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- PDB-3o39: Crystal Structure of SPY -

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Basic information

Entry
Database: PDB / ID: 3o39
TitleCrystal Structure of SPY
ComponentsPeriplasmic protein related to spheroblast formation
KeywordsCHAPERONE / alpha-helical / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homologyLTXXQ motif family protein / LTXXQ motif family protein / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1490 / Four Helix Bundle (Hemerythrin (Met), subunit A) / periplasmic space / Up-down Bundle / Mainly Alpha / : / Periplasmic chaperone Spy
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.599 Å
AuthorsRuane, K.M. / Shi, R. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Genetic selection designed to stabilize proteins uncovers a chaperone called Spy.
Authors: Quan, S. / Koldewey, P. / Tapley, T. / Kirsch, N. / Ruane, K.M. / Pfizenmaier, J. / Shi, R. / Hofmann, S. / Foit, L. / Ren, G. / Jakob, U. / Xu, Z. / Cygler, M. / Bardwell, J.C.
History
DepositionJul 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Periplasmic protein related to spheroblast formation
B: Periplasmic protein related to spheroblast formation
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,18911
Polymers26,1782
Non-polymers1,0129
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.971, 68.971, 124.281
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein Periplasmic protein related to spheroblast formation / Spheroplast protein Y


Mass: 13088.823 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) / Strain: O157:H7 EDL933 / Gene: ECs2449, spy, Z2775 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8XDZ4
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.28 Å3/Da / Density % sol: 62.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.3M CdCl2, 2.4M Ammonium Sulphate, vapor diffusion, sitting drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97923 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 10, 2010
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 19671 / Redundancy: 9.3 % / Rsym value: 0.116 / Net I/σ(I): 37.07

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
PHENIX1.6_289refinement
SCALEPACKdata scaling
SHARPphasing
RESOLVEphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.599→43.063 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.829 / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.44 / σ(F): 1.89 / Phase error: 30.1 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2808 949 4.86 %
Rwork0.2431 --
obs0.245 19513 95.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.47 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.5639 Å2-0 Å2-0 Å2
2--0.5639 Å20 Å2
3----1.1277 Å2
Refinement stepCycle: LAST / Resolution: 2.599→43.063 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1479 0 9 21 1509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141542
X-RAY DIFFRACTIONf_angle_d1.3242070
X-RAY DIFFRACTIONf_dihedral_angle_d20.732602
X-RAY DIFFRACTIONf_chiral_restr0.077232
X-RAY DIFFRACTIONf_plane_restr0.005274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.599-2.7360.2854840.27082209X-RAY DIFFRACTION79
2.736-2.90740.30671200.26212681X-RAY DIFFRACTION96
2.9074-3.13180.28531520.24212766X-RAY DIFFRACTION100
3.1318-3.44680.27481510.22572772X-RAY DIFFRACTION100
3.4468-3.94530.25461420.20362627X-RAY DIFFRACTION97
3.9453-4.96950.21191670.19892738X-RAY DIFFRACTION100
4.9695-43.06860.31471330.27062771X-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)
11.4814-0.65011.18513.51521.78682.8360.64210.0557-0.2202-0.1774-0.5093-0.25830.38890.6448-0.01750.4228-0.0007-0.15780.28610.02150.21573.7331-9.138218.7795
24.2426-2.3501-2.87984.0424-0.11423.68640.2004-0.3003-0.2428-0.2776-0.17720.3621.40450.4628-0.00060.90160.36-0.24810.2331-0.06990.29865.3584-21.1245-8.5423
33.37030.5639-1.58964.66111.17652.66150.29260.387-0.49950.3272-0.005-0.73681.3665-0.08570.00340.9569-0.3573-0.28210.22910.10980.3837-5.5427-21.18223.874
42.11991.22611.17184.1428-2.35273.20020.79880.1758-0.53660.1792-0.14870.3841-0.1309-0.39860.0010.49430.0372-0.2040.28060.00980.2661-3.4845-8.8404-3.4959
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain X and resid 79:115)
2X-RAY DIFFRACTION2(chain X and (resid 52:78 or resid 116:147))
3X-RAY DIFFRACTION3(chain C and (resid 52:78 or resid 116:147))
4X-RAY DIFFRACTION4(chain C and resid 79:115)

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