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- PDB-6d34: Apo Crystal Structure of TerC, a Terfestatin Biosynthesis Enzyme -

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Basic information

Entry
Database: PDB / ID: 6d34
TitleApo Crystal Structure of TerC, a Terfestatin Biosynthesis Enzyme
ComponentsTerC
KeywordsBIOSYNTHETIC PROTEIN / NADPH reductase / natural products
Function / homologySnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / ISOPROPYL ALCOHOL / TerC
Function and homology information
Biological speciesStreptomyces (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.2Oct 4, 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 / 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: TerC
B: TerC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0875
Polymers39,9062
Non-polymers1803
Water3,675204
1
A: TerC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1344
Polymers19,9531
Non-polymers1803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TerC


Theoretical massNumber of molelcules
Total (without water)19,9531
Polymers19,9531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.721, 31.020, 101.258
Angle α, β, γ (deg.)90.000, 130.660, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 56 through 69 or resid 71 through 119 or resid 121 through 186))
21(chain B and (resid 56 through 69 or resid 71 through 119 or resid 121 through 186))

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
11ALAALAGLYGLY(chain A and (resid 56 through 69 or resid 71 through 119 or resid 121 through 186))AA56 - 6956 - 69
12ARGARGVALVAL(chain A and (resid 56 through 69 or resid 71 through 119 or resid 121 through 186))AA71 - 11971 - 119
13GLYGLYSERSER(chain A and (resid 56 through 69 or resid 71 through 119 or resid 121 through 186))AA121 - 186121 - 186
21ALAALAGLYGLY(chain B and (resid 56 through 69 or resid 71 through 119 or resid 121 through 186))BB56 - 6956 - 69
22ARGARGVALVAL(chain B and (resid 56 through 69 or resid 71 through 119 or resid 121 through 186))BB71 - 11971 - 119
23GLYGLYSERSER(chain B and (resid 56 through 69 or resid 71 through 119 or resid 121 through 186))BB121 - 186121 - 186

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Components

#1: Protein TerC


Mass: 19953.242 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 (E. coli) / References: UniProt: A0A3B6UEU1*PLUS
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.76 Å3/Da / Density % sol: 55.51 % / Description: long rods
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% v/v 2-propanol, 100 mM HEPES pH 7.5, 30% w/v PEG 3350, 50 mM sodium chloride

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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: Nov 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.8→38.408 Å / Num. obs: 30175 / % possible obs: 99.3 % / Redundancy: 5.556 % / Biso Wilson estimate: 23.55 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.136 / Rrim(I) all: 0.15 / Χ2: 0.99 / Net I/σ(I): 8.97 / Num. measured all: 167645
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.95.5371.391.1947560.6311.54198.3
1.9-2.045.5840.7392.3145550.8510.81999.7
2.04-2.25.6010.4773.742250.9170.5399.6
2.2-2.415.6050.3165.3639290.9670.3599.5
2.41-2.695.60.1988.0335200.9840.2299.5
2.69-3.15.590.13111.5731720.9920.14599.4
3.1-3.85.5490.06620.1726680.9970.07399.4
3.8-5.345.4870.04529.0621170.9990.04999.3
5.34-38.4085.1270.04230.4412330.9980.04697.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(1.13rc1_2954)refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ebt

3ebt


Resolution: 2.1→38.408 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.68
RfactorNum. reflection% reflection
Rfree0.2277 1257 6.61 %
Rwork0.1904 --
obs0.193 19007 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 162.87 Å2 / Biso mean: 42.2757 Å2 / Biso min: 20.93 Å2
Refinement stepCycle: final / Resolution: 2.1→38.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2035 0 36 204 2275
Biso mean--69.57 43.44 -
Num. residues----263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032113
X-RAY DIFFRACTIONf_angle_d0.5562857
X-RAY DIFFRACTIONf_chiral_restr0.043310
X-RAY DIFFRACTIONf_plane_restr0.003372
X-RAY DIFFRACTIONf_dihedral_angle_d18.797760
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1532X-RAY DIFFRACTION12.145TORSIONAL
12B1532X-RAY DIFFRACTION12.145TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.18410.38141410.299619412082100
2.1841-2.28350.35561290.2671931206099
2.2835-2.40390.25331340.23081963209799
2.4039-2.55440.26211390.215219512090100
2.5544-2.75160.24731400.19819472087100
2.7516-3.02840.24481410.20419772118100
3.0284-3.46640.21061430.175919752118100
3.4664-4.36630.19081420.147819942136100
4.3663-38.41420.17811480.166320712219100

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