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- PDB-2oqt: Structural Genomics, the crystal structure of a putative PTS IIA ... -

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Basic information

Entry
Database: PDB / ID: 2oqt
TitleStructural Genomics, the crystal structure of a putative PTS IIA domain from Streptococcus pyogenes M1 GAS
ComponentsHypothetical protein SPy0176
KeywordsTRANSFERASE / APC29699 / putative PTS IIA domain / Streptococcus pyogenes M1 GAS / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / cytoplasm
Similarity search - Function
: / PTS EIIA type-2 domain / Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2 / PTS_EIIA type-2 domain profile. / Mannitol-specific EII; Chain A / Mannitol-specific EII; Chain A / Phosphotransferase/anion transporter / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ascorbate-specific PTS system EIIA component
Similarity search - Component
Biological speciesStreptococcus pyogenes serotype M1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.41 Å
AuthorsTan, K. / Wu, R. / Osipiuk, J. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a putative PTS IIA domain from Streptococcus pyogenes M1 GAS
Authors: Tan, K. / Wu, R. / Osipiuk, J. / Clancy, S. / Joachimiak, A.
History
DepositionFeb 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 300 BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ... BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS POLYPEPTIDE IS A MONOMER. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).
Remark 999 SEQUENCE AUTHORS STATE THAT THERE IS A MUTATION F7L FROM UNKNOWN SOURCE IN COMPARISON TO THE ... SEQUENCE AUTHORS STATE THAT THERE IS A MUTATION F7L FROM UNKNOWN SOURCE IN COMPARISON TO THE DATABASE SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein SPy0176
B: Hypothetical protein SPy0176
C: Hypothetical protein SPy0176
D: Hypothetical protein SPy0176


Theoretical massNumber of molelcules
Total (without water)71,2264
Polymers71,2264
Non-polymers00
Water25214
1
A: Hypothetical protein SPy0176


Theoretical massNumber of molelcules
Total (without water)17,8061
Polymers17,8061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hypothetical protein SPy0176


Theoretical massNumber of molelcules
Total (without water)17,8061
Polymers17,8061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Hypothetical protein SPy0176


Theoretical massNumber of molelcules
Total (without water)17,8061
Polymers17,8061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Hypothetical protein SPy0176


Theoretical massNumber of molelcules
Total (without water)17,8061
Polymers17,8061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
C: Hypothetical protein SPy0176
D: Hypothetical protein SPy0176


Theoretical massNumber of molelcules
Total (without water)35,6132
Polymers35,6132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-16 kcal/mol
Surface area12760 Å2
MethodPISA
6
A: Hypothetical protein SPy0176
B: Hypothetical protein SPy0176


Theoretical massNumber of molelcules
Total (without water)35,6132
Polymers35,6132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-12 kcal/mol
Surface area12650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.224, 112.781, 60.401
Angle α, β, γ (deg.)90.00, 99.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Hypothetical protein SPy0176


Mass: 17806.418 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria)
Species: Streptococcus pyogenes / Strain: M1 GAS, SF370 / Gene: SPy0176 / Plasmid: pMCSG19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9A1N7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 20% PEG3350, 0.2M Li2SO4, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924, 0.97938
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 11, 2006 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979241
20.979381
ReflectionResolution: 2.4→35.85 Å / Num. all: 23714 / Num. obs: 23714 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 34.86
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 5 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.02 / Num. unique all: 912 / % possible all: 52.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MAD / Resolution: 2.41→35.85 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / SU B: 21.172 / SU ML: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.593 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25445 1196 5 %RANDOM
Rwork0.20787 ---
all0.21024 22509 --
obs0.21024 22509 90.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.214 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å2-0.05 Å2
2--0.05 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.41→35.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4679 0 0 14 4693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224763
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9271.9856502
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8375617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.06325.543184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.36115813
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0871518
X-RAY DIFFRACTIONr_chiral_restr0.1380.2795
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023502
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2580.22428
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.23262
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2164
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0140.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0251.53155
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.69624996
X-RAY DIFFRACTIONr_scbond_it2.26331800
X-RAY DIFFRACTIONr_scangle_it3.5614.51501
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.41→2.47 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 44 -
Rwork0.287 936 -
obs-980 50.96 %

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