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- PDB-6d2v: Apo Structure of TerB, an NADP Dependent Oxidoreductase in the Te... -

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Basic information

Entry
Database: PDB / ID: 6d2v
TitleApo Structure of TerB, an NADP Dependent Oxidoreductase in the Terfestatin Biosynthesis Pathway
ComponentsTerB Oxidoreductase
KeywordsOXIDOREDUCTASE / NADPH reductase / natural products
Function / homologyNAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily / nucleotide binding / Chem-NDP / THIOCYANATE ION / TerB Oxidoreductase
Function and homology information
Biological speciesStreptomyces (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.901 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) United States
National Institutes of Health/National Cancer Institute (NIH/NCI) 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
DepositionApr 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)70,6489
Polymers68,9122
Non-polymers1,7367
Water8,575476
1
A: TerB Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3305
Polymers34,4561
Non-polymers8744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TerB Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3184
Polymers34,4561
Non-polymers8623
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-45 kcal/mol
Surface area24670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.516, 80.598, 139.518
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 20 or resid 22...
21(chain B and (resid 2 through 20 or resid 22...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUALAALA(chain A and (resid 2 through 20 or resid 22...AA2 - 2010 - 28
12ALAALAPHEPHE(chain A and (resid 2 through 20 or resid 22...AA22 - 5230 - 60
13TRPTRPALAALA(chain A and (resid 2 through 20 or resid 22...AA54 - 11862 - 126
14TYRTYRVALVAL(chain A and (resid 2 through 20 or resid 22...AA120 - 248128 - 256
15GLYGLYSERSER(chain A and (resid 2 through 20 or resid 22...AA-7 - 3071 - 315
16GLUGLUTHRTHR(chain A and (resid 2 through 20 or resid 22...AA253 - 276261 - 284
17VALVALPROPRO(chain A and (resid 2 through 20 or resid 22...AA287 - 306295 - 314
21GLUGLUALAALA(chain B and (resid 2 through 20 or resid 22...BB2 - 2010 - 28
22ALAALAPHEPHE(chain B and (resid 2 through 20 or resid 22...BB22 - 5230 - 60
23METMETPROPRO(chain B and (resid 2 through 20 or resid 22...BB1 - 3069 - 314
24METMETPROPRO(chain B and (resid 2 through 20 or resid 22...BB1 - 3069 - 314
25TYRTYRVALVAL(chain B and (resid 2 through 20 or resid 22...BB120 - 248128 - 256
26TYRTYRLEULEU(chain B and (resid 2 through 20 or resid 22...BB250 - 251258 - 259
27GLUGLUTHRTHR(chain B and (resid 2 through 20 or resid 22...BB253 - 276261 - 284
28ARGARGCYSCYS(chain B and (resid 2 through 20 or resid 22...BB278 - 285286 - 293
29VALVALPROPRO(chain B and (resid 2 through 20 or resid 22...BB287 - 306295 - 314

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Components

#1: Protein TerB Oxidoreductase


Mass: 34455.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces (bacteria) / Strain: RM. 5-8 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL 21 / References: UniProt: A0A3B6UEU0*PLUS
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 2.25 Å3/Da / Density % sol: 45.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Potassium thiocyanate, 30% w/v PEG Monomethyl ether 2000, 50 mM NaCl, 10 mM HEPES buffer pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.9→47.346 Å / Num. obs: 52609 / % possible obs: 99.7 % / Redundancy: 7.374 % / Biso Wilson estimate: 24.76 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.089 / Χ2: 1.027 / Net I/σ(I): 18.51 / Num. measured all: 387913
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.9-2.027.3480.7163.1461523843383730.9190.76999.3
2.02-2.157.4610.4445.0658763788978760.9570.47799.8
2.15-2.337.4550.2817.8255062739273860.9820.30299.9
2.33-2.557.4580.18511.3450737681268030.990.19999.9
2.55-2.857.4470.11816.9146014619061790.9950.12799.8
2.85-3.297.4020.06926.8140511548454730.9980.07499.8
3.29-4.027.3120.03943.2634250469046840.9990.04299.9
4.02-5.677.1880.02953.526517369336890.9990.03299.9
5.67-47.3466.7740.02556.63145362175214610.02798.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.12_2829)refinement
XDSdata reduction
XDSdata scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.901→38.716 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.44
RfactorNum. reflection% reflection
Rfree0.1978 2630 5 %
Rwork0.1613 --
obs0.1632 52578 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.06 Å2 / Biso mean: 34.9591 Å2 / Biso min: 12.37 Å2
Refinement stepCycle: final / Resolution: 1.901→38.716 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4785 0 167 476 5428
Biso mean--26.57 37.89 -
Num. residues----621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055114
X-RAY DIFFRACTIONf_angle_d0.8536997
X-RAY DIFFRACTIONf_chiral_restr0.05761
X-RAY DIFFRACTIONf_plane_restr0.005956
X-RAY DIFFRACTIONf_dihedral_angle_d13.7071910
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3378X-RAY DIFFRACTION10.895TORSIONAL
12B3378X-RAY DIFFRACTION10.895TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9009-1.93550.28451350.23742555269098
1.9355-1.97270.26421370.211426132750100
1.9727-2.0130.24611370.19725832720100
2.013-2.05670.26381350.194725712706100
2.0567-2.10460.24471360.189325892725100
2.1046-2.15720.19321380.173426082746100
2.1572-2.21550.24821360.162225942730100
2.2155-2.28070.20391380.158926072745100
2.2807-2.35430.19651380.150626262764100
2.3543-2.43840.20471380.156326332771100
2.4384-2.53610.1961370.161426012738100
2.5361-2.65140.22691380.157926142752100
2.6514-2.79120.21821390.162926392778100
2.7912-2.9660.20831380.165926252763100
2.966-3.19490.21351380.175426262764100
3.1949-3.51620.19841410.164926752816100
3.5162-4.02460.1521410.138326662807100
4.0246-5.06880.15071420.125227152857100
5.0688-38.72430.19211480.17412808295699

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