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- PDB-6jqh: Crystal structure of MaDA -

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Basic information

Entry
Database: PDB / ID: 6jqh
TitleCrystal structure of MaDA
ComponentsMaDA
KeywordsPLANT PROTEIN / Diels-Alder reaction / FAD-dependent enzyme
Function / homology
Function and homology information


Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / 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 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE
Similarity search - Component
Biological speciesMorus alba (white mulberry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.303 Å
AuthorsDu, X.X. / Lei, X.G.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China21625201 China
National Natural Science Foundation of China21661140001 China
National Natural Science Foundation of China21561142002 China
National Natural Science Foundation of China91853202 China
CitationJournal: Nat.Chem. / Year: 2020
Title: FAD-dependent enzyme-catalysed intermolecular [4+2] cycloaddition in natural product biosynthesis.
Authors: Gao, L. / Su, C. / Du, X. / Wang, R. / Chen, S. / Zhou, Y. / Liu, C. / Liu, X. / Tian, R. / Zhang, L. / Xie, K. / Chen, S. / Guo, Q. / Guo, L. / Hano, Y. / Shimazaki, M. / Minami, A. / ...Authors: Gao, L. / Su, C. / Du, X. / Wang, R. / Chen, S. / Zhou, Y. / Liu, C. / Liu, X. / Tian, R. / Zhang, L. / Xie, K. / Chen, S. / Guo, Q. / Guo, L. / Hano, Y. / Shimazaki, M. / Minami, A. / Oikawa, H. / Huang, N. / Houk, K.N. / Huang, L. / Dai, J. / Lei, X.
History
DepositionMar 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MaDA
B: MaDA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,5434
Polymers116,9722
Non-polymers1,5712
Water8,521473
1
A: MaDA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2712
Polymers58,4861
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MaDA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2712
Polymers58,4861
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.665, 115.381, 95.870
Angle α, β, γ (deg.)90.00, 96.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MaDA


Mass: 58485.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Morus alba (white mulberry) / Production host: Trichoplusia ni (cabbage looper)
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 3.51 Å3/Da / Density % sol: 64.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Zinc acetate dihydrate, 0.1 M Sodium cacodylate trihydrate, pH 6.5, 18% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 65797 / % possible obs: 92.4 % / Redundancy: 7.3 % / Biso Wilson estimate: 25.74 Å2 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.052 / Rrim(I) all: 0.143 / Χ2: 1.131 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.347.10.61733970.9020.2420.6630.55295.2
2.34-2.3870.56433090.8920.2220.6070.57394.2
2.38-2.4370.49533690.9260.1960.5330.5995.2
2.43-2.487.10.44533620.9360.1760.4790.62894.3
2.48-2.537.10.38433070.9460.1520.4140.6694
2.53-2.597.10.33333770.9590.1310.3580.65294.1
2.59-2.667.10.29133130.9660.1150.3130.71193.3
2.66-2.737.20.24532790.9740.0970.2640.76692.6
2.73-2.817.20.2132190.9770.0830.2260.80791.1
2.81-2.97.30.19131940.9810.0750.2060.91889.3
2.9-37.20.16730220.9860.0660.1791.05884.9
3-3.127.40.14727600.9870.0570.1571.22977.5
3.12-3.267.50.13333910.9870.0520.1431.34495.3
3.26-3.447.60.11834320.990.0460.1271.52396.9
3.44-3.657.60.10634320.9930.0410.1141.67996.3
3.65-3.937.50.09534110.9940.0370.1021.77995.7
3.93-4.337.40.0933850.9940.0350.0971.8395
4.33-4.957.40.08233330.9950.0320.0881.77492.7
4.95-6.247.30.0829610.9940.0320.0861.7182.3
6.24-507.20.0735440.9960.0280.0751.57497.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VTE

3vte


Resolution: 2.303→44.044 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2264 1999 3.04 %
Rwork0.1856 --
obs0.1868 65780 92.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.303→44.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8228 0 0 473 8701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098439
X-RAY DIFFRACTIONf_angle_d0.99611455
X-RAY DIFFRACTIONf_dihedral_angle_d17.1924943
X-RAY DIFFRACTIONf_chiral_restr0.0551243
X-RAY DIFFRACTIONf_plane_restr0.0061446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3026-2.36020.26181400.20744467X-RAY DIFFRACTION91
2.3602-2.4240.26321460.20444647X-RAY DIFFRACTION95
2.424-2.49540.24631460.20184664X-RAY DIFFRACTION94
2.4954-2.57590.25041460.19294654X-RAY DIFFRACTION94
2.5759-2.66790.25431440.19574602X-RAY DIFFRACTION93
2.6679-2.77480.23281430.19044548X-RAY DIFFRACTION92
2.7748-2.9010.21481370.19584425X-RAY DIFFRACTION90
2.901-3.05390.2541270.19084044X-RAY DIFFRACTION82
3.0539-3.24520.22451380.19484389X-RAY DIFFRACTION88
3.2452-3.49570.22881490.19174768X-RAY DIFFRACTION97
3.4957-3.84730.23451500.17334775X-RAY DIFFRACTION96
3.8473-4.40350.20661490.15334729X-RAY DIFFRACTION95
4.4035-5.54630.16891390.15964473X-RAY DIFFRACTION90
5.5463-44.05160.24261450.21644596X-RAY DIFFRACTION91

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