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- PDB-5wo2: Chaperone Spy bound to Casein Fragment (Casein un-modeled) -

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Basic information

Entry
Database: PDB / ID: 5wo2
TitleChaperone Spy bound to Casein Fragment (Casein 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: 1.769 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: 5IOG
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 / pdbx_struct_special_symmetry / 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_alt_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_alt_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)24,61326
Polymers23,0812
Non-polymers1,53224
Water2,162120
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)42.960, 42.960, 258.169
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-213-

ZN

21A-310-

HOH

31B-326-

HOH

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Components

#1: Protein Periplasmic chaperone Spy / Spheroplast protein Y


Mass: 11540.274 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-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 0.97861 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 1.77→36.88 Å / Num. obs: 25052 / % possible obs: 99.99 % / Redundancy: 8.7 % / CC1/2: 0.999 / Net I/σ(I): 15.3

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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: 1.769→35.762 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.252 1268 5.08 %
Rwork0.2146 --
obs0.2165 24952 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.769→35.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1423 0 48 120 1591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141547
X-RAY DIFFRACTIONf_angle_d1.3032065
X-RAY DIFFRACTIONf_dihedral_angle_d20.654614
X-RAY DIFFRACTIONf_chiral_restr0.057221
X-RAY DIFFRACTIONf_plane_restr0.006277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.769-1.83980.40481300.3282552X-RAY DIFFRACTION100
1.8398-1.92360.26851380.28692556X-RAY DIFFRACTION100
1.9236-2.0250.29021410.25682573X-RAY DIFFRACTION100
2.025-2.15180.28451520.24292575X-RAY DIFFRACTION100
2.1518-2.31790.27381260.21722580X-RAY DIFFRACTION100
2.3179-2.55110.25231430.2152634X-RAY DIFFRACTION100
2.5511-2.92010.21261260.20772647X-RAY DIFFRACTION100
2.9201-3.67850.24361500.20252679X-RAY DIFFRACTION100
3.6785-35.76970.24671620.20292888X-RAY DIFFRACTION100
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)
14.7511-5.55861.70196.5061-2.05973.0111-0.08930.43651.40480.365-0.3583-1.1546-1.05082.48490.19570.5499-0.138-0.10921.0021-0.03750.4023-8.3917-3.2649260.4043
28.1839-2.9829-2.22639.35596.05144.21090.05770.24960.5777-0.5648-0.38820.396-0.6208-0.31910.25980.3266-0.0035-0.05430.5510.03260.2898-19.086-0.9533262.2026
39.66652.0799-1.62323.4902-2.28054.26110.22660.24861.3094-0.6692-0.03730.2912-1.9748-0.4426-0.2731.10510.1635-0.24630.584-0.21510.7432-18.03216.2208267.114
43.5293.35975.13194.69696.05348.79820.0090.5224-0.0084-0.4029-0.17250.90240.2663-0.56370.09610.5144-0.1511-0.09560.46610.03770.4682-1.042727.2695278.1549
52.76061.4901-1.59453.10110.23112.19190.1349-0.27170.62810.233-0.0950.34330.08260.2974-0.08460.3185-0.1033-0.09140.2120.00940.33472.649924.7724287.0594
64.56374.86663.63586.91665.38074.7364-0.20660.02840.4247-0.5537-0.18210.7193-0.5364-0.0690.2960.4038-0.1051-0.05170.32250.01190.2544-11.14175.0265277.2584
75.08481.07712.35584.76893.38314.45490.14091.2887-0.4884-0.5133-0.1124-0.4777-0.82930.5285-0.01810.4129-0.1039-0.07750.4743-0.01960.2971-3.1339-7.3117267.3098
86.6693-2.40713.62416.38283.0087.39920.5646-0.67390.37220.0486-0.2902-0.451-0.21180.3928-0.09570.4632-0.1685-0.05520.3608-0.02230.2823-4.0292-2.7539279.2033
92.92223.0174-0.73936.3221-2.7683.1669-0.21870.3832-0.1665-0.09070.0639-0.6331-0.07250.13710.09830.2681-0.09310.01470.3159-0.05450.29665.573120.8118279.2368
101.6705-2.9742-0.93527.082-1.21075.15311.02490.2742-1.6641-0.2038-0.4484-0.3052-0.5724-0.0907-0.72410.7806-0.2745-0.1690.7658-0.06061.131616.416329.9088266.3459
119.74364.0961-3.45241.9835-0.52974.4854-0.34350.7215-0.856-0.5697-0.2991-1.76950.14711.23360.93010.3504-0.06210.18360.65780.17311.187222.541923.3972275.1436
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 28 THROUGH 35 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 36 THROUGH 45 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 46 THROUGH 47 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 56 THROUGH 68 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 69 THROUGH 85 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 86 THROUGH 106 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 107 THROUGH 123 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 57 THROUGH 74 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 75 THROUGH 124 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 29 THROUGH 35 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 36 THROUGH 49 )

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