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- PDB-2fu2: Crystal structure of protein SPy2152 from Streptococcus pyogenes -

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Basic information

Entry
Database: PDB / ID: 2fu2
TitleCrystal structure of protein SPy2152 from Streptococcus pyogenes
ComponentsHypothetical protein SPy2152
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyTa0600-like / Ta0600-like superfamily / Bacteriocin immunity protein family / bacteriocin immunity / de novo design (two linked rop proteins) / Up-down Bundle / Mainly Alpha / Bacteriocin / Bacteriocin
Function and homology information
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsChang, C. / Cymborowski, M. / Otwinowski, Z. / Minor, W. / Lezondra, L.-E. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Bmc Struct.Biol. / Year: 2009
Title: The structure of pyogenecin immunity protein, a novel bacteriocin-like immunity protein from Streptococcus pyogenes.
Authors: Chang, C. / Coggill, P. / Bateman, A. / Finn, R.D. / Cymborowski, M. / Otwinowski, Z. / Minor, W. / Volkart, L. / Joachimiak, A.
History
DepositionJan 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein SPy2152


Theoretical massNumber of molelcules
Total (without water)11,4691
Polymers11,4691
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.087, 30.280, 35.855
Angle α, β, γ (deg.)90.00, 113.26, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hypothetical protein SPy2152


Mass: 11468.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Plasmid: pMCSG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Derivatives / References: UniProt: Q99XL4, UniProt: Q48QT2*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.65 Å3/Da / Density % sol: 25.63 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20 % PEG 8000, Mes pH 6.0, Ca(OAc)2 , VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97907 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2005
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. all: 5139 / Num. obs: 4682 / % possible obs: 91.1 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 30.26
Reflection shellResolution: 2.01→2.03 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 3.62 / Num. unique all: 75 / % possible all: 58.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.15→34.94 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.909 / SU B: 12.189 / SU ML: 0.15 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.279 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25389 185 4.6 %RANDOM
Rwork0.15732 ---
all0.1611 3855 --
obs0.16111 3855 96.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.876 Å2
Baniso -1Baniso -2Baniso -3
1-3.81 Å20 Å2-0.16 Å2
2---2.12 Å20 Å2
3----1.83 Å2
Refinement stepCycle: LAST / Resolution: 2.15→34.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms627 0 0 67 694
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.022636
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8131.98855
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.349577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.80325.86229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.8115125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.406152
X-RAY DIFFRACTIONr_chiral_restr0.1020.2100
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02456
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2350.2326
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.2454
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2210.249
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.330.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2720.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.951.5410
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5382630
X-RAY DIFFRACTIONr_scbond_it2.8883262
X-RAY DIFFRACTIONr_scangle_it4.3234.5225
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.207 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.167 13 -
Rwork0.187 230 -
obs--81 %
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)
14.365-1.42213.91645.7137-3.06347.14180.11230.13110.1667-0.234-0.01690.0407-0.09860.1067-0.09540.0077-0.02210.0646-0.11260.0124-0.132817.859-6.9853.55
28.576-2.47595.76752.9278-3.23759.34720.18240.2013-0.4766-0.3672-0.01280.16850.25180.2448-0.16950.0325-0.0240.0225-0.1435-0.0304-0.106314.133-15.8684.679
310.8730.65312.21843.67042.11214.6591-0.21-0.46010.12370.00750.09090.1753-0.147-0.4430.1191-0.1123-0.007-0.0022-0.05830.0193-0.125810.877-8.61713.766
43.9556-4.42090.65197.14340.94113.83270.39710.07360.3351-0.495-0.2971-0.1117-0.33970.0241-0.10.0209-0.01420.0213-0.11050.0244-0.101812.786-0.8699.626
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 222 - 22
2X-RAY DIFFRACTION2AA23 - 4123 - 41
3X-RAY DIFFRACTION3AA42 - 6442 - 64
4X-RAY DIFFRACTION4AA65 - 7965 - 79

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