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- PDB-5wpp: Crystal structure HpiC1 W73M/K132M -

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Basic information

Entry
Database: PDB / ID: 5wpp
TitleCrystal structure HpiC1 W73M/K132M
Components12-epi-hapalindole C/U synthase
KeywordsISOMERASE / cyclase / hapalindole
Function / homologymetal ion binding / TRIETHYLENE GLYCOL / 12-epi-hapalindole C/U synthase
Function and homology information
Biological speciesFischerella sp. ATCC 43239 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 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 1.5Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,68914
Polymers48,9442
Non-polymers74512
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-48 kcal/mol
Surface area16520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.920, 81.140, 131.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 24472.117 Da / Num. of mol.: 2 / Fragment: residues 26-227 / Mutation: W73M, K132M
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.: 10 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 23% PEG 3350, 200 mM CaCl2, 5% trehalose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2016
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→39.3 Å / Num. obs: 53625 / % possible obs: 99 % / Redundancy: 6.7 % / Net I/σ(I): 16.97

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→39.3 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.02
RfactorNum. reflection% reflection
Rfree0.2148 2704 5.04 %
Rwork0.1809 --
obs0.1826 53625 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.47 Å2 / Biso mean: 29.1047 Å2 / Biso min: 17.04 Å2
Refinement stepCycle: final / Resolution: 1.7→39.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3024 0 33 426 3483
Biso mean--42.59 36.26 -
Num. residues----397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053119
X-RAY DIFFRACTIONf_angle_d0.8114261
X-RAY DIFFRACTIONf_chiral_restr0.06480
X-RAY DIFFRACTIONf_plane_restr0.006566
X-RAY DIFFRACTIONf_dihedral_angle_d4.3171819
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 (%)
1.7-1.73090.33711240.32482666279098
1.7309-1.76420.3171370.290826012738100
1.7642-1.80020.29911400.25742640278099
1.8002-1.83940.29621520.241926062758100
1.8394-1.88210.25231370.21612675281299
1.8821-1.92920.22641460.198226242770100
1.9292-1.98140.20651310.18122636276799
1.9814-2.03970.20631380.18742668280699
2.0397-2.10550.25281490.188526252774100
2.1055-2.18080.20311430.184826692812100
2.1808-2.26810.25521520.189626552807100
2.2681-2.37130.23241390.192726992838100
2.3713-2.49630.19711220.192926892811100
2.4963-2.65260.23821420.193826962838100
2.6526-2.85740.24191390.201926982837100
2.8574-3.14480.21141540.189926902844100
3.1448-3.59960.20081520.167627202872100
3.5996-4.53410.18111430.141227812924100
4.5341-39.310.18411640.15822883304799

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