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- PDB-5wgt: Crystal Structure of MalA' H253A, premalbrancheamide complex -

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Basic information

Entry
Database: PDB / ID: 5wgt
TitleCrystal Structure of MalA' H253A, 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: 2.093 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)77,11815
Polymers74,6301
Non-polymers2,48714
Water7,963442
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-100 kcal/mol
Surface area24710 Å2
2
A: Flavin-dependent halogenase
hetero molecules

A: Flavin-dependent halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,23530
Polymers149,2612
Non-polymers4,97528
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_756-x+2,y,-z+11
Buried area8050 Å2
ΔGint-193 kcal/mol
Surface area46560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.176, 120.451, 170.271
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-806-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Flavin-dependent halogenase


Mass: 74630.422 Da / Num. of mol.: 1 / Mutation: His253Ala, 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, 456 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 112.411 Da / Num. of mol.: 4 / 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


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION


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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.73 Å3/Da / Density % sol: 54.94 % / Mosaicity: 0.1 °
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: Feb 8, 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: 2.093→46.14 Å / Num. obs: 48238 / % possible obs: 99.76 % / Redundancy: 6.8 % / Biso Wilson estimate: 39.72 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07229 / Rpim(I) all: 0.031 / Rrim(I) all: 0.081 / Net I/σ(I): 16.58
Reflection shellResolution: 2.093→2.168 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.007 / Mean I/σ(I) obs: 1.83 / CC1/2: 0.703 / Rpim(I) all: 0.458 / Rrim(I) all: 1.187 / % possible all: 98.82

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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: 2.093→46.14 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.76
RfactorNum. reflection% reflection
Rfree0.2075 2316 4.8 %
Rwork0.1624 --
obs0.1647 48221 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 138.68 Å2 / Biso mean: 46.0537 Å2 / Biso min: 23.53 Å2
Refinement stepCycle: final / Resolution: 2.093→46.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5243 0 134 442 5819
Biso mean--56.91 50.18 -
Num. residues----664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075542
X-RAY DIFFRACTIONf_angle_d0.7487557
X-RAY DIFFRACTIONf_chiral_restr0.047797
X-RAY DIFFRACTIONf_plane_restr0.005987
X-RAY DIFFRACTIONf_dihedral_angle_d14.8133249
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.093-2.13580.26421310.24012632276398
2.1358-2.18220.3071180.231726852803100
2.1822-2.2330.27411300.223126772807100
2.233-2.28880.26171440.208626482792100
2.2888-2.35070.30191390.203926622801100
2.3507-2.41990.25161210.195527032824100
2.4199-2.4980.22331400.195726702810100
2.498-2.58720.30241360.185626942830100
2.5872-2.69080.24131350.183526702805100
2.6908-2.81330.24331400.190126912831100
2.8133-2.96160.2271400.185326942834100
2.9616-3.14710.2481130.190827182831100
3.1471-3.390.26371430.171127132856100
3.39-3.7310.16861520.151426972849100
3.731-4.27050.16541510.121627212872100
4.2705-5.37910.15621490.115627452894100
5.3791-46.15190.18181340.157328853019100
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)
10.68410.7134-0.52244.5535-2.9153.94140.0634-0.07840.18060.0135-0.1967-0.2126-0.23990.44540.1320.2601-0.0745-0.01020.3264-0.03270.339280.563439.602865.7641
21.36820.37230.38310.67590.11450.91580.00910.02540.0163-0.1092-0.02610.02310.00050.06140.01610.3114-0.0174-0.00940.2613-0.00960.243469.315730.431861.0397
31.13310.58630.05021.62660.53790.9751-0.03820.12330.091-0.20370.03380.1201-0.0457-0.14360.01220.31930.0045-0.04670.32020.00440.243158.448732.340853.1714
41.55520.93910.38111.50540.1491.4086-0.02180.29150.1283-0.31010.01160.0469-0.0856-0.10980.02750.33580.0348-0.04720.3160.02130.312259.728235.424948.1415
51.6513-0.38961.9230.4156-0.62133.99450.02660.06170.0247-0.1363-0.03520.03660.0432-0.01530.00650.2933-0.0256-0.00290.2341-0.02440.264164.796923.66655.9316
62.51850.22520.67140.75570.35881.28670.0154-0.1701-0.1807-0.0441-0.02310.1510.0926-0.3322-0.00570.302-0.0613-0.01010.32340.00990.30551.143316.356167.5909
71.89461.1189-0.9073.0804-0.7190.92150.1071-0.14070.42250.2014-0.0680.4335-0.2215-0.1754-0.04780.40620.0509-0.01160.4772-0.08620.434346.075539.147470.004
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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