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- PDB-5wgu: Crystal Structure of MalA' E494D, premalbrancheamide complex -

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Basic information

Entry
Database: PDB / ID: 5wgu
TitleCrystal Structure of MalA' E494D, premalbrancheamide complex
ComponentsFlavin-dependent halogenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / flavin-dependent halogenase / malbrancheamide / zinc / Zn / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


flavin-dependent halogenase activity / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / secondary metabolite biosynthetic process / monooxygenase activity
Similarity search - Function
Flavin-dependent halogenase / Tryptophan halogenase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / FLAVIN-ADENINE DINUCLEOTIDE / Chem-PM7 / Flavin-dependent halogenase malA
Similarity search - Component
Biological speciesMalbranchea aurantiaca (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.052 Å
AuthorsFraley, A.E. / Smith, J.L.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01-CA70375 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01-CA047135 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-086374 United States
National Science Foundation (NSF, United States)CHE-1205646 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Function and Structure of MalA/MalA', Iterative Halogenases for Late-Stage C-H Functionalization of Indole Alkaloids.
Authors: Fraley, A.E. / Garcia-Borras, M. / Tripathi, A. / Khare, D. / Mercado-Marin, E.V. / Tran, H. / Dan, Q. / Webb, G.P. / Watts, K.R. / Crews, P. / Sarpong, R. / Williams, R.M. / Smith, J.L. / ...Authors: Fraley, A.E. / Garcia-Borras, M. / Tripathi, A. / Khare, D. / Mercado-Marin, E.V. / Tran, H. / Dan, Q. / Webb, G.P. / Watts, K.R. / Crews, P. / Sarpong, R. / Williams, R.M. / Smith, J.L. / Houk, K.N. / Sherman, D.H.
History
DepositionJul 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.classification
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flavin-dependent halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,15415
Polymers74,6831
Non-polymers2,47114
Water8,233457
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-108 kcal/mol
Surface area24920 Å2
2
A: Flavin-dependent halogenase
hetero molecules

A: Flavin-dependent halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,30930
Polymers149,3672
Non-polymers4,94228
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_756-x+2,y,-z+11
Buried area8340 Å2
ΔGint-207 kcal/mol
Surface area46970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.637, 121.300, 170.625
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-702-

CD

21A-703-

CD

31A-1192-

HOH

41A-1224-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Flavin-dependent halogenase


Mass: 74683.469 Da / Num. of mol.: 1 / Mutation: Glu494Asp, Leu276Pro, Arg428Pro
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Malbranchea aurantiaca (fungus) / Gene: malA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: L0E155

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Non-polymers , 7 types, 471 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PM7 / (5aS,12aS,13aS)-12,12-dimethyl-2,3,11,12,12a,13-hexahydro-1H,5H,6H-5a,13a-(epiminomethano)indolizino[7,6-b]carbazol-14-one / premalbrancheamide E


Mass: 335.443 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H25N3O / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 2.77 Å3/Da / Density % sol: 55.58 % / Mosaicity: 0.13 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2 M ammonium sulfate, 0.2 M lithium sulfate, 0.1 M Bis-Tris pH 5.5, 5 mM cadmium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2017
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.052→49.43 Å / Num. obs: 51808 / % possible obs: 99.58 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1102 / Rpim(I) all: 0.053 / Rrim(I) all: 0.137 / Net I/σ(I): 12.29
Reflection shellResolution: 2.052→2.125 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.146 / Mean I/σ(I) obs: 1.25 / CC1/2: 0.592 / Rpim(I) all: 0.585 / Rrim(I) all: 1.393 / % possible all: 96.51

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Processing

Software
NameVersionClassification
XDSdata scaling
Aimless0.5.26data scaling
PHENIX1.11.1_2575refinement
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WGR

5wgr


Resolution: 2.052→49.43 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.18
RfactorNum. reflection% reflection
Rfree0.2002 2511 4.85 %
Rwork0.1624 --
obs0.1643 51793 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 146.64 Å2 / Biso mean: 40.8031 Å2 / Biso min: 17.16 Å2
Refinement stepCycle: final / Resolution: 2.052→49.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5247 0 138 457 5842
Biso mean--55.37 44.87 -
Num. residues----664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085548
X-RAY DIFFRACTIONf_angle_d0.8637570
X-RAY DIFFRACTIONf_chiral_restr0.052797
X-RAY DIFFRACTIONf_plane_restr0.006988
X-RAY DIFFRACTIONf_dihedral_angle_d14.2923250
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0515-2.0910.32721430.27592515265893
2.091-2.13370.29321230.246427042827100
2.1337-2.18010.28221410.222627242865100
2.1801-2.23080.28841340.218927322866100
2.2308-2.28660.28461210.202627332854100
2.2866-2.34840.22741290.187627292858100
2.3484-2.41750.22671390.183227442883100
2.4175-2.49550.20671580.17826942852100
2.4955-2.58470.25111430.178927232866100
2.5847-2.68820.23181420.178827442886100
2.6882-2.81050.2311390.179827262865100
2.8105-2.95870.20181450.176527602905100
2.9587-3.1440.22391170.180327402857100
3.144-3.38670.23251430.162527732916100
3.3867-3.72740.16491540.142327502904100
3.7274-4.26650.14381530.122627692922100
4.2665-5.37430.16341500.117627952945100
5.3743-49.44590.17681370.160729313068100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.57360.6244-0.31944.3595-2.34383.24280.1004-0.12910.21810.1632-0.1653-0.1067-0.22270.32610.08730.1908-0.0629-0.02050.2635-0.03410.25280.8939.938365.8485
21.54620.31050.21880.50090.07110.73690.0288-0.05710.07590.0145-0.03760.02920.00280.05580.0050.2665-0.0136-0.00190.26680.0030.216569.597330.701961.1526
31.61640.92960.13691.73030.55221.05220.00480.06950.169-0.0263-0.01480.1639-0.0255-0.0930.02540.22640.0159-0.0150.22160.00860.176158.587732.642553.3131
41.48480.71320.35362.4230.68831.48980.04250.17030.2044-0.1447-0.07890.1539-0.1142-0.0940.02980.23530.0384-0.02460.27380.03050.269660.011735.620148.2443
51.6229-0.21521.45550.3078-0.32462.70330.0799-0.0027-0.0149-0.0219-0.03870.030.12660.0065-0.03850.2477-0.0185-0.00010.2061-0.00790.223965.064423.914356.0729
61.87630.5060.7770.43830.42951.14310.0465-0.2898-0.05910.0804-0.03820.14250.0531-0.2299-0.02290.3253-0.05770.02050.35610.01830.291551.405716.508867.7276
72.00661.4649-1.00783.2663-0.70121.31650.1349-0.44660.31390.4816-0.15420.3647-0.0996-0.1160.00690.41220.01180.03990.5681-0.08240.412846.316139.390370.1367
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 69 )A3 - 69
2X-RAY DIFFRACTION2chain 'A' and (resid 70 through 217 )A70 - 217
3X-RAY DIFFRACTION3chain 'A' and (resid 218 through 293 )A218 - 293
4X-RAY DIFFRACTION4chain 'A' and (resid 294 through 340 )A294 - 340
5X-RAY DIFFRACTION5chain 'A' and (resid 341 through 437 )A341 - 437
6X-RAY DIFFRACTION6chain 'A' and (resid 438 through 579 )A438 - 579
7X-RAY DIFFRACTION7chain 'A' and (resid 580 through 666 )A580 - 666

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