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Basic information

Entry
Database: PDB / ID: 4ud8
TitleAtBBE15
ComponentsFAD-BINDING AND BBE DOMAIN-CONTAINING PROTEIN
KeywordsOXIDOREDUCTASE / MONOLIGNOL OXIDASE / FAD / BERBERINE BRIDGE ENZYME-LIKE
Function / homology
Function and homology information


coniferyl-alcohol dehydrogenase / polar nucleus fusion / coniferyl-alcohol dehydrogenase activity / cinnamyl-alcohol dehydrogenase / sinapyl alcohol dehydrogenase activity / cinnamyl-alcohol dehydrogenase activity / embryo development ending in seed dormancy / plasmodesma / cell wall / FAD binding / extracellular region
Similarity search - Function
Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Berberine/berberine-like / Berberine and berberine like / 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 ...Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Berberine/berberine-like / Berberine and berberine like / 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-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / : / Berberine bridge enzyme-like 15
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.088 Å
AuthorsDaniel, B. / Steiner, B. / Pavkov-Keller, T. / Dordic, A. / Gutmann, A. / Sensen, C.W. / Nidetzky, B. / van der Graaff, E. / Wallner, S. / Gruber, K. / Macheroux, P.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Oxidation of Monolignols by Members of the Berberine Bridge Enzyme Family Suggests a Role in Cell Wall Metabolism.
Authors: Daniel, B. / Pavkov-Keller, T. / Steiner, B. / Dordic, A. / Gutmann, A. / Nidetzky, B. / Sensen, C.W. / Van Der Graaff, E. / Wallner, S. / Gruber, K. / Macheroux, P.
History
DepositionDec 9, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / 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.pdbx_synonyms / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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_auth_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 / _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 2.1Dec 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: FAD-BINDING AND BBE DOMAIN-CONTAINING PROTEIN
B: FAD-BINDING AND BBE DOMAIN-CONTAINING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,19714
Polymers119,4302
Non-polymers3,76712
Water11,079615
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A: FAD-BINDING AND BBE DOMAIN-CONTAINING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5676
Polymers59,7151
Non-polymers1,8535
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FAD-BINDING AND BBE DOMAIN-CONTAINING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6308
Polymers59,7151
Non-polymers1,9157
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.596, 94.742, 188.298
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein FAD-BINDING AND BBE DOMAIN-CONTAINING PROTEIN / ATBBE15


Mass: 59714.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: THE FAD COFACTOR IS BICOVALENTLY LINKED TO THE PEPTIDE CHAIN VIA A COVALENT BOND OF HIS115 TO 8-ALPHA- METHYL GROUP AND CYS179 TO THE 6-POSITION OF THE ISOALLOXAZINE RING.
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PPICZALPHA / Production host: KOMAGATELLA PASTORIS (fungus) / Strain (production host): KM71H / References: UniProt: O64743

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Sugars , 2 types, 4 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.: 2
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.: 2
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 , 5 types, 623 molecules

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


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 398.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 615 / 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: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 8.5 / Details: pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.97167
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Sep 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97167 Å / Relative weight: 1
ReflectionResolution: 2.09→47.38 Å / Num. obs: 67102 / % possible obs: 97.8 % / Observed criterion σ(I): 1.6 / Redundancy: 6.2 % / Biso Wilson estimate: 32.02 Å2 / Rmerge(I) obs: 0.191 / Net I/σ(I): 7.73
Reflection shellResolution: 2.09→2.21 Å / Redundancy: 3.2627 % / Rmerge(I) obs: 0.794 / Mean I/σ(I) obs: 2.23 / % possible all: 87

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3D2H

3d2h


Resolution: 2.088→47.371 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 21.46 / Stereochemistry target values: ML
Details: A FEW RESIDUES POSITIONED AT THE N-TERMINAL PART COULD NOT BE MODELED INTO THE ELECTRON DENSITY MOST LIKELY DUE TO THEIR HIGH FLEXIBILITY (VAL43 AND SER44 IN CHAIN A AS WELL GLN40, SER41 AND ...Details: A FEW RESIDUES POSITIONED AT THE N-TERMINAL PART COULD NOT BE MODELED INTO THE ELECTRON DENSITY MOST LIKELY DUE TO THEIR HIGH FLEXIBILITY (VAL43 AND SER44 IN CHAIN A AS WELL GLN40, SER41 AND ASP42 IN CHAIN B). NO CLEAR ELECTRON DENSITY WAS VISIBLE FOR THE SAME LOOP REGION (RESIDUES 301 TO 305) IN BOTH CHAINS.
RfactorNum. reflection% reflection
Rfree0.2209 3397 5.1 %
Rwork0.1835 --
obs0.1855 67070 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.09 Å2
Refinement stepCycle: LAST / Resolution: 2.088→47.371 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7919 0 248 615 8782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088430
X-RAY DIFFRACTIONf_angle_d0.82511436
X-RAY DIFFRACTIONf_dihedral_angle_d16.1363099
X-RAY DIFFRACTIONf_chiral_restr0.0541215
X-RAY DIFFRACTIONf_plane_restr0.0041437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0878-2.11760.3438680.32351452X-RAY DIFFRACTION53
2.1176-2.14920.29061480.2472629X-RAY DIFFRACTION100
2.1492-2.18280.27611330.23462690X-RAY DIFFRACTION100
2.1828-2.21860.27641340.23432675X-RAY DIFFRACTION100
2.2186-2.25680.27471450.22312670X-RAY DIFFRACTION100
2.2568-2.29790.29421790.22372650X-RAY DIFFRACTION100
2.2979-2.34210.27591370.22162671X-RAY DIFFRACTION100
2.3421-2.38990.27631380.21882676X-RAY DIFFRACTION100
2.3899-2.44180.29461310.21852701X-RAY DIFFRACTION100
2.4418-2.49860.27331380.20852653X-RAY DIFFRACTION100
2.4986-2.56110.24691570.20952710X-RAY DIFFRACTION100
2.5611-2.63040.27861710.21052631X-RAY DIFFRACTION100
2.6304-2.70780.24711480.21042699X-RAY DIFFRACTION100
2.7078-2.79510.27721600.20152662X-RAY DIFFRACTION100
2.7951-2.8950.22431340.18922716X-RAY DIFFRACTION100
2.895-3.01090.20651380.18572693X-RAY DIFFRACTION100
3.0109-3.14790.22151230.18582730X-RAY DIFFRACTION100
3.1479-3.31390.20941360.18282703X-RAY DIFFRACTION100
3.3139-3.52140.22391550.16982729X-RAY DIFFRACTION100
3.5214-3.79320.18061360.15782728X-RAY DIFFRACTION100
3.7932-4.17470.17651520.14412718X-RAY DIFFRACTION100
4.1747-4.77830.16151350.13412761X-RAY DIFFRACTION100
4.7783-6.01830.16981360.15292799X-RAY DIFFRACTION100
6.0183-47.38320.18551650.17692927X-RAY DIFFRACTION100
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)
11.5101-0.0994-0.00020.7506-0.25531.03260.07160.22830.1134-0.076-0.07420.1868-0.134-0.19590.00850.22850.0528-0.02830.2560.00040.2197-1.30299.4001-54.759
21.1176-0.4861-0.45340.78170.16750.74460.0417-0.04820.08940.01020.0452-0.0914-0.05770.1223-0.07740.1608-0.0037-0.00520.1772-0.02340.132822.9774.0441-37.559
30.845-0.1762-0.23790.5566-0.00420.84480.01960.1004-0.1512-0.0828-0.03320.07760.0628-0.05930.00930.15470.0095-0.00810.1556-0.04780.173516.5046-10.333-48.9906
40.61920.4787-0.0241.06850.34960.3679-0.0833-0.1143-0.2132-0.02490.05560.52990.2819-0.20410.00680.3646-0.0499-0.01250.29290.11630.5007-15.1414-17.81118.9645
51.62550.84290.74811.2873-0.26670.8467-0.0373-0.191-0.24160.06010.19530.48960.0248-0.3575-0.0970.2344-0.02180.0060.25940.12240.4196-16.6902-10.83142.3528
60.9729-0.04490.08690.72120.00641.07710.0108-0.0375-0.06650.00030.01240.031-0.03810.0344-0.02270.17150.0054-0.01950.12790.0240.14475.12553.0323-2.6712
71.66110.61130.18781.5454-0.19221.00940.0738-0.2433-0.02290.0366-0.07330.4036-0.1386-0.333-0.02940.19230.045-0.00470.27790.03550.261-18.98377.2484-1.8334
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 27:140)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 141:371)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 372:532)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 28:84)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 85:129)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 130:486)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 487:532)

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