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- PDB-5d79: Structure of BBE-like #28 from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 5d79
TitleStructure of BBE-like #28 from Arabidopsis thaliana
ComponentsBerberine bridge enzyme-like protein
KeywordsOXIDOREDUCTASE / covalent FAD binding / berberine bridge enzyme like / plant enzyme
Function / homology
Function and homology information


plant-type cell wall / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / response to salt stress / FAD binding / oxidoreductase activity / 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, subdomain 2 / FAD-binding, type PCMH-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHATE ION / Berberine bridge enzyme-like 28
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.849 Å
AuthorsDaniel, B. / Kumar, P. / Gruber, K.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundW901 Austria
CitationJournal: Plos One / Year: 2016
Title: Structure of a Berberine Bridge Enzyme-Like Enzyme with an Active Site Specific to the Plant Family Brassicaceae.
Authors: Daniel, B. / Wallner, S. / Steiner, B. / Oberdorfer, G. / Kumar, P. / van der Graaff, E. / Roitsch, T. / Sensen, C.W. / Gruber, K. / Macheroux, P.
History
DepositionAug 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_validate_close_contact / struct_conn
Item: _pdbx_audit_support.funding_organization
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _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: Berberine bridge enzyme-like protein
B: Berberine bridge enzyme-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,2578
Polymers120,4252
Non-polymers1,8326
Water8,575476
1
A: Berberine bridge enzyme-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1294
Polymers60,2131
Non-polymers9163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Berberine bridge enzyme-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1294
Polymers60,2131
Non-polymers9163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.024, 133.132, 138.999
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-921-

HOH

21A-966-

HOH

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Components

#1: Protein Berberine bridge enzyme-like protein / FAD-binding and BBE domain-containing protein


Mass: 60212.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: THE FAD COFACTOR IS COVALENTLY LINKED TO THE PEPTIDE CHAIN VIA A COVALENT BOND BETWEEN ND1 OF HIS111 AND THE 8-ALPHA-METHYL GROUP OF THE ISOALLOXAZINE RING.
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g44440 / Plasmid: pPICZa / Production host: Komagataella pastoris (fungus) / Strain (production host): KM71H / References: UniProt: Q9FI21
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.83 % / Description: tetragonal bipyramidal
Crystal growTemperature: 293 K / Method: microbatch / pH: 7
Details: 0.1 M HEPES buffer pH 7.0, 30 % v/v Jeffamine ED 2001

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.91964 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 20, 2013 / Details: bent collimating mirror and toroid
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91964 Å / Relative weight: 1
ReflectionResolution: 1.849→15.89 Å / Num. all: 93337 / Num. obs: 93337 / % possible obs: 93.16 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.1224 / Net I/σ(I): 7.22
Reflection shellResolution: 1.849→1.915 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.5576 / % possible all: 91.72

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Processing

Software
NameVersionClassification
PHENIX1.8.3_1479refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D2H

3d2h


Resolution: 1.849→15.887 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.43 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2429 4947 5.3 %random selection
Rwork0.1965 ---
obs0.1988 93334 93.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.849→15.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7875 0 118 476 8469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088199
X-RAY DIFFRACTIONf_angle_d1.0511106
X-RAY DIFFRACTIONf_dihedral_angle_d13.2783012
X-RAY DIFFRACTIONf_chiral_restr0.0391192
X-RAY DIFFRACTIONf_plane_restr0.0051399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8515-1.88330.32912190.30654384X-RAY DIFFRACTION89
1.8833-1.91750.2922400.28994553X-RAY DIFFRACTION92
1.9175-1.95430.29822370.26394515X-RAY DIFFRACTION91
1.9543-1.99410.29232330.26334497X-RAY DIFFRACTION91
1.9941-2.03740.29222280.25784512X-RAY DIFFRACTION91
2.0374-2.08470.2842300.24864537X-RAY DIFFRACTION91
2.0847-2.13670.26392290.24134490X-RAY DIFFRACTION91
2.1367-2.19430.29762350.23864479X-RAY DIFFRACTION90
2.1943-2.25860.24712660.2364418X-RAY DIFFRACTION89
2.2586-2.33130.27792480.23344441X-RAY DIFFRACTION90
2.3313-2.41430.27922120.22574502X-RAY DIFFRACTION90
2.4143-2.51060.27462450.22794368X-RAY DIFFRACTION89
2.5106-2.62430.26122240.2224448X-RAY DIFFRACTION89
2.6243-2.76190.25742480.21684382X-RAY DIFFRACTION88
2.7619-2.93370.24762240.20654364X-RAY DIFFRACTION88
2.9337-3.15840.25442260.19714368X-RAY DIFFRACTION87
3.1584-3.47280.24412290.17854325X-RAY DIFFRACTION86
3.4728-3.96760.20772280.15094330X-RAY DIFFRACTION86
3.9676-4.96970.18872390.12344295X-RAY DIFFRACTION85
4.9697-15.22550.20122220.1534401X-RAY DIFFRACTION84
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)
15.9271-1.77142.44336.4156-0.58241.08940.1123-0.3829-0.44360.1725-0.1208-0.1710.1769-0.0568-0.05540.49650.2950.06670.70920.23080.40898.7904-11.6586118.492
20.4238-0.3613-0.35481.17-0.45051.0007-0.1226-0.3229-0.11610.38330.0144-0.19120.18680.49280.09670.25380.11750.00450.46870.11140.213595.06331.9053109.3993
31.0101-0.12-0.50480.8071-0.1091.4716-0.04820.0236-0.1197-0.05210.00270.01050.08750.07640.03860.09770.01660.01370.1287-0.00580.116382.39558.66286.9382
40.89780.1124-0.43210.89240.0021.1196-0.0071-0.19450.03080.1199-0.0105-0.0289-0.04420.1548-0.00480.11660.01770.00620.1676-0.01160.123583.508918.6765100.9296
54.08655.10284.74297.65227.66937.88780.4557-0.96921.1972-0.06470.3574-0.3198-2.03480.0519-0.8091.0971-0.04240.5151.0334-0.27980.657669.858226.532249.3171
60.0241-0.01050.05060.2175-0.13330.77570.3330.9021-0.4888-0.1971-0.1858-0.30190.370.35050.04410.39810.2731-0.03440.6408-0.35010.356259.92131.594264.4621
72.1991-0.19720.63080.57230.12721.13820.11090.1936-0.1522-0.032-0.0340.02410.04980.0633-0.04480.16490.05490.0110.13590.00560.119252.066345.505984.1906
80.56120.0677-0.07940.4262-0.15341.9255-0.00650.6555-0.0473-0.1615-0.01630.01570.0016-0.1120.01890.23810.0965-0.00150.4510.00960.163945.875648.846863.5946
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 33:47)
2X-RAY DIFFRACTION2(chain A and resid 48:143)
3X-RAY DIFFRACTION3(chain A and resid 144:344)
4X-RAY DIFFRACTION4(chain A and resid 345:530)
5X-RAY DIFFRACTION5(chain B and resid 33:47)
6X-RAY DIFFRACTION6(chain B and resid 48:143)
7X-RAY DIFFRACTION7(chain B and resid 144:444)
8X-RAY DIFFRACTION8(chain B and resid 445:530)

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