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- PDB-8kif: The structure of MmaE with substrate -

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Basic information

Entry
Database: PDB / ID: 8kif
TitleThe structure of MmaE with substrate
ComponentsPutative dioxygenase
KeywordsOXIDOREDUCTASE / MmaE / Fe/2OG enzymes
Function / homology: / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily / : / dioxygenase activity / : / : / Putative dioxygenase
Function and homology information
Biological speciesMycobacterium marinum M (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsChen, J. / Zhou, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0901900 China
CitationJournal: Acs Catalysis / Year: 2024
Title: Variation in biosynthesis and metal-binding properties of isonitrile-containing peptides produced by Mycobacteria versus Streptomyces.
Authors: Chen, T.Y. / Chen, J. / Ruszczycky, M.W. / Hilovsky, D. / Hostetler, T. / Liu, X. / Zhou, J. / Chang, W.C.
History
DepositionAug 23, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Putative dioxygenase
A: Putative dioxygenase
C: Putative dioxygenase
D: Putative dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,63512
Polymers136,4314
Non-polymers1,2058
Water9,764542
1
B: Putative dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4093
Polymers34,1081
Non-polymers3012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4093
Polymers34,1081
Non-polymers3012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4093
Polymers34,1081
Non-polymers3012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4093
Polymers34,1081
Non-polymers3012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.822, 77.951, 99.833
Angle α, β, γ (deg.)82.814, 78.341, 75.588
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Putative dioxygenase


Mass: 34107.648 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum M (bacteria) / Gene: MMRN_02610 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2Z5Y839
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-VY9 / (3R)-3-(2-hydroxy-2-oxoethylamino)decanoic acid


Mass: 245.315 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H23NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / 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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium acetate trihydrate, 0.1 M Tris/HCl (pH 8.5), 30% Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.13→61.98 Å / Num. obs: 65034 / % possible obs: 93.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 31.74 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.5
Reflection shellResolution: 2.13→2.25 Å / Num. unique obs: 9227 / CC1/2: 0.851

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→24.48 Å / SU ML: 0.256 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.3736 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2325 3217 4.95 %
Rwork0.1806 61708 -
obs0.1831 64925 93.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.05 Å2
Refinement stepCycle: LAST / Resolution: 2.13→24.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8959 0 72 542 9573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089295
X-RAY DIFFRACTIONf_angle_d0.943312686
X-RAY DIFFRACTIONf_chiral_restr0.05771398
X-RAY DIFFRACTIONf_plane_restr0.00681646
X-RAY DIFFRACTIONf_dihedral_angle_d4.83576080
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.170.30871440.24392813X-RAY DIFFRACTION96.7
2.17-2.20.31011430.23752842X-RAY DIFFRACTION97.45
2.2-2.230.28221420.23852758X-RAY DIFFRACTION97.25
2.23-2.270.4291480.2455952X-RAY DIFFRACTION32.96
2.27-2.310.31451300.23532831X-RAY DIFFRACTION97.47
2.31-2.360.31671670.22222755X-RAY DIFFRACTION97.53
2.36-2.410.26151640.21532779X-RAY DIFFRACTION97.61
2.41-2.460.25881500.21672822X-RAY DIFFRACTION97.54
2.46-2.520.2861240.20382828X-RAY DIFFRACTION97.91
2.52-2.580.26331240.20572875X-RAY DIFFRACTION97.81
2.58-2.650.26971340.20112773X-RAY DIFFRACTION97.78
2.65-2.730.28771150.21961789X-RAY DIFFRACTION62.22
2.73-2.810.2561450.21282781X-RAY DIFFRACTION97.79
2.81-2.920.27281610.2132857X-RAY DIFFRACTION98.18
2.92-3.030.2521680.21632727X-RAY DIFFRACTION97.97
3.03-3.170.25191560.20562842X-RAY DIFFRACTION98.07
3.17-3.340.26591520.19012806X-RAY DIFFRACTION97.79
3.34-3.540.2221260.18192831X-RAY DIFFRACTION98.11
3.54-3.820.22581570.16392787X-RAY DIFFRACTION98.17
3.82-4.20.18851700.14762800X-RAY DIFFRACTION97.67
4.2-4.80.16671500.13082811X-RAY DIFFRACTION98.08
4.8-6.040.19481310.14492845X-RAY DIFFRACTION98.12
6.04-24.480.17621160.14712804X-RAY DIFFRACTION96.59

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