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- PDB-6owy: Spy H96L:Im7 K20pI-Phe complex; multiple anomalous datasets conta... -

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Basic information

Entry
Database: PDB / ID: 6owy
TitleSpy H96L:Im7 K20pI-Phe complex; multiple anomalous datasets contained herein for element identification
ComponentsPeriplasmic chaperone Spy
KeywordsCHAPERONE / periplasmic
Function / homology
Function and homology information


chaperone-mediated protein folding / protein folding chaperone / response to organic cyclic compound / unfolded protein binding / outer membrane-bounded periplasmic space / protein homodimerization activity
Similarity search - Function
: / LTXXQ motif family protein / LTXXQ motif family protein / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1490 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
IMIDAZOLE / IODIDE ION / Periplasmic chaperone Spy
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsRocchio, S. / Duman, R. / El Omari, K. / Mykhaylyk, V. / Yan, Z. / Wagner, A. / Bardwell, J.C.A. / Horowitz, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R00 GM120388 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Identifying dynamic, partially occupied residues using anomalous scattering.
Authors: Rocchio, S. / Duman, R. / El Omari, K. / Mykhaylyk, V. / Orr, C. / Yan, Z. / Salmon, L. / Wagner, A. / Bardwell, J.C.A. / Horowitz, S.
History
DepositionMay 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 2.0Oct 9, 2019Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Other / Refinement description / Structure summary
Category: atom_site / cell ...atom_site / cell / computing / pdbx_entity_instance_feature / pdbx_entry_details / pdbx_refine_tls / pdbx_refine_tls_group / refine / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / symmetry
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_z ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_z / _atom_site.occupancy / _cell.volume / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.percent_reflns_obs / _reflns.pdbx_CC_half / _reflns_shell.pdbx_CC_half / _symmetry.space_group_name_Hall
Description: Atoms with unrealistic or zero occupancies / Provider: author / Type: Coordinate replacement
Revision 2.1Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.3Oct 11, 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_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.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_label_seq_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: Periplasmic chaperone Spy
B: Periplasmic chaperone Spy
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,15519
Polymers23,0312
Non-polymers1,12517
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, analytical ultracentrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-24 kcal/mol
Surface area11940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.840, 42.840, 257.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Space group name HallP4w2c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+3/4
#8: -y,-x,-z+1/4
Components on special symmetry positions
IDModelComponents
11A-209-

ZN

21B-311-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Periplasmic chaperone Spy / Spheroplast protein Y


Mass: 11515.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P77754

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Non-polymers , 5 types, 75 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 55.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 22-34% PEG 3000, 70-270 mM zinc acetate, and 0.1 M imidazole, pH 8.0

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Data collection

DiffractionMean temperature: 75 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 2.3843, 2.7552
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
12.38431
22.75521
ReflectionResolution: 2.07→42.84 Å / Num. obs: 15762 / % possible obs: 99.7 % / Redundancy: 7.7 % / Biso Wilson estimate: 46.91 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.9
Reflection shellResolution: 2.07→2.12 Å / Num. unique obs: 1115 / CC1/2: 0.691

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5wnw

5wnw


Resolution: 2.07→42.84 Å / SU ML: 0.3322 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.9121
RfactorNum. reflection% reflection
Rfree0.2728 939 5.99 %
Rwork0.2272 --
obs0.23 15674 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 58.31 Å2
Refinement stepCycle: LAST / Resolution: 2.07→42.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1371 0 29 58 1458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01291432
X-RAY DIFFRACTIONf_angle_d1.22661917
X-RAY DIFFRACTIONf_chiral_restr0.054215
X-RAY DIFFRACTIONf_plane_restr0.0072257
X-RAY DIFFRACTIONf_dihedral_angle_d24.5366551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.180.41181280.35792023X-RAY DIFFRACTION98.58
2.18-2.320.38311290.31372023X-RAY DIFFRACTION99.63
2.32-2.490.32031320.27622051X-RAY DIFFRACTION99.36
2.49-2.750.32741320.24522088X-RAY DIFFRACTION99.95
2.75-3.140.30891330.23182083X-RAY DIFFRACTION100
3.14-3.960.22461370.21132149X-RAY DIFFRACTION99.91
3.96-42.260.25251480.20562318X-RAY DIFFRACTION99.92

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