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- PDB-3fw7: Structure of berberine bridge enzyme, H104A variant -

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Basic information

Entry
Database: PDB / ID: 3fw7
TitleStructure of berberine bridge enzyme, H104A variant
ComponentsReticuline oxidase
KeywordsFLAVOPROTEIN / BI-COVALENT FLAVINYLATION / N-GLYCOSYLATION / ALAKLOID BIOSYNTHESIS / OXIDOREDUCTASE / Alkaloid metabolism / Cytoplasmic vesicle / FAD / Glycoprotein
Function / homology
Function and homology information


reticuline oxidase / reticuline oxidase activity / alkaloid metabolic process / FAD binding / cytoplasmic vesicle
Similarity search - Function
Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Berberine/berberine-like / Berberine and berberine like / Oxygen oxidoreductase covalent FAD-binding site / Oxygen oxidoreductases covalent FAD-binding site. / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 ...Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Berberine/berberine-like / Berberine and berberine like / Oxygen oxidoreductase covalent FAD-binding site / Oxygen oxidoreductases covalent FAD-binding site. / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Reticuline oxidase
Similarity search - Component
Biological speciesEschscholzia californica (California poppy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.825 Å
AuthorsWinkler, A. / Macheroux, P. / Gruber, K.
Citation
Journal: to be published
Title: Structural roles of biocovalent flaninylation in berberine bridge enzyme
Authors: Winkler, A. / Motz, K. / Riedl, S. / Puhl, M. / Macheroux, P. / Gruber, K.
#1: Journal: Nat. Chem. Biol. / Year: 2008
Title: A concerted mechanism for berberine bridge enzyme.
Authors: Winkler, A. / Lyskowski, A. / Riedl, S. / Puhl, M. / Kutchan, T.M. / Macheroux, P. / Gruber, K.
History
DepositionJan 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_label_asym_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 / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Reticuline oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1575
Polymers55,5401
Non-polymers1,6184
Water8,971498
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.800, 68.800, 247.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-748-

HOH

Detailsbiological unit is the same as asymmetric unit.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Reticuline oxidase / Berberine bridge-forming enzyme / BBE / Tetrahydroprotoberberine synthase


Mass: 55539.836 Da / Num. of mol.: 1 / Mutation: H104A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eschscholzia californica (California poppy)
Gene: BBE1 / Plasmid: PPICZA / Production host: Pichia pastoris (fungus) / Strain (production host): KM71H / References: UniProt: P30986, reticuline oxidase

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 500 molecules

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


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / 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: 2.63 Å3/Da / Density % sol: 53.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 0.2 M MAGNESIUMCHLORIDE, 30% PEG-4000, 0.1 M TRIS/HCL, pH 8.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.825→47.7 Å / Num. all: 53899 / Num. obs: 53899 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 % / Rsym value: 0.106 / Net I/σ(I): 14.4
Reflection shellResolution: 1.83→1.94 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 3 / Rsym value: 0.773 / % possible all: 98.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3d2j

3d2j


Resolution: 1.825→47.7 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.194 2743 5.09 %random
Rwork0.166 ---
obs0.168 53899 99.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.46 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso max: 128.79 Å2 / Biso mean: 27.032 Å2 / Biso min: 9.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.009 Å20 Å2-0 Å2
2--1.009 Å2-0 Å2
3----2.018 Å2
Refinement stepCycle: LAST / Resolution: 1.825→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3919 0 107 498 4524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114324
X-RAY DIFFRACTIONf_angle_d1.0135912
X-RAY DIFFRACTIONf_chiral_restr0.068653
X-RAY DIFFRACTIONf_plane_restr0.004746
X-RAY DIFFRACTIONf_dihedral_angle_d17.491605
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.825-1.8570.2481380.1932409254796
1.857-1.890.2481290.19424862615100
1.89-1.9270.2261260.20425252651100
1.927-1.9660.2221320.17625292661100
1.966-2.0090.2181460.16624782624100
2.009-2.0560.2071200.15525312651100
2.056-2.1070.2041400.15725262666100
2.107-2.1640.1981430.15125332676100
2.164-2.2280.2041400.16525342674100
2.228-2.2990.2481270.17725312658100
2.299-2.3820.1821430.16425372680100
2.382-2.4770.2221330.16425472680100
2.477-2.590.191320.17125422674100
2.59-2.7260.2211380.16425682706100
2.726-2.8970.1751560.16925542710100
2.897-3.1210.2051340.17125882722100
3.121-3.4350.1761410.16326002741100
3.435-3.9310.1671250.14426302755100
3.931-4.9520.1491540.13526702824100
4.952-47.750.1921460.18828382984100
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)
13.11310.77430.77232.0705-0.0137-3.3598-0.03550.8372-0.2875-0.57030.13840.03870.23410.0862-0.03950.28910.02590.0410.3995-0.0430.1929-9.34663.2768-41.7642
21.10830.0177-0.12341.84230.82090.65710.03240.4172-0.2573-0.1997-0.1422-0.05670.1649-0.0440.06630.1769-0.0088-0.00480.3033-0.05780.1609-18.3792-4.1278-33.7992
30.774-0.0147-0.02240.78680.01781.01440.08460.0818-0.036-0.01970.0132-0.01810.01030.0231-0.07380.0921-0.0148-0.00520.09960.00070.1043-18.20816.8673-16.1927
42.1150.3297-0.06540.3135-0.36850.62340.1128-0.1533-0.18080.0399-0.07910.0040.0947-0.0055-0.03980.0853-0.0243-0.01940.05290.00490.0848-28.8208-6.91362.0288
51.3390.6067-0.15870.7396-0.54780.59780.01580.1447-0.0636-0.04190.08710.06670.0454-0.1292-0.06470.0764-0.0272-0.00390.1279-0.00210.1046-39.7754-3.8165-9.685
60.727-0.29510.28190.2104-0.00890.75550.09810.21790.1185-0.08420.01310.1188-0.0894-0.243-0.11210.10390.04650.00930.16070.04970.108-36.637611.3575-26.8318
7-0.9618-0.37592.6945-2.38964.98235.074-0.01520.01620.13770.1224-0.02290.0012-0.109-0.1210.03950.52260.16180.04910.33870.23860.5003-36.213620.9961-32.5402
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 23:39)
2X-RAY DIFFRACTION2(chain A and resid 40:95)
3X-RAY DIFFRACTION3(chain A and resid 96:242)
4X-RAY DIFFRACTION4(chain A and resid 245:367)
5X-RAY DIFFRACTION5(chain A and resid 368:458)
6X-RAY DIFFRACTION6(chain A and resid 459:518)
7X-RAY DIFFRACTION7(chain A and resid 519:524)

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