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- PDB-4pzf: Berberine bridge enzyme G164A variant, a reticuline dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 4pzf
TitleBerberine bridge enzyme G164A variant, a reticuline dehydrogenase
ComponentsReticuline oxidase
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / BI-COVALENT FLAVINYLATION / Reticuline oxidase / Berberine bridge-forming enzyme / Tetrahydroprotoberberine synthase
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 / Oxygen oxidoreductase covalent FAD-binding site / Berberine/berberine-like / Berberine and berberine like / 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 / Oxygen oxidoreductase covalent FAD-binding site / Berberine/berberine-like / Berberine and berberine like / 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 / Resolution: 2.2 Å
AuthorsZafred, D. / Wallner, S. / Steiner, B. / Macheroux, P.
CitationJournal: Febs J. / Year: 2015
Title: Rationally engineered flavin-dependent oxidase reveals steric control of dioxygen reduction.
Authors: Zafred, D. / Steiner, B. / Teufelberger, A.R. / Hromic, A. / Karplus, P.A. / Schofield, C.J. / Wallner, S. / Macheroux, P.
History
DepositionMar 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Mar 4, 2015Group: Database references
Revision 1.3Mar 25, 2015Group: Database references
Revision 1.4Apr 1, 2015Group: Structure summary
Revision 1.5Apr 22, 2015Group: Other
Revision 1.6Sep 2, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Reticuline oxidase
B: Reticuline oxidase
C: Reticuline oxidase
D: Reticuline oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,54223
Polymers240,2444
Non-polymers7,29819
Water5,549308
1
A: Reticuline oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4924
Polymers60,0611
Non-polymers1,4313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Reticuline oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5885
Polymers60,0611
Non-polymers1,5274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Reticuline oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2317
Polymers60,0611
Non-polymers2,1706
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Reticuline oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2317
Polymers60,0611
Non-polymers2,1706
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Reticuline oxidase
C: Reticuline oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,72311
Polymers120,1222
Non-polymers3,6019
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-37 kcal/mol
Surface area37570 Å2
MethodPISA
6
B: Reticuline oxidase
D: Reticuline oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,81912
Polymers120,1222
Non-polymers3,69710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-51 kcal/mol
Surface area37150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.820, 175.440, 195.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 60061.008 Da / Num. of mol.: 4 / Mutation: G164A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eschscholzia californica (California poppy)
Gene: BBE1 / Production host: Komagataella pastoris (fungus) / References: UniProt: P30986, reticuline oxidase

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Sugars , 2 types, 8 molecules

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


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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 , 4 types, 319 molecules

#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 546.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsCONFLICT MUTATIONS ARE CLEAVING SITES.

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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: 2.89 Å3/Da / Density % sol: 57.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30mg/mL protein + 0.1 M HEPES pH 7.5, 2.0 M Ammonium sulfate, BATCH, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 10, 2014
RadiationMonochromator: carved single silicon (111) crystal with a channel in the middle (called channel-cut design)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 141762 / Num. obs: 140296 / % possible obs: 99 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 8.2 % / Net I/σ(I): 11.78
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 1.63 / Num. unique all: 17490 / % possible all: 98.4

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Processing

Software
NameVersionClassification
ProDCdata collection
PHASERmrphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3D2H

3d2h


Resolution: 2.2→47.378 Å / SU ML: 0.27 / σ(F): 1.35 / Phase error: 28.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2419 7008 5 %random
Rwork0.2198 ---
obs0.2209 140140 98.87 %-
all-141762 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→47.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15713 0 455 308 16476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416596
X-RAY DIFFRACTIONf_angle_d0.8422482
X-RAY DIFFRACTIONf_dihedral_angle_d15.0945955
X-RAY DIFFRACTIONf_chiral_restr0.0312453
X-RAY DIFFRACTIONf_plane_restr0.0032814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2250.37162290.35394341X-RAY DIFFRACTION98
2.225-2.25120.39552320.32754402X-RAY DIFFRACTION98
2.2512-2.27860.32422280.31424330X-RAY DIFFRACTION98
2.2786-2.30750.33782310.29624401X-RAY DIFFRACTION98
2.3075-2.33780.31152270.30194319X-RAY DIFFRACTION98
2.3378-2.36990.31952330.29344419X-RAY DIFFRACTION99
2.3699-2.40370.33752270.29484318X-RAY DIFFRACTION98
2.4037-2.43960.31242320.2844419X-RAY DIFFRACTION98
2.4396-2.47770.2932290.2714372X-RAY DIFFRACTION99
2.4777-2.51830.2942320.27254403X-RAY DIFFRACTION99
2.5183-2.56180.31992290.26694349X-RAY DIFFRACTION99
2.5618-2.60830.30392350.25914451X-RAY DIFFRACTION99
2.6083-2.65850.27152290.25574351X-RAY DIFFRACTION99
2.6585-2.71280.28082330.24664418X-RAY DIFFRACTION98
2.7128-2.77170.28312320.25724404X-RAY DIFFRACTION99
2.7717-2.83620.27262320.25434415X-RAY DIFFRACTION99
2.8362-2.90710.32242320.25814414X-RAY DIFFRACTION99
2.9071-2.98570.28242340.25864446X-RAY DIFFRACTION99
2.9857-3.07360.26632320.24974405X-RAY DIFFRACTION99
3.0736-3.17270.26312340.24384435X-RAY DIFFRACTION99
3.1727-3.28610.24092340.23174452X-RAY DIFFRACTION99
3.2861-3.41760.24472350.2264460X-RAY DIFFRACTION99
3.4176-3.57310.23852360.2244476X-RAY DIFFRACTION99
3.5731-3.76140.23152350.20184473X-RAY DIFFRACTION99
3.7614-3.9970.22642370.19144501X-RAY DIFFRACTION99
3.997-4.30540.20772370.18034505X-RAY DIFFRACTION100
4.3054-4.73830.18252390.16814536X-RAY DIFFRACTION100
4.7383-5.42310.19812400.17594551X-RAY DIFFRACTION99
5.4231-6.82930.1962420.18754604X-RAY DIFFRACTION100
6.8293-47.38890.18142510.17754762X-RAY DIFFRACTION99

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