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- PDB-3fw8: Structure of berberine bridge enzyme, C166A variant -

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Basic information

Entry
Database: PDB / ID: 3fw8
TitleStructure of berberine bridge enzyme, C166A 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 / Resolution: 1.5 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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)56,9505
Polymers55,3331
Non-polymers1,6184
Water10,629590
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.090, 69.090, 247.070
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-1026-

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: 55332.613 Da / Num. of mol.: 1 / Mutation: C166A
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, 592 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.: 590 / 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: 2.66 Å3/Da / Density % sol: 53.83 %
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: 1.39→47.9 Å / Num. all: 118784 / Num. obs: 118784 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Biso Wilson estimate: 14.52 Å2 / Rsym value: 0.075 / Net I/σ(I): 13.9
Reflection shellResolution: 1.39→1.48 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.932 / % possible all: 92.3

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementStarting model: 3d2j

3d2j


Resolution: 1.5→42.017 Å / Occupancy max: 1 / Occupancy min: 0.21 / FOM work R set: 0.911 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.189 4875 5.04 %random
Rwork0.168 ---
all0.169 96810 --
obs0.169 96810 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.961 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso max: 99.05 Å2 / Biso mean: 25.791 Å2 / Biso min: 12.49 Å2
Baniso -1Baniso -2Baniso -3
1--6.071 Å2-0 Å2-0 Å2
2---6.071 Å2-0 Å2
3----6.448 Å2
Refinement stepCycle: LAST / Resolution: 1.5→42.017 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3906 0 107 590 4603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014307
X-RAY DIFFRACTIONf_angle_d1.0285883
X-RAY DIFFRACTIONf_chiral_restr0.067647
X-RAY DIFFRACTIONf_plane_restr0.005741
X-RAY DIFFRACTIONf_dihedral_angle_d18.3461589
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.5170.2231710.18829533124100
1.517-1.5350.2131650.1830363201100
1.535-1.5540.1961620.1829733135100
1.554-1.5730.1991530.17230703223100
1.573-1.5940.1971420.16930023144100
1.594-1.6160.1781640.16630103174100
1.616-1.6390.1671570.15330353192100
1.639-1.6630.1791440.15930313175100
1.663-1.6890.1961520.16130373189100
1.689-1.7170.191650.1630343199100
1.717-1.7470.1781670.15930233190100
1.747-1.7780.2121550.16230533208100
1.778-1.8130.1951850.16730003185100
1.813-1.850.1771510.16130233174100
1.85-1.890.1891600.16130323192100
1.89-1.9340.1731690.15830473216100
1.934-1.9820.1811650.16330653230100
1.982-2.0360.1841550.1630653220100
2.036-2.0960.1981420.16330573199100
2.096-2.1630.1681740.16430523226100
2.163-2.2410.2161570.16130663223100
2.241-2.330.1971460.16730843230100
2.33-2.4360.1861670.17130613228100
2.436-2.5650.1871700.16831003270100
2.565-2.7260.2031770.17430713248100
2.726-2.9360.2051560.17831073263100
2.936-3.2310.1771820.17531253307100
3.231-3.6990.1741700.15931673337100
3.699-4.6590.1591770.14532003377100
4.659-42.0340.1881750.1753356353198
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)
10.867-0.1656-0.13860.87770.33710.53990.05160.2596-0.062-0.1464-0.0411-0.0551-0.00950.0517-0.00860.17440.028-0.0140.275-0.01010.162-18.3918-2.2867-33.2342
20.7485-0.05280.08470.53120.1280.58130.08230.03730.0180.0150.0012-0.0251-0.04050.0818-0.05930.1554-0.01930.00240.15890.00840.1524-16.92898.1533-13.9505
31.63320.5760.07660.39-0.30730.48660.082-0.2232-0.02940.0487-0.05920.04090.0823-0.0088-0.02780.1619-0.0302-0.01830.15440.00630.1647-27.6585-7.21234.2501
40.88740.5026-0.14030.6422-0.18490.62180.03310.0927-0.0187-0.010.05890.02620.0298-0.0822-0.07880.1442-0.0139-0.00380.17740.01070.1723-39.1416-3.6561-10.4814
50.758-0.084-0.0264-0.0583-0.32361.16740.1660.21620.1855-0.03930.02260.1208-0.2569-0.2746-0.17150.20980.06470.01290.23560.07390.2112-36.371413.1803-27.5931
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 26:114)
2X-RAY DIFFRACTION2(chain A and resid 115:244)
3X-RAY DIFFRACTION3(chain A and resid 245:350)
4X-RAY DIFFRACTION4(chain A and resid 351:465)
5X-RAY DIFFRACTION5(chain A and resid 466:520)

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