-NDP / TerB Oxidoreductase
Function and homology information
Biological speciesStreptomyces (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.36 Å
AuthorsClinger, J.A. / Elshahawi, S.I. / Zhang, Y. / Hall, R.P. / Liu, Y. / Thorson, J.S. / Phillips Jr., G.N.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115261 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA217255 United States
CitationJournal: To Be Published
Title: Structure and Function of Terfestatin Biosynthesis Enzymes TerB and TerC
Authors: Clinger, J.A. / Elshahawi, S.I. / Zhang, Y. / Hall, R.P. / Liu, Y. / Miller, M.D. / Thorson, J.S. / Phillips Jr., G.N.
History
DepositionDec 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 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

Downloads & links

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Assembly

Deposited unit
A: TerB Oxidoreductase
B: TerB Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,96114
Polymers73,1802
Non-polymers2,78012
Water14,124784
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-22 kcal/mol
Surface area23460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.498, 80.991, 139.955
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein TerB Oxidoreductase


Mass: 36590.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces (bacteria) / Strain: Streptomyces sp LC 6-2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3B6UEU0*PLUS

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Non-polymers , 5 types, 796 molecules

#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-KJG / 2~3~,2~6~-dihydroxy[1~1~,2~1~:2~4~,3~1~-terphenyl]-2~2~,2~5~-dione


Mass: 292.285 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H12O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


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


Mass: 18.015 Da / Num. of mol.: 784 / 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: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1:1 6mg/mL TerB protein 3mM polyporic acid in 33% isopropyl to 25% PEG 3350, 200 mM NaCl, 100mM HEPES, pH 7.5. Cryoprotected with 20% glycerol addition to mother liquor

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033, 1.319
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0331
21.3191
ReflectionResolution: 1.25→47.422 Å / Num. obs: 292990 / % possible obs: 82.9 % / Redundancy: 2.08 % / Biso Wilson estimate: 23.158 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.068 / Χ2: 1.026 / Net I/σ(I): 7.93 / Num. measured all: 609294 / Scaling rejects: 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) all% possible allCC1/2
1.25-1.291.2281.7720.367432.44225.7
1.29-1.321.741.2040.52116871.59145.90.227
1.32-1.361.8240.9420.73145941.24658.80.321
1.36-1.41.8810.7371193850.97780.50.476
1.4-1.452.0840.531.5216650.69992.70.678
1.45-1.52.1850.3592.24211100.47293.40.837
1.5-1.552.1050.2493.16202940.32993.60.904
1.55-1.622.1220.1834.15197530.24194.10.946
1.62-1.692.2040.145.41191020.18394.90.965
1.69-1.772.1670.1056.9182270.138950.978
1.77-1.872.1150.0818.79174650.10695.80.985
1.87-1.982.1420.06611.1166440.08696.40.988
1.98-2.122.2170.05613.44155420.07395.80.99
2.12-2.292.1180.0514.81145510.06596.40.992
2.29-2.512.140.04516.46134730.059970.992
2.51-2.82.2420.04218.12121990.05596.80.993
2.8-3.232.1130.04118.97107520.05496.80.993
3.23-3.962.1690.03920.7890080.05196.70.993
3.96-5.62.2050.03921.6369700.05196.60.994
5.6-47.4222.1940.03821.3938260.0596.50.994

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassificationNB
PHENIX(1.14_3260)refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SIRAS / Resolution: 1.36→47.422 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.04
RfactorNum. reflection% reflection
Rfree0.1468 6859 5 %
Rwork0.1161 --
obs0.1176 137194 95.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 128.69 Å2 / Biso mean: 23.9414 Å2 / Biso min: 9.27 Å2
Refinement stepCycle: final / Resolution: 1.36→47.422 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4739 0 323 804 5866
Biso mean--32.69 42.27 -
Num. residues----620
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.36-1.37550.33561810.31833429361077
1.3755-1.39160.31632050.29023911411687
1.3916-1.40860.31242180.24884155437393
1.4086-1.42640.26982230.23024224444793
1.4264-1.44520.25272240.20734275449996
1.4452-1.4650.22762240.18054260448495
1.465-1.48590.2092260.17174287451396
1.4859-1.50810.21172260.16534299452595
1.5081-1.53170.2032260.15854307453396
1.5317-1.55680.20192250.14614281450696
1.5568-1.58370.16472290.12314338456796
1.5837-1.61240.17512250.11434290451596
1.6124-1.64350.14372280.10944324455296
1.6435-1.6770.15622290.1034356458597
1.677-1.71350.14212300.09964355458597
1.7135-1.75330.15622300.09914387461797
1.7533-1.79720.1422310.09434379461097
1.7972-1.84580.13542300.09754366459697
1.8458-1.90010.13772300.09644383461397
1.9001-1.96140.13032330.09274428466198
1.9614-2.03150.13912330.09414413464697
2.0315-2.11290.14692320.09464418465098
2.1129-2.2090.12192350.09274467470298
2.209-2.32550.12732360.09124481471798
2.3255-2.47120.11752360.09314470470699
2.4712-2.6620.1242380.09854523476199
2.662-2.92980.13552390.10324551479099
2.9298-3.35370.13462400.10944561480199
3.3537-4.22490.13252450.1074641488699
4.2249-47.45070.15592520.15484776502898

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