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- PDB-6owx: Spy H96L:Im7 L18pI-Phe complex; multiple anomalous datasets conta... -

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Basic information

Entry
Database: PDB / ID: 6owx
TitleSpy H96L:Im7 L18pI-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: 2.06 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: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / computing / pdbx_entity_instance_feature / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_conn_angle / pdbx_validate_close_contact / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / struct_asym / struct_conn / struct_site / struct_site_gen / symmetry
Item: _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] ..._atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _cell.volume / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.selection_details / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.d_res_low / _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 / _struct_asym.entity_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id / _struct_site_gen.symmetry / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_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)24,42423
Polymers23,0312
Non-polymers1,39421
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, analytical ultracentrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-21 kcal/mol
Surface area11880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.800, 42.800, 253.780
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

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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, 63 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 13 / 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.: 5 / 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.: 42 / 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: 2.75 Å3/Da / Density % sol: 55.22 %
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 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.3843 Å / Relative weight: 1
ReflectionResolution: 2.06→42.3 Å / Num. obs: 15670 / % possible obs: 99.9 % / Redundancy: 8.2 % / Biso Wilson estimate: 49.05 Å2 / CC1/2: 1 / Net I/σ(I): 21
Reflection shellResolution: 2.06→2.1 Å / Num. unique obs: 1112 / CC1/2: 0.651

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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: 2.06→42.2 Å / SU ML: 0.3119 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 29.1666
RfactorNum. reflection% reflection
Rfree0.2768 1716 6.17 %
Rwork0.2408 --
obs0.243 27823 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 66.97 Å2
Refinement stepCycle: LAST / Resolution: 2.06→42.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1356 0 41 42 1439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01171410
X-RAY DIFFRACTIONf_angle_d1.21611887
X-RAY DIFFRACTIONf_chiral_restr0.0518214
X-RAY DIFFRACTIONf_plane_restr0.0081254
X-RAY DIFFRACTIONf_dihedral_angle_d19.7703522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.120.39361400.34742180X-RAY DIFFRACTION99.19
2.12-2.190.33181390.34812134X-RAY DIFFRACTION99.82
2.19-2.270.28791470.30292212X-RAY DIFFRACTION99.96
2.27-2.360.28931370.27672166X-RAY DIFFRACTION100
2.36-2.470.29991450.26442157X-RAY DIFFRACTION99.87
2.47-2.60.2651470.26052195X-RAY DIFFRACTION99.96
2.6-2.760.32511430.26482181X-RAY DIFFRACTION100
2.76-2.970.27841420.25772161X-RAY DIFFRACTION100
2.97-3.270.28761480.25712182X-RAY DIFFRACTION100
3.27-3.740.26811450.23562165X-RAY DIFFRACTION99.91
3.74-4.710.24681410.20242195X-RAY DIFFRACTION99.96
4.71-40.560.28051420.22932179X-RAY DIFFRACTION99.91
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.9181384915-3.83761338844.700817963557.015793575851.657304963941.929799264060.6081465296851.007007747830.112836414208-0.5009696351170.109440793405-1.52188334924-0.4369294412981.45729401243-0.4918098011570.4613116535-0.02078297546970.0551895367591.02875258110.01659233831190.696872176424-9.25230724533-4.10005968305254.330706378
22.77809453144-4.09977816618-2.107420776362.505588928641.7177101986710.01725484810.004180586751610.1210863656280.180023475367-0.0824677372696-0.524646665530.159371056314-1.00291651403-0.5788000133920.6061185566070.409610277573-0.0334597449180.02167835835570.521069119693-0.02310890437320.518392954091-18.78208626411.40790866633260.54212579
39.03362378201-0.647502868043-0.1315099934816.27424803178-3.241430035476.730209577330.528688093050.571636008988-0.4534744223970.1287443831710.1491737346931.491568243821.45920094071-1.01837787742-0.4970007488050.446499671221-0.123135241004-0.03699954115490.527830746830.02817498190410.5937913169061.8053848163227.4044429266274.614996675
43.87812663855.449204183513.551495762377.983046679615.021427367332.15366165916-0.2236155344840.1205253928560.496892643673-0.1229554517690.03987927938630.624687837905-0.1562173344230.1547714534860.2039739012830.492329334353-0.111000803364-0.0455103006390.439215291693-0.006054612417070.495579118535-6.025210897879.86517784774275.267297274
52.064044822541.51503761471-0.6392582468748.51158882823-4.38465599082.06487410349-0.8977192767982.02312679459-1.39238787429-1.644348158840.7388818230841.049424260070.5565147565920.7315717852440.2853394795960.800280422637-0.243069767870.08391671369340.976665568894-0.2159646907610.9778181788519.063300765729.9865185971261.170739184
61.886943850151.936888490011.545974532142.082969868872.016430882122.131809582240.189532138131-0.714111134699-2.722167239270.838080180702-1.0207430485-2.967363468290.3105157516631.376609365951.860222169590.71333809333-0.08967834675470.04309019110420.6579588404480.05530314141821.8650676184521.613187874620.7639161839271.782649667
71.982355488319.440762769437.918094722926.119032749375.101928540444.342887126590.253359830123-0.4107561998381.763063135820.475400047096-0.0985253801686-2.12881459433-0.000653586993382-0.314237775691-0.2492775558171.6951482148-0.3420793156670.04658689886971.13626785052-0.1584035608911.245704393587.534736210671.23446098402276.636808455
86.811979323652.25066866576-0.4511631483857.931106734380.608786124748.393564039380.589073378059-0.6930925358160.2243855067340.647461819584-0.5038608691890.09964362436730.03389571799770.3241819827-0.03100396260580.440063307693-0.117469405695-0.08319435089320.528291902031-0.001814227724290.481367369571-6.19475837538-5.53110903766273.467935288
97.741131162438.23514240483-2.365108404328.59703591945-2.321150282631.11293247916-0.2914518424570.517477106175-0.146476012372-0.3345145897490.431466995972-0.05410586163920.356642478802-0.18320952823-0.02674227858520.395547550425-0.0978394138914-0.02696594399090.444708249704-0.06922369852060.4046636088994.2735835308514.7058576773277.795627749
103.017729264073.081523311463.7932302818910.0558873431-0.1118733734523.040660627540.3926675379371.21723899887-0.187010122072-0.3900514070190.0163290093856-0.340917319567-0.1409038317270.784112799634-0.2916527838440.4760523581570.00390277514258-0.002307491055530.668494170327-0.0241927411550.469496070951-2.29333052178-7.86800967865262.563889789
118.885932766143.662610379970.96252092808410.0045433784-1.120003861887.3745167905-0.545493462651.17016306646-0.11363503797-0.778402986880.25018989263-0.1590601334230.00923622607971-0.3516434764120.1862000827590.415809618821-0.05185980059870.005505588215050.6316796565540.008009624817130.3362321085338.6986782023632.5532939328266.044755502
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 28 THROUGH 36 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 37 THROUGH 50 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 57 THROUGH 71 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 72 THROUGH 108 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 29 THROUGH 36 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 37 THROUGH 52 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 57 THROUGH 61 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 62 THROUGH 72 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 73 THROUGH 108 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 109 THROUGH 122 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 109 THROUGH 122 )

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