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- PDB-5uao: Crystal structure of MibH, a lathipeptide tryptophan 5-halogenase -

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Basic information

Entry
Database: PDB / ID: 5uao
TitleCrystal structure of MibH, a lathipeptide tryptophan 5-halogenase
ComponentsTryptophane-5-halogenase
KeywordsOXIDOREDUCTASE / halogenase / lanthipeptide / tryptophan / NAI-107
Function / homology
Function and homology information


monooxygenase activity / nucleotide binding
Similarity search - Function
Flavin-dependent halogenase / Tryptophan halogenase / : / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Tryptophane-5-halogenase
Similarity search - Component
Biological speciesMicrobispora sp. ATCC PTA-5024 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsCogan, D.P. / Nair, S.K.
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Two Flavoenzymes Catalyze the Post-Translational Generation of 5-Chlorotryptophan and 2-Aminovinyl-Cysteine during NAI-107 Biosynthesis.
Authors: Ortega, M.A. / Cogan, D.P. / Mukherjee, S. / Garg, N. / Li, B. / Thibodeaux, G.N. / Maffioli, S.I. / Donadio, S. / Sosio, M. / Escano, J. / Smith, L. / Nair, S.K. / van der Donk, W.A.
History
DepositionDec 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.3Oct 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptophane-5-halogenase
B: Tryptophane-5-halogenase
C: Tryptophane-5-halogenase
D: Tryptophane-5-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,5948
Polymers236,9524
Non-polymers1,6424
Water24,2661347
1
A: Tryptophane-5-halogenase
C: Tryptophane-5-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,2974
Polymers118,4762
Non-polymers8212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-39 kcal/mol
Surface area37880 Å2
MethodPISA
2
B: Tryptophane-5-halogenase
D: Tryptophane-5-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,2974
Polymers118,4762
Non-polymers8212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-43 kcal/mol
Surface area37840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.436, 87.887, 100.632
Angle α, β, γ (deg.)64.58, 69.90, 76.26
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Tryptophane-5-halogenase


Mass: 59237.973 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microbispora sp. ATCC PTA-5024 (bacteria)
Gene: mlbH, MPTA5024_21495 / Production host: Escherichia coli (E. coli) / References: UniProt: W2EQU4
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1347 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 45.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12.5% MPD, 12.5% PEG 3.35K, 0.1 M MES/imidazole pH 6.5, and 0.09 M NPS (1:1:1 NaNO3, Na2HPO4, (NH4)2SO4)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.88→87.38 Å / Num. obs: 170761 / % possible obs: 97.8 % / Redundancy: 7.9 % / Net I/σ(I): 16.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WET

2wet


Resolution: 1.88→87.38 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.767 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.131 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20362 8242 5 %RANDOM
Rwork0.15618 ---
obs0.15855 155653 97.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.207 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å21.63 Å2-1.95 Å2
2---2.4 Å2-0.4 Å2
3---0.54 Å2
Refinement stepCycle: 1 / Resolution: 1.88→87.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15908 0 108 1347 17363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01916430
X-RAY DIFFRACTIONr_bond_other_d0.0010.0215385
X-RAY DIFFRACTIONr_angle_refined_deg1.9421.96222404
X-RAY DIFFRACTIONr_angle_other_deg0.947335180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.92552058
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.05421.644724
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.442152433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.07115175
X-RAY DIFFRACTIONr_chiral_restr0.1220.22441
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02118710
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023983
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1763.3088244
X-RAY DIFFRACTIONr_mcbond_other3.1773.3078243
X-RAY DIFFRACTIONr_mcangle_it4.3214.94310298
X-RAY DIFFRACTIONr_mcangle_other4.3224.94310299
X-RAY DIFFRACTIONr_scbond_it4.3363.7838186
X-RAY DIFFRACTIONr_scbond_other4.3353.7838187
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4635.48612107
X-RAY DIFFRACTIONr_long_range_B_refined9.38928.89720224
X-RAY DIFFRACTIONr_long_range_B_other9.26628.47619623
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.881→1.93 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 617 -
Rwork0.304 11268 -
obs--96.2 %

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