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- PDB-5wgr: Crystal Structure of Wild-type MalA', premalbrancheamide complex -

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Basic information

Entry
Database: PDB / ID: 5wgr
TitleCrystal Structure of Wild-type MalA', 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: 2.362 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_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_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)76,99313
Polymers74,6971
Non-polymers2,29512
Water7,206400
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-81 kcal/mol
Surface area24680 Å2
2
A: Flavin-dependent halogenase
hetero molecules

A: Flavin-dependent halogenase
hetero molecules

A: Flavin-dependent halogenase
hetero molecules

A: Flavin-dependent halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)307,97052
Polymers298,7904
Non-polymers9,18148
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_756-x+2,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area15410 Å2
ΔGint-337 kcal/mol
Surface area92950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.284, 120.619, 170.388
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-1147-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Flavin-dependent halogenase


Mass: 74697.492 Da / Num. of mol.: 1 / Mutation: 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, 412 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.: 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.: 3 / 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.: 400 / 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: 0.1 °
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: Dec 14, 2016
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.362→39.64 Å / Num. obs: 33624 / % possible obs: 99.11 % / Redundancy: 6.8 % / Biso Wilson estimate: 43.84 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1064 / Rpim(I) all: 0.048 / Rrim(I) all: 0.126 / Net I/σ(I): 14.08
Reflection shellResolution: 2.362→2.45 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 1.93 / CC1/2: 0.69 / Rpim(I) all: 0.439 / Rrim(I) all: 1.184 / % possible all: 97.72

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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: 5WGS

5wgs


Resolution: 2.362→39.64 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.3
RfactorNum. reflection% reflection
Rfree0.2048 1672 4.97 %
Rwork0.1511 --
obs0.1538 33618 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 301.09 Å2 / Biso mean: 50.4925 Å2 / Biso min: 23.03 Å2
Refinement stepCycle: final / Resolution: 2.362→39.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5248 0 124 400 5772
Biso mean--64.55 56.28 -
Num. residues----664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055541
X-RAY DIFFRACTIONf_angle_d0.7297553
X-RAY DIFFRACTIONf_chiral_restr0.046797
X-RAY DIFFRACTIONf_plane_restr0.005988
X-RAY DIFFRACTIONf_dihedral_angle_d14.1583251
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3621-2.43160.33281530.25392568272197
2.4316-2.51010.29581530.22882588274199
2.5101-2.59980.30951280.21162657278599
2.5998-2.70390.26991380.20052634277299
2.7039-2.82690.25191360.18812653278999
2.8269-2.9760.22731320.17762633276599
2.976-3.16240.26521160.17842706282299
3.1624-3.40650.24551410.16512603274498
3.4065-3.74910.18291460.136626822828100
3.7491-4.29130.15781460.112726922838100
4.2913-5.40530.15781510.106527012852100
5.4053-46.18020.17181320.1452830296299
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)
10.830.4571-0.11886.389-3.63294.7230.0155-0.0730.30150.0414-0.2116-0.2999-0.28110.44150.20640.2709-0.0662-0.00150.3413-0.03820.372880.629139.68265.8062
21.50080.21910.28520.57050.06470.8853-0.0078-0.0180.0264-0.1165-0.02060.0434-0.02550.08690.03690.3081-0.037-0.01590.2985-0.00330.273769.363830.422161.1034
31.54220.98050.3061.90420.67411.1037-0.04440.13190.1287-0.21090.01680.16-0.0212-0.14340.04570.34350.0088-0.03080.314-0.00330.249158.377632.426353.2282
41.98560.94140.22531.99750.25470.8008-0.06450.32570.1669-0.30250.09920.0615-0.02720.01770.01250.43910.0194-0.0840.39330.03650.31659.786735.450348.168
52.5832-0.59352.66950.3714-0.95815.0647-0.00870.0450.0493-0.0876-0.03670.0010.05020.03790.04870.2895-0.0302-00.2187-0.02170.281464.844823.695755.9637
62.7180.56810.93690.92520.57191.54730.0704-0.2646-0.1158-0.0012-0.06480.16720.1064-0.3538-0.02270.3209-0.07240.00040.34230.02430.325351.173916.397267.6532
71.57921.5207-1.07913.7128-1.35141.31570.1075-0.19550.48820.3062-0.02450.4852-0.2154-0.2362-0.09870.41990.08-0.00360.5348-0.11850.490246.071539.213370.0603
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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