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- PDB-5wgv: Crystal Structure of MalA' C112S/C128S, premalbrancheamide complex -

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Basic information

Entry
Database: PDB / ID: 5wgv
TitleCrystal Structure of MalA' C112S/C128S, 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: 2.3 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
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)77,04014
Polymers74,6651
Non-polymers2,37513
Water6,449358
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-96 kcal/mol
Surface area24940 Å2
2
A: Flavin-dependent halogenase
hetero molecules

A: Flavin-dependent halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,08028
Polymers149,3312
Non-polymers4,75026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_756-x+2,y,-z+11
Buried area7970 Å2
ΔGint-187 kcal/mol
Surface area47020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.376, 120.711, 170.003
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

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Flavin-dependent halogenase


Mass: 74665.359 Da / Num. of mol.: 1 / Mutation: Cys112Ser, Cys128Ser, 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, 371 molecules

#2: Chemical ChemComp-FAD / 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


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 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.74 Å3/Da / Density % sol: 55.06 % / Mosaicity: 0.11 °
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: Mar 7, 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: 2.3→49.21 Å / Num. obs: 36691 / % possible obs: 99.94 % / Redundancy: 6.8 % / Biso Wilson estimate: 44.22 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1146 / Rpim(I) all: 0.049 / Rrim(I) all: 0.129 / Net I/σ(I): 13.43
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.227 / Mean I/σ(I) obs: 1.57 / CC1/2: 0.665 / Rpim(I) all: 0.54 / Rrim(I) all: 1.414 / % possible all: 99.97

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.11.1_2575refinement
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WGR

5wgr


Resolution: 2.3→49.21 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.63
RfactorNum. reflection% reflection
Rfree0.2145 1807 4.93 %
Rwork0.1633 --
obs0.1658 36680 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 215.11 Å2 / Biso mean: 53.1107 Å2 / Biso min: 22.9 Å2
Refinement stepCycle: final / Resolution: 2.3→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5248 0 133 358 5739
Biso mean--87.76 52.1 -
Num. residues----664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075546
X-RAY DIFFRACTIONf_angle_d0.7467565
X-RAY DIFFRACTIONf_chiral_restr0.047797
X-RAY DIFFRACTIONf_plane_restr0.005988
X-RAY DIFFRACTIONf_dihedral_angle_d13.6163251
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3-2.36220.29661550.256626462801
2.3622-2.43170.31111330.243926592792
2.4317-2.51020.26461430.232626102753
2.5102-2.59990.31961290.226926622791
2.5999-2.7040.30761400.218726612801
2.704-2.8270.28291370.207526602797
2.827-2.97610.26061340.192426532787
2.9761-3.16250.27951140.197727122826
3.1625-3.40660.22451430.165926542797
3.4066-3.74930.181470.142226882835
3.7493-4.29160.17191490.118726982847
4.2916-5.40590.16691510.11627092860
5.4059-49.22290.18791320.160328612993
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)
10.43880.9041-0.41244.6447-3.22084.16080.0669-0.03530.23340.1684-0.2049-0.1791-0.29170.45420.17650.3482-0.0749-0.02460.368-0.03540.42980.724839.707965.6369
21.45170.5480.29230.76290.27550.9249-0.0235-0.00630.0461-0.0599-0.03310.0421-0.05310.05890.05960.3625-0.0181-0.02280.33790.0130.281369.494230.51560.9594
31.17130.70140.37811.14820.43531.0068-0.01960.09170.0977-0.16050.01820.13570.0198-0.10590.01890.33070.0107-0.03290.310700.272958.450432.459553.1674
41.69370.85730.51121.51370.63341.2066-0.0330.30890.1308-0.4080.0633-0.0447-0.1442-0.07380.02020.4270.0406-0.04980.40080.00510.359259.884435.510648.0746
51.5301-0.54831.9290.6095-0.87154.14350.0564-0.0350.0227-0.0976-0.03960.04840.1693-0.0699-0.04060.315-0.0298-0.00240.2767-0.0170.326764.901623.750255.8424
62.4330.2560.69460.99050.33361.48960.0343-0.2293-0.06970.0212-0.05120.17660.0685-0.3483-0.00040.3124-0.07010.0080.33290.00910.304951.246916.406967.5009
71.28531.4709-1.50034.0039-1.38061.11960.2201-0.27340.4370.5584-0.0960.5567-0.2862-0.2257-0.11610.50470.01790.00170.561-0.08250.518946.196239.276269.9864
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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