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- PDB-5wpu: Crystal structure HpiC1 Y101S -

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Basic information

Entry
Database: PDB / ID: 5wpu
TitleCrystal structure HpiC1 Y101S
Components12-epi-hapalindole C/U synthase
KeywordsISOMERASE / cyclase
Function / homology12-epi-hapalindole C/U synthase
Function and homology information
Biological speciesFischerella sp. ATCC 43239 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsNewmister, S.A. / Li, S. / Garcia-Borras, M. / Sanders, J.N. / Yang, S. / Lowell, A.N. / Yu, F. / Smith, J.L. / Williams, R.M. / Houk, K.N. / Sherman, D.H.
Funding support United States, 5items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1205646 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA70375 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118101 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM076477 United States
National Science Foundation (NSF, United States)OCI-1053575 United States
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: Structural basis of the Cope rearrangement and cyclization in hapalindole biogenesis.
Authors: Newmister, S.A. / Li, S. / Garcia-Borras, M. / Sanders, J.N. / Yang, S. / Lowell, A.N. / Yu, F. / Smith, J.L. / Williams, R.M. / Houk, K.N. / Sherman, D.H.
History
DepositionAug 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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: 12-epi-hapalindole C/U synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6514
Polymers24,4491
Non-polymers2023
Water5,693316
1
A: 12-epi-hapalindole C/U synthase
hetero molecules

A: 12-epi-hapalindole C/U synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3038
Polymers48,8982
Non-polymers4056
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2740 Å2
ΔGint-23 kcal/mol
Surface area15880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.936, 49.622, 53.438
Angle α, β, γ (deg.)90.000, 110.310, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

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Components

#1: Protein 12-epi-hapalindole C/U synthase / HpiU5


Mass: 24449.018 Da / Num. of mol.: 1 / Mutation: Y101S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fischerella sp. ATCC 43239 (bacteria) / Gene: hpiU5 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A076NBW8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.9 Å3/Da / Density % sol: 57.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% MEPEG 5000, 150 mM CaCl2, 100 mM Tris pH 8.5, 5% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 7, 2017
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.39→45.213 Å / Num. obs: 52971 / % possible obs: 93.6 % / Redundancy: 6.3 % / Net I/σ(I): 18.24

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WPP

5wpp


Resolution: 1.39→45.213 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.48
RfactorNum. reflection% reflection
Rfree0.1817 2623 4.96 %
Rwork0.1495 --
obs0.1512 52840 93.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 65.33 Å2 / Biso mean: 24.5082 Å2 / Biso min: 12.15 Å2
Refinement stepCycle: final / Resolution: 1.39→45.213 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1524 0 10 316 1850
Biso mean--36.28 40.38 -
Num. residues----199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051582
X-RAY DIFFRACTIONf_angle_d0.7942170
X-RAY DIFFRACTIONf_chiral_restr0.086243
X-RAY DIFFRACTIONf_plane_restr0.006290
X-RAY DIFFRACTIONf_dihedral_angle_d3.629898
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3897-1.41490.5183840.58861486157053
1.4149-1.44210.4954890.50241816190565
1.4421-1.47160.44011010.41162086218775
1.4716-1.50360.3591270.3212483261087
1.5036-1.53860.29291630.26362735289899
1.5386-1.5770.27231530.21728112964100
1.577-1.61970.23371340.198328432977100
1.6197-1.66730.20911240.177427932917100
1.6673-1.72120.16961510.135228172968100
1.7212-1.78270.21171520.13528352987100
1.7827-1.85410.16821370.121327662903100
1.8541-1.93840.16531290.123528632992100
1.9384-2.04060.15831500.124928092959100
2.0406-2.16850.18421420.130128402982100
2.1685-2.33590.18331550.141928202975100
2.3359-2.5710.17761440.142928352979100
2.571-2.94290.17031730.149328373010100
2.9429-3.70750.15631570.133528172974100
3.7075-45.23650.15771580.138729253083100

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