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- PDB-5wps: Crystal structure HpiC1 Y101F -

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Basic information

Entry
Database: PDB / ID: 5wps
TitleCrystal structure HpiC1 Y101F
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: 1.389 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 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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)24,8526
Polymers24,5091
Non-polymers3435
Water5,729318
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)49,70312
Polymers49,0182
Non-polymers68510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3570 Å2
ΔGint-13 kcal/mol
Surface area16010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.797, 49.814, 53.367
Angle α, β, γ (deg.)90.000, 110.420, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 24509.115 Da / Num. of mol.: 1 / Fragment: residues 26-227 / Mutation: Y101F
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

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Non-polymers , 5 types, 323 molecules

#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: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.89 Å3/Da / Density % sol: 57.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: containing 22% PEG 4000, 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: 1.389→45.133 Å / Num. obs: 51294 / % possible obs: 90.5 % / Redundancy: 6.6 % / Net I/σ(I): 20.44

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Processing

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

5wpp


Resolution: 1.389→45.133 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.2
RfactorNum. reflection% reflection
Rfree0.1684 2532 4.94 %
Rwork0.137 --
obs0.1386 51234 90.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 98.61 Å2 / Biso mean: 26.6008 Å2 / Biso min: 15.33 Å2
Refinement stepCycle: final / Resolution: 1.389→45.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1538 0 18 318 1874
Biso mean--33.21 43.58 -
Num. residues----199

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