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- PDB-7scp: The crystal structure of ScoE in complex with intermediate -

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Basic information

Entry
Database: PDB / ID: 7scp
TitleThe crystal structure of ScoE in complex with intermediate
ComponentsScoE protein
KeywordsBIOSYNTHETIC PROTEIN / Iron/2-oxoglutarate dependent / Fe/2OG / isonitrile biosynthesis
Function / homology
Function and homology information


(R)-3-[(carboxymethyl)amino]fatty acid dioxygenase/decarboxylase / : / : / dioxygenase activity / metal ion binding
Similarity search - Function
TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily
Similarity search - Domain/homology
(3R)-3-(oxaloamino)butanoic acid / : / (3R)-3-[(carboxymethyl)amino]fatty acid oxygenase/decarboxylase
Similarity search - Component
Biological speciesStreptomyces coeruleorubidus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsCha, L. / Chen, J. / Zhou, J. / Chang, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM127588 United States
CitationJournal: Acs Catalysis / Year: 2022
Title: Deciphering the Reaction Pathway of Mononuclear Iron Enzyme-Catalyzed N-C Triple Bond Formation in Isocyanide Lipopeptide and Polyketide Biosynthesis
Authors: Chen, T.Y. / Zheng, Z. / Zhang, X. / Chen, J. / Cha, L. / Tang, Y. / Guo, Y. / Zhou, J. / Wang, B. / Liu, H.W. / Chang, W.C.
History
DepositionSep 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ScoE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,30819
Polymers39,0541
Non-polymers1,25418
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.820, 96.820, 69.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number77
Space group name H-MP42
Space group name HallP4c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/2
#3: y,-x,z+1/2
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-30-

ARG

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ScoE protein


Mass: 39053.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coeruleorubidus (bacteria)
Gene: ScoE / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A3B6UEU3

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Non-polymers , 5 types, 143 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-8S6 / (3R)-3-(oxaloamino)butanoic acid


Mass: 175.139 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H9NO5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.19 Å3/Da / Density % sol: 70.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD 0.03 M of each divalent cation 0.1 M MOPS/HEPES-Na pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97917 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 1.99→48.89 Å / Num. obs: 44184 / % possible obs: 99.4 % / Redundancy: 13.5 % / CC1/2: 0.999 / Net I/σ(I): 19.5
Reflection shellResolution: 1.99→2.04 Å / Num. unique obs: 3076 / CC1/2: 0.725

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Processing

Software
NameVersionClassification
PHENIXv1.18.2-3874refinement
XDSdata reduction
XDSdata scaling
PHENIXv1.18.2-3874phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L6X

6l6x


Resolution: 1.99→48.89 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.1406 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2534 2214 5.01 %
Rwork0.2273 41970 -
obs0.2293 44184 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.16 Å2
Refinement stepCycle: LAST / Resolution: 1.99→48.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2373 0 79 125 2577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00182494
X-RAY DIFFRACTIONf_angle_d0.44183350
X-RAY DIFFRACTIONf_chiral_restr0.0439355
X-RAY DIFFRACTIONf_plane_restr0.0042439
X-RAY DIFFRACTIONf_dihedral_angle_d8.58241485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.030.33641370.33862559X-RAY DIFFRACTION94.15
2.03-2.080.2961680.32862575X-RAY DIFFRACTION92.69
2.08-2.130.28251210.30742576X-RAY DIFFRACTION94.08
2.13-2.190.26661240.30622605X-RAY DIFFRACTION94.38
2.19-2.260.35751410.31412625X-RAY DIFFRACTION94.22
2.26-2.330.30231380.30732598X-RAY DIFFRACTION94.34
2.33-2.410.30611330.29562601X-RAY DIFFRACTION94.62
2.41-2.510.27171470.28472599X-RAY DIFFRACTION94.2
2.51-2.620.30111270.28072603X-RAY DIFFRACTION95.03
2.62-2.760.28951300.27672642X-RAY DIFFRACTION94.97
2.76-2.930.3071330.2552618X-RAY DIFFRACTION94.75
2.93-3.160.24871350.24242635X-RAY DIFFRACTION94.95
3.16-3.470.23241540.22162613X-RAY DIFFRACTION94.23
3.47-3.970.2171480.19162629X-RAY DIFFRACTION94.5
3.97-4.990.20491260.17022677X-RAY DIFFRACTION95.47
4.99-18.880.27341520.19832695X-RAY DIFFRACTION94.53
Refinement TLS params.Method: refined / Origin x: 25.6231916369 Å / Origin y: 44.7101356987 Å / Origin z: 3.84326626137 Å
111213212223313233
T0.243357574384 Å2-0.00133738031512 Å20.00804434620976 Å2-0.370435720279 Å2-0.0158347556138 Å2--0.201135468591 Å2
L1.28760910613 °20.0429028185491 °2-0.065843970923 °2-0.757879007368 °2-0.0083605510714 °2--1.37270139296 °2
S0.0139851236054 Å °0.159812304344 Å °-0.0435951718239 Å °0.0978181478745 Å °0.0260520055235 Å °0.0453790459026 Å °0.0582156873863 Å °-0.237434485165 Å °-0.0422025660059 Å °
Refinement TLS groupSelection details: all

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