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- PDB-5wo3: Chaperone Spy bound to Im7 (Im7 un-modeled) -

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Basic information

Entry
Database: PDB / ID: 5wo3
TitleChaperone Spy bound to Im7 (Im7 un-modeled)
ComponentsPeriplasmic chaperone Spy
KeywordsCHAPERONE
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 / Periplasmic chaperone Spy
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsHorowitz, S. / Koldewey, P. / Martin, R. / Bardwell, J.C.A.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2016
Title: Visualizing chaperone-assisted protein folding.
Authors: Horowitz, S. / Salmon, L. / Koldewey, P. / Ahlstrom, L.S. / Martin, R. / Quan, S. / Afonine, P.V. / van den Bedem, H. / Wang, L. / Xu, Q. / Trievel, R.C. / Brooks, C.L. / Bardwell, J.C.
History
DepositionAug 1, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionAug 16, 2017ID: 5IOA
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 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_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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)24,09419
Polymers23,0312
Non-polymers1,06317
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-21 kcal/mol
Surface area12180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.150, 43.150, 260.159
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-317-

HOH

21A-371-

HOH

31A-392-

HOH

41B-328-

HOH

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Components

#1: Protein Periplasmic chaperone Spy / Spheroplast protein Y


Mass: 11515.285 Da / Num. of mol.: 2 / Fragment: UNP residues 52-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P77754
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8 / Details: PEG 3000, imidazole, zinc acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97933 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.87→33.21 Å / Num. obs: 20932 / % possible obs: 96.8 % / Redundancy: 8.2 % / CC1/2: 0.998 / Net I/σ(I): 13.2

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5INA

5ina
PDB Unreleased entry


Resolution: 1.87→33.214 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2528 1982 9.57 %
Rwork0.2191 --
obs0.2223 20701 95.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.87→33.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1404 0 29 179 1612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141474
X-RAY DIFFRACTIONf_angle_d1.3891965
X-RAY DIFFRACTIONf_dihedral_angle_d24.117586
X-RAY DIFFRACTIONf_chiral_restr0.063215
X-RAY DIFFRACTIONf_plane_restr0.005262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8701-1.91690.50751220.50621186X-RAY DIFFRACTION88
1.9169-1.96870.4671270.41541178X-RAY DIFFRACTION86
1.9687-2.02660.32461340.28551262X-RAY DIFFRACTION96
2.0266-2.0920.31311330.24891266X-RAY DIFFRACTION93
2.092-2.16680.29391370.23031277X-RAY DIFFRACTION93
2.1668-2.25350.35511370.27011302X-RAY DIFFRACTION96
2.2535-2.3560.26421380.21541323X-RAY DIFFRACTION97
2.356-2.48020.25371420.2191332X-RAY DIFFRACTION98
2.4802-2.63560.24171450.20361363X-RAY DIFFRACTION99
2.6356-2.8390.25791470.20511389X-RAY DIFFRACTION99
2.839-3.12450.22731490.21291400X-RAY DIFFRACTION100
3.1245-3.57610.2491500.19161426X-RAY DIFFRACTION100
3.5761-4.50370.20621530.16641434X-RAY DIFFRACTION100
4.5037-33.21970.22051680.22541581X-RAY DIFFRACTION99
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)
13.95170.0856-0.55922.8716-0.34043.012-0.22320.3151-0.49770.0982-0.01330.22480.4758-0.1203-0.03920.3222-0.02150.11740.3653-0.03060.275915.5325-0.26384.8041
24.71940.1003-1.57012.48680.35013.47770.18270.03770.2143-0.43590.0829-0.3407-0.38230.3573-0.02130.3592-0.09150.11350.2888-0.03020.28990.9321-28.003920.2198
30.96090.8205-0.30671.5204-1.0340.4358-0.06610.0114-0.203-0.1321-0.0558-0.23810.1078-0.09630.02250.3061-0.10550.08510.1986-0.01470.22134.8214-13.556623.3725
46.39191.1113-1.36812.844-0.534.04390.29780.53230.1196-0.376-0.29940.24260.3388-0.4319-0.01910.2848-0.01250.06710.2774-0.00910.26052.74847.07359.0255
52.45820.60120.53134.82662.09293.4534-0.2430.46150.9091-0.6711-0.12840.3354-0.2569-0.58880.03340.21340.0237-0.05670.4485-0.07240.6767-21.2301-25.228615.0966
60.77590.5655-0.90410.96070.57410.39030.12590.26230.07820.17580.00520.2229-0.1391-0.0958-0.01410.2449-0.0949-0.02320.23640.06890.2874-0.9116-9.529323.9433
76.81610.911-0.69542.63750.5713.4345-0.05061.04170.1418-0.4208-0.45910.5010.53760.21710.03690.2178-0.19760.01980.3624-0.10780.3314-9.4897-33.384912.76
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 28 THROUGH 50 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 57 THROUGH 68 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 69 THROUGH 106 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 107 THROUGH 123 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 29 THROUGH 50 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 60 THROUGH 106 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 107 THROUGH 122 )

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