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- PDB-6al6: Crystal structure HpiC1 in P42 space group -

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Basic information

Entry
Database: PDB / ID: 6al6
TitleCrystal structure HpiC1 in P42 space group
Components12-epi-hapalindole C/U synthase
KeywordsISOMERASE / cyclase
Function / homologymetal ion binding / 12-epi-hapalindole C/U synthase
Function and homology information
Biological speciesFischerella sp. ATCC 43239 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.088 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.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_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_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.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)49,2918
Polymers49,0502
Non-polymers2406
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-31 kcal/mol
Surface area15550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.339, 71.339, 80.623
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number77
Space group name H-MP42
Components on special symmetry positions
IDModelComponents
11B-303-

CA

21B-449-

HOH

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Components

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


Mass: 24525.115 Da / Num. of mol.: 2 / Fragment: residues 26-227
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.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.09 Å3/Da / Density % sol: 41.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 22% PEG 4000, 200 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: Oct 9, 2016
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.09→42.76 Å / Num. obs: 24033 / % possible obs: 98.9 % / Redundancy: 13.5 % / Net I/σ(I): 18.94

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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: 2.088→42.764 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2533 1215 5.06 %
Rwork0.2064 22814 -
obs0.2089 24029 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.72 Å2 / Biso mean: 46.0328 Å2 / Biso min: 25.07 Å2
Refinement stepCycle: final / Resolution: 2.088→42.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2953 0 6 107 3066
Biso mean--45.92 47.04 -
Num. residues----391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083026
X-RAY DIFFRACTIONf_angle_d0.9754149
X-RAY DIFFRACTIONf_chiral_restr0.061472
X-RAY DIFFRACTIONf_plane_restr0.007552
X-RAY DIFFRACTIONf_dihedral_angle_d3.6661748
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0883-2.17190.40981350.32222486262199
2.1719-2.27070.35381380.306325152653100
2.2707-2.39040.34351110.290325822693100
2.3904-2.54020.37881180.277525242642100
2.5402-2.73630.321590.269424962655100
2.7363-3.01150.2981320.239925452677100
3.0115-3.44720.28521100.212625542664100
3.4472-4.34240.2211490.171225412690100
4.3424-42.77250.18451630.154425712734100

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