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- PDB-5xgv: The structure of Diels-Alderase PyrE3 in the biosynthetic pathway... -

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Basic information

Entry
Database: PDB / ID: 5xgv
TitleThe structure of Diels-Alderase PyrE3 in the biosynthetic pathway of pyrroindomycins
ComponentsPyrE3
KeywordsOXIDOREDUCTASE / Diels-Alderase / pyrroindomycins
Function / homology
Function and homology information


Isomerases; Intramolecular lyases / antibiotic biosynthetic process / isomerase activity / FAD binding
Similarity search - Function
Glutaredoxin - #120 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / Glutaredoxin / FAD/NAD(P)-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Dialkyldecalin synthase
Similarity search - Component
Biological speciesStreptomyces rugosporus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 Å
AuthorsPan, L. / Gong, Y. / Guo, Y.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (General Program)21672253 China
the Foundation for Innovative Research Groups of the National Natural Science Foundation of China21621002 China
the Foundation for key projects of basic research of Shanghai Committee of Science and Technology, China15JC1400400 China
CitationJournal: Cell Chem Biol / Year: 2018
Title: Structural Insights into a Flavin-Dependent [4 + 2] Cyclase that Catalyzes trans-Decalin Formation in Pyrroindomycin Biosynthesis.
Authors: Zheng, Q. / Gong, Y. / Guo, Y. / Zhao, Z. / Wu, Z. / Zhou, Z. / Chen, D. / Pan, L. / Liu, W.
History
DepositionApr 18, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / 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: PyrE3
B: PyrE3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1364
Polymers98,5652
Non-polymers1,5712
Water14,088782
1
A: PyrE3
hetero molecules

B: PyrE3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1364
Polymers98,5652
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4840 Å2
ΔGint-29 kcal/mol
Surface area37130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.617, 58.022, 127.150
Angle α, β, γ (deg.)90.000, 127.460, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-861-

HOH

21A-963-

HOH

31A-985-

HOH

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Components

#1: Protein PyrE3


Mass: 49282.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces rugosporus (bacteria) / Gene: pyrE3
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: K7QRJ5
#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.: 782 / 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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: Sodium acetate trihydrate, PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97845 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97845 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 61958 / % possible obs: 99.2 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.05 / Rrim(I) all: 0.092 / Χ2: 0.531 / Net I/σ(I): 4.6 / Num. measured all: 197419
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.143.10.31530510.8540.2120.3810.46298.8
2.14-2.182.90.26930340.8890.1870.3290.46498.3
2.18-2.2230.23230840.910.1590.2830.49898.8
2.22-2.263.30.22130790.9310.1440.2650.49299.7
2.26-2.313.30.20431170.9390.1330.2440.50799.7
2.31-2.373.30.18530630.950.120.2210.51199.4
2.37-2.423.30.16731040.9610.1080.1990.50299.4
2.42-2.493.30.15630630.9640.1010.1860.49899.4
2.49-2.563.30.14130660.9680.0920.1690.52199.4
2.56-2.653.20.12631260.9730.0820.1510.5199.2
2.65-2.743.10.11130780.9770.0740.1340.53499.1
2.74-2.852.90.09730380.9820.0670.1190.55398.1
2.85-2.983.30.08931120.9860.0570.1060.56799.7
2.98-3.143.40.0831040.9870.0510.0960.59199.7
3.14-3.333.30.06931330.990.0450.0830.58699.7
3.33-3.593.30.05931110.9920.0380.070.59699.4
3.59-3.953.10.04931020.9940.0320.0590.54498.6
3.95-4.5230.04431110.9940.030.0530.50298.6
4.52-5.73.30.04431690.9950.0280.0530.505100
5.7-503.10.04932130.9940.0330.0590.65698.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
PHASERphasing
HKLdata scaling
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IGH

3igh


Resolution: 2.099→47.042 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2002 3149 5.08 %
Rwork0.1651 58800 -
obs0.167 61949 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.02 Å2 / Biso mean: 26.4834 Å2 / Biso min: 10.86 Å2
Refinement stepCycle: final / Resolution: 2.099→47.042 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6926 0 106 782 7814
Biso mean--20.71 32.17 -
Num. residues----922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087196
X-RAY DIFFRACTIONf_angle_d1.1639828
X-RAY DIFFRACTIONf_chiral_restr0.0471104
X-RAY DIFFRACTIONf_plane_restr0.0051300
X-RAY DIFFRACTIONf_dihedral_angle_d14.1642624
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0988-2.13160.23771360.20032573270996
2.1316-2.16660.27961310.19992637276898
2.1666-2.2040.25271260.18922627275398
2.204-2.2440.21681680.186826822850100
2.244-2.28720.2481470.179326602807100
2.2872-2.33390.20271360.1812657279399
2.3339-2.38460.24061310.172926752806100
2.3846-2.44010.21581350.17612678281399
2.4401-2.50110.23021490.18132664281399
2.5011-2.56870.20541410.18042657279899
2.5687-2.64430.24181400.18512714285499
2.6443-2.72960.21291390.17682636277599
2.7296-2.82720.23911430.18252627277098
2.8272-2.94040.23361330.183327082841100
2.9404-3.07420.20061550.18326732828100
3.0742-3.23620.23691680.181826702838100
3.2362-3.43890.19651470.164927062853100
3.4389-3.70430.16291400.15112657279799
3.7043-4.07690.17721400.13612690283098
4.0769-4.66640.1441430.12742695283899
4.6664-5.87740.17031440.148827472891100
5.8774-47.05360.16851570.15292767292498
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)
11.60260.22520.48270.73710.03681.46620.0039-0.0312-0.1688-0.0816-0.02140.01630.1439-0.25210.00250.1928-0.04590.01940.2227-0.0120.1656-29.94696.548524.5411
21.0918-0.2263-0.30330.29730.14440.62940.0176-0.0473-0.0466-0.0194-0.02380.00320.0791-0.11660.01530.1896-0.0343-0.00280.1544-0.00460.1814-17.07186.874419.6619
31.15630.00620.16081.4003-0.00891.5973-0.0175-0.51840.11570.29120.0707-0.02320.0057-0.1516-0.05190.2579-0.00660.0180.4512-0.07150.2197-24.455418.315147.7296
41.2977-0.3896-0.71260.9762-0.15391.85550.007-0.06130.20870.12050.028-0.0079-0.2468-0.42120.03460.21250.0557-0.01890.2755-0.03050.1875-38.527921.0519-16.9714
51.2401-0.20340.11580.35950.16491.35690.03460.06430.26690.05220.00960.0704-0.1933-0.41540.00070.23150.05380.0040.2336-0.02850.2297-35.180722.0434-17.2834
60.7810.39930.01650.76910.33740.3847-0.0213-0.02280.2122-0.08560.02930.0068-0.1425-0.05790.03030.27160.0004-0.02190.1776-0.0080.25-17.513528.6683-9.3855
70.347-0.23960.03821.6652-0.28341.01370.0054-0.06720.03660.1456-0.04380.2081-0.12270.00310.00640.2683-0.0018-0.01690.1704-0.02650.2589-14.578732.6791-3.0799
81.19330.124-0.06040.33660.12760.66520.04860.0711-0.03420.0315-0.0439-0.03250.0581-0.12370.00670.17930.0059-0.00690.1416-0.01480.1789-23.740312.3991-20.3182
90.96350.0914-0.04741.645-0.15121.7389-0.0530.4528-0.0509-0.32420.09580.0720.0221-0.3034-0.05280.2593-0.0145-0.02020.4518-0.05580.2189-38.01869.2663-40.7956
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 57 )A2 - 57
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 381 )A58 - 381
3X-RAY DIFFRACTION3chain 'A' and (resid 382 through 462 )A382 - 463
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 57 )B2 - 57
5X-RAY DIFFRACTION5chain 'B' and (resid 58 through 154 )B58 - 154
6X-RAY DIFFRACTION6chain 'B' and (resid 155 through 208 )B155 - 208
7X-RAY DIFFRACTION7chain 'B' and (resid 209 through 255 )B209 - 255
8X-RAY DIFFRACTION8chain 'B' and (resid 256 through 381 )B256 - 381
9X-RAY DIFFRACTION9chain 'B' and (resid 382 through 462 )B382 - 463

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