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- PDB-1yhf: Crystal Structure of Conserved SPY1581 Protein of Unknown Functio... -

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Basic information

Entry
Database: PDB / ID: 1yhf
TitleCrystal Structure of Conserved SPY1581 Protein of Unknown Function from Streptococcus pyogenes
Componentshypothetical protein SPy1581
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / conserved hypothetical protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyCupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta / Cupin type-2 domain-containing protein
Function and homology information
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsOsipiuk, J. / Lezondra, L. / Moy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of conserved hypothetical SPy1581 protein from Streptococcus pyogenes.
Authors: Osipiuk, J. / Lezondra, L. / Moy, S. / Collart, F. / Joachimiak, A.
History
DepositionJan 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein SPy1581


Theoretical massNumber of molelcules
Total (without water)12,9321
Polymers12,9321
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: hypothetical protein SPy1581

A: hypothetical protein SPy1581


Theoretical massNumber of molelcules
Total (without water)25,8642
Polymers25,8642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/41
Buried area3380 Å2
ΔGint-25 kcal/mol
Surface area10340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.897, 39.897, 144.758
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-214-

HOH

21A-215-

HOH

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Components

#1: Protein hypothetical protein SPy1581


Mass: 12931.826 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: M1 GAS / Gene: SPy1581 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99YR1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.3 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 293 K / pH: 4.5
Details: 30% PEG 3000, 0.1 M Sodium Acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 4.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97946
DetectorType: SBC-3 / Detector: CCD / Date: Dec 2, 2004
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 8535 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 23.4 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 33.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.746 / Mean I/σ(I) obs: 2.62 / % possible all: 94.8

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Phasing

PhasingMethod: SAD
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.45-10010.40.718502
4.23-5.457.50.872505
3.66-4.2311.50.864506
3.31-3.669.90.812502
3.06-3.3113.40.795504
2.87-3.0611.30.782506
2.72-2.878.60.751503
2.6-2.728.90.746504
2.49-2.65.80.772509
2.4-2.495.90.773503
2.32-2.45.30.758509
2.25-2.323.40.798512
2.19-2.253.40.777505
2.13-2.193.60.709503
2.08-2.133.20.741501
2.04-2.0820.783507
1.95-2.042.20.655974

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MLPHAREphasing
DM5phasing
REFMACrefinement
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2→39.9 Å / Cor.coef. Fo:Fc: 0.958 / SU B: 5.982 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / σ(F): 0 / ESU R: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ALL DATA WERE USED IN FINAL ROUND OF REFINEMENT. R-FACTOR-ALL CORRESPONDS TO DEPOSITED FILE. R- FACTORS, R-WORK AND R-FREE, ARE TAKEN FROM SECOND TO LAST ROUND OF REFINEMENT WHICH USED TEST DATA SET.
RfactorNum. reflection% reflection
Rfree0.248 843 -
Rwork0.19 --
obs0.192 8492 99.3 %
all-8492 -
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.75 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å20 Å20 Å2
2--1.42 Å20 Å2
3----2.85 Å2
Refinement stepCycle: LAST / Resolution: 2→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms878 0 0 103 981
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022889
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9741206
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6345113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.07225.89739
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34915161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.461154
X-RAY DIFFRACTIONr_chiral_restr0.0910.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02656
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.2345
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2597
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.283
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9451.5588
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2292920
X-RAY DIFFRACTIONr_scbond_it2.413334
X-RAY DIFFRACTIONr_scangle_it3.9144.5286
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 50 -
Rwork0.235 554 -
obs--95.35 %
Refinement TLS params.Method: refined / Origin x: 22.7025 Å / Origin y: 14.9165 Å / Origin z: 27.3086 Å
111213212223313233
T-0.0596 Å20.0244 Å20.005 Å2--0.0087 Å20.0038 Å2---0.0357 Å2
L0.6212 °20.2018 °20.1299 °2-1.0165 °2-0.1391 °2--1.8851 °2
S0.0182 Å °-0.1027 Å °-0.0067 Å °0.0228 Å °-0.0298 Å °0.0289 Å °0.0685 Å °-0.045 Å °0.0116 Å °

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