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- PDB-5btu: The structure of Diels-Alderase PyrI4 in the biosynthetic pathway... -

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Basic information

Entry
Database: PDB / ID: 5btu
TitleThe structure of Diels-Alderase PyrI4 in the biosynthetic pathway of pyrroindomycins
ComponentsPyrI4
KeywordsLYASE / beta-barrel / Diels-Alderase / pyrroindomycins
Function / homologyAllene oxide cyclase barrel-like domain / Allene oxide cyclase barrel like domain / Isomerases / antibiotic biosynthetic process / isomerase activity / DI(HYDROXYETHYL)ETHER / Spiro-conjugate synthase
Function and homology information
Biological speciesStreptomyces rugosporus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.503 Å
AuthorsPan, L. / Guo, Y. / Liu, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Basic Research Program of China2013CB836900 China
a Shanghai Rising Star Scholar award13QA1404300 China
CitationJournal: Cell Chem Biol / Year: 2016
Title: Enzyme-Dependent [4 + 2] Cycloaddition Depends on Lid-like Interaction of the N-Terminal Sequence with the Catalytic Core in PyrI4
Authors: Zheng, Q. / Guo, Y. / Yang, L. / Zhao, Z. / Wu, Z. / Zhang, H. / Liu, J. / Cheng, X. / Wu, J. / Yang, H. / Jiang, H. / Pan, L. / Liu, W.
History
DepositionJun 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PyrI4
B: PyrI4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3849
Polymers39,6552
Non-polymers7297
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-11 kcal/mol
Surface area14270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.379, 47.379, 131.209
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein PyrI4


Mass: 19827.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces rugosporus (bacteria) / Gene: pyrI4 / Plasmid: pET28a
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: K7QVW7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 1000, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 20, 2014
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 11339 / % possible obs: 99.7 % / Observed criterion σ(I): 5.42 / Redundancy: 10.1 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 43.45
Reflection shellResolution: 2.5→2.75 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.969 / Mean I/σ(I) obs: 7.62 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data processing
PHENIX1.8.2_1309phasing
Cootmodel building
PHENIX1.8.2_1309refinement
RefinementMethod to determine structure: SAD / Resolution: 2.503→39.161 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 33.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2506 536 4.78 %Random selection
Rwork0.1801 ---
obs0.1835 11215 98.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.61 Å2
Refinement stepCycle: LAST / Resolution: 2.503→39.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2382 0 48 10 2440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162467
X-RAY DIFFRACTIONf_angle_d1.7533339
X-RAY DIFFRACTIONf_dihedral_angle_d19.575888
X-RAY DIFFRACTIONf_chiral_restr0.084394
X-RAY DIFFRACTIONf_plane_restr0.008432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.503-2.75480.37031450.24482634X-RAY DIFFRACTION99
2.7548-3.15330.32351350.22912687X-RAY DIFFRACTION99
3.1533-3.97220.27581320.18932703X-RAY DIFFRACTION100
3.9722-39.1660.20121240.15582655X-RAY DIFFRACTION98
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)
10.27150.22070.21730.17910.04380.58810.511-0.54940.01950.26680.0697-0.20810.57730.07050.00140.92950.12690.00730.7913-0.00890.836618.7585-10.034427.84
20.27520.00790.26230.332-0.11660.27170.2923-0.662-0.79180.47410.22710.36131.04630.34110.00751.2936-0.01070.17680.93250.1690.82510.3225-16.550330.2452
30.62850.28470.79190.2050.15670.888-0.06630.03640.1343-0.02660.38610.3920.0669-0.05150.00040.906-0.20030.04760.687-0.01770.652717.1382-6.21425.3787
40.0521-0.1810.04250.6455-0.05290.797-0.71950.431-0.1249-0.32050.8126-0.10180.06130.2315-0.0010.7513-0.1440.03570.8016-0.05270.631514.9473-2.925712.0753
50.0625-0.08070.02350.10550.00360.0474-0.21271.3274-0.1954-0.66590.92090.0291-0.68850.96750.00280.5512-0.12490.04820.9559-0.17660.75524.194-0.713115.2965
60.3122-0.51360.13121.25630.09310.509-0.39051.02650.37660.10050.28490.04860.1164-0.03310.00030.5187-0.14870.03520.7582-0.06280.666312.475-8.359818.8487
7-0.00010.0054-0.00640.09790.0109-0.00210.44431.4860.0139-0.3704-0.05370.0660.7472-1.136-0.00520.8649-0.0687-0.05010.6491-0.01030.726216.537-8.519.331
80.32360.12990.31781.0565-0.01750.3216-0.0238-0.365-0.1141-0.08680.5168-0.27081.11880.11970.00760.6191-0.08910.0730.7415-0.20540.759823.2452-11.48813.3576
90.1976-0.2151-0.25350.1940.30160.46770.19321.14510.5063-0.37520.0184-0.2359-0.71270.7416-0.00060.9677-0.0770.06590.8194-0.04390.851318.668310.06116.7619
100.0940.5837-0.07691.72650.86952.7763-0.2734-0.1520.03340.20640.4786-0.0674-0.1656-0.1528-00.6380.1149-0.01380.6927-0.00880.626115.95016.72731.9273
110.5771-0.0702-0.36330.95150.5831.0111-0.0049-0.1257-0.0352-0.13250.1983-0.1902-0.0723-0.1550.00010.52550.0833-0.0130.6244-0.02090.634917.34089.584427.9021
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 41 )
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 62 )
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 108 )
4X-RAY DIFFRACTION4chain 'A' and (resid 109 through 131 )
5X-RAY DIFFRACTION5chain 'A' and (resid 132 through 140 )
6X-RAY DIFFRACTION6chain 'A' and (resid 141 through 159 )
7X-RAY DIFFRACTION7chain 'A' and (resid 160 through 167 )
8X-RAY DIFFRACTION8chain 'A' and (resid 168 through 184 )
9X-RAY DIFFRACTION9chain 'B' and (resid 23 through 41 )
10X-RAY DIFFRACTION10chain 'B' and (resid 42 through 140 )
11X-RAY DIFFRACTION11chain 'B' and (resid 141 through 184 )

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