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- PDB-6eo5: Physcomitrella patens BBE-like 1 variant D396N -

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Basic information

Entry
Database: PDB / ID: 6eo5
TitlePhyscomitrella patens BBE-like 1 variant D396N
ComponentsPpBBE-like 1 D396N
KeywordsOXIDOREDUCTASE / BBE-like / VAO / cellobiose / bi-covalent / flavin
Function / homology
Function and homology information


FAD binding / oxidoreductase activity
Similarity search - Function
Berberine/berberine-like / Berberine and berberine like / 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 ...Berberine/berberine-like / Berberine and berberine like / 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 / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FAD-binding PCMH-type domain-containing protein
Similarity search - Component
Biological speciesPhyscomitrella patens subsp. patens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsToplak, M. / Winkler, A. / Macheroux, P.
Funding support Austria, 2items
OrganizationGrant numberCountry
Austrian Science FundP28678 Austria
Austrian Science FundW901 Austria
CitationJournal: FEBS J. / Year: 2018
Title: The single berberine bridge enzyme homolog of Physcomitrella patens is a cellobiose oxidase.
Authors: Toplak, M. / Wiedemann, G. / Ulicevic, J. / Daniel, B. / Hoernstein, S.N.W. / Kothe, J. / Niederhauser, J. / Reski, R. / Winkler, A. / Macheroux, P.
History
DepositionOct 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 17, 2024Group: 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: PpBBE-like 1 D396N
B: PpBBE-like 1 D396N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,2566
Polymers105,2432
Non-polymers2,0144
Water2,360131
1
A: PpBBE-like 1 D396N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6283
Polymers52,6211
Non-polymers1,0072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PpBBE-like 1 D396N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6283
Polymers52,6211
Non-polymers1,0072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.670, 148.670, 204.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein PpBBE-like 1 D396N


Mass: 52621.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physcomitrella patens subsp. patens (plant)
Gene: PHYPADRAFT_234241 / Variant: D396N / Production host: Komagataella phaffii (fungus) / Strain (production host): KM71H - PDI / References: UniProt: A0A2K1JP57*PLUS
#2: 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
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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

CrystalDescription: bipyramid
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Mg(OOCH)2, 13/14 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.009 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 2.6→48.416 Å / Num. obs: 70960 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 14.72 % / Biso Wilson estimate: 64.26 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.167 / Rrim(I) all: 0.173 / Χ2: 1.062 / Net I/σ(I): 12.08
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.6-2.6714.5892.2431.1251750.5962.32399.7
2.67-2.7415.0951.7411.4950170.7081.80299.6
2.74-2.8214.5431.3121.9949120.821.35999.8
2.82-2.9114.60.9882.7147590.8891.02399.8
2.91-315.1410.83.3946090.9130.82899.8
3-3.1115.4220.6064.5745070.9450.627100
3.11-3.2215.2760.4466.1843370.9710.46299.9
3.22-3.3614.9070.3218.4641600.9840.33399.9
3.36-3.5114.240.26110.1940120.9890.2799.9
3.51-3.6814.6180.19313.5638410.9930.299.9
3.68-3.8815.340.15417.3536600.9950.15999.9
3.88-4.1115.0560.1320.0534930.9960.135100
4.11-4.3914.5840.10923.1632750.9960.11399.9
4.39-4.7513.9670.09725.3330620.9960.101100
4.75-5.214.7910.0927.6828290.9970.093100
5.2-5.8114.9310.09525.8525840.9960.099100
5.81-6.7113.8110.09325.4722890.9970.097100
6.71-8.2214.0940.07829.6619730.9970.081100
8.22-11.6313.7940.06633.5215570.9980.068100
11.63-48.41612.0240.06231.949090.9970.06598.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.22 Å48.42 Å
Translation7.22 Å48.42 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.6.0phasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model based on 4ud8 (Swiss model)

4ud8


Resolution: 2.6→48.416 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.15
RfactorNum. reflection% reflection
Rfree0.2095 3547 5 %
Rwork0.1829 --
obs0.1843 70947 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.16 Å2 / Biso mean: 63.3582 Å2 / Biso min: 38.43 Å2
Refinement stepCycle: final / Resolution: 2.6→48.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7158 0 134 131 7423
Biso mean--68.55 58.57 -
Num. residues----925
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067505
X-RAY DIFFRACTIONf_angle_d0.88410257
X-RAY DIFFRACTIONf_chiral_restr0.0521117
X-RAY DIFFRACTIONf_plane_restr0.0051298
X-RAY DIFFRACTIONf_dihedral_angle_d10.3624297
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.63570.35041390.330326442783100
2.6357-2.67330.34741390.29726412780100
2.6733-2.71320.30391400.279226632803100
2.7132-2.75560.31431390.27692644278399
2.7556-2.80080.2941410.26426682809100
2.8008-2.84910.30771400.246126632803100
2.8491-2.90090.2791380.231826262764100
2.9009-2.95660.24231410.235326722813100
2.9566-3.0170.28151400.240526602800100
3.017-3.08260.28991410.239126762817100
3.0826-3.15430.27821400.239726732813100
3.1543-3.23310.26241410.238526722813100
3.2331-3.32050.28741400.230626672807100
3.3205-3.41820.28921410.222126812822100
3.4182-3.52850.21891410.211226822823100
3.5285-3.65460.20241420.204626952837100
3.6546-3.80090.22791420.192426952837100
3.8009-3.97380.22671410.185526902831100
3.9738-4.18320.20821420.165727012843100
4.1832-4.44510.17421430.1427252868100
4.4451-4.7880.16751440.135427252869100
4.788-5.26930.15231440.129727412885100
5.2693-6.03060.18611450.157427572902100
6.0306-7.59320.16121470.159927902937100
7.5932-48.42440.151560.145829493105100

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