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- PDB-3oeo: The crystal structure E. coli Spy -

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Basic information

Entry
Database: PDB / ID: 3oeo
TitleThe crystal structure E. coli Spy
ComponentsSpheroplast protein Y
KeywordsSIGNALING PROTEIN / LTxxQ / extracytoplasmic stress response-related
Function / homology
Function and homology information


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
: / Periplasmic chaperone Spy / Periplasmic chaperone Spy
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsKwon, E. / Kim, D.Y. / Gross, C.A. / Gross, J.D. / Kim, K.K.
CitationJournal: Protein Sci. / Year: 2010
Title: The crystal structure Escherichia coli Spy.
Authors: Kwon, E. / Kim, D.Y. / Gross, C.A. / Gross, J.D. / Kim, K.K.
History
DepositionAug 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spheroplast protein Y
B: Spheroplast protein Y
C: Spheroplast protein Y
D: Spheroplast protein Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,21926
Polymers63,7464
Non-polymers2,47322
Water1,58588
1
A: Spheroplast protein Y
C: Spheroplast protein Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,33415
Polymers31,8732
Non-polymers1,46113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Spheroplast protein Y
D: Spheroplast protein Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,88411
Polymers31,8732
Non-polymers1,0129
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.195, 69.195, 126.347
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Spheroplast protein Y


Mass: 15936.379 Da / Num. of mol.: 4 / Fragment: mature form of EcSpy, UNP residues 24-161
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: spy, b1743, JW1732 / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C5W4R8, UniProt: C6ECL5*PLUS
#2: Chemical...
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.74 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 4.6
Details: 0.1 M acetate pH 4.6, 26-32% (w/v) PEG400, 0.2 M CdCl2, and 2 mM TCEP, EVAPORATION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587, 0.97944, 0.97976, 0.98771, 0.97220
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 26, 2009
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.115871
20.979441
30.979761
40.987711
50.97221
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.263
11-H, H+K, -L20.25
11-h,-k,l30.237
11-H-K, K, -L40.25
ReflectionResolution: 2.7→20 Å / Num. all: 18617 / Num. obs: 18354 / % possible obs: 98.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 15.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.7-2.82.80.38595.3
2.8-2.9130.36595.7
2.91-3.043.20.28696.7
3.04-3.23.60.18698.4
3.2-3.43.80.1798.6
3.4-3.664.40.10299.1
3.66-4.034.70.07199.7
4.03-4.64.90.05799.8
4.6-5.774.90.05699.7
5.77-205.40.0399.6

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.894 / Occupancy max: 1 / Occupancy min: 1 / SU B: 24.139 / SU ML: 0.226 / SU R Cruickshank DPI: 0.1226 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29973 915 5 %RANDOM
Rwork0.25227 ---
obs0.25462 17348 98.2 %-
all-18263 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.503 Å2
Baniso -1Baniso -2Baniso -3
1--30.89 Å2-0 Å20 Å2
2---30.89 Å2-0 Å2
3---61.78 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3016 0 22 88 3126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223048
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.9594060
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0045360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.66125.814172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.76615668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2261524
X-RAY DIFFRACTIONr_chiral_restr0.0760.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212268
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3921.51824
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.72622944
X-RAY DIFFRACTIONr_scbond_it0.74631224
X-RAY DIFFRACTIONr_scangle_it1.2614.51116
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.767 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 76 -
Rwork0.318 1252 -
obs--93.98 %
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)
11.97750.4863-2.52450.6319-1.95719.9880.14160.2-0.269-0.1256-0.0840.19260.2507-0.5468-0.05760.2501-0.0352-0.13080.2194-0.13080.2095-5.883-16.6226.044
22.1259-0.3922.57311.4166-2.61689.81380.1981-0.00850.09660.1007-0.25940.2569-0.6627-0.13650.06130.42740.14240.0810.1529-0.08870.1666-5.80516.352-5.726
31.1029-0.5496-3.07952.70013.201510.0665-0.0364-0.1715-0.23310.1937-0.2972-0.20860.44820.33480.33350.17380.0654-0.09120.13780.04120.15065.921-16.504-6.084
41.76820.5753.72152.07562.66789.82060.17510.36380.0705-0.0821-0.1278-0.1691-0.19280.7168-0.04730.3694-0.10650.11330.22980.03550.18885.7816.5766.146
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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