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- PDB-4d3g: Structure of PstA -

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Basic information

Entry
Database: PDB / ID: 4d3g
TitleStructure of PstA
ComponentsPSTA
KeywordsSIGNALING PROTEIN / GRAM-POSITIVE / C-DI-AMP / PSTA
Function / homology
Function and homology information


Cyclic-di-AMP receptor / Cyclic-di-AMP receptor / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein from nitrogen regulatory protein P-II (GLNB) family / Uncharacterized protein
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCampeotto, I. / Freemont, P. / Grundling, A.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Complex Structure and Biochemical Characterization of the Staphylococcus Aureus Cyclic Di-AMP Binding Protein Psta, the Founding Member of a New Signal Transduction Protein Family
Authors: Campeotto, I. / Zhang, Y. / Mladenov, M.G. / Freemont, P.S. / Grundling, A.
History
DepositionOct 22, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Feb 11, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PSTA


Theoretical massNumber of molelcules
Total (without water)13,8871
Polymers13,8871
Non-polymers00
Water00
1
A: PSTA

A: PSTA

A: PSTA


Theoretical massNumber of molelcules
Total (without water)41,6603
Polymers41,6603
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area4740 Å2
ΔGint-31 kcal/mol
Surface area11320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.753, 56.753, 66.165
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein PSTA


Mass: 13886.558 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99WC0, UniProt: Q2G229*PLUS
Sequence details19 AA EXPRESSION TAG ATTACHED AT THE N-TERMINAL, ONLY 1 ( HIS0) IS VISIBLE IN THE STRUCTURE

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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: 2.22 Å3/Da / Density % sol: 44.61 % / Description: NONE
Crystal growpH: 4.6 / Details: 200 MM NA MALONATE PH=4.6 AND 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.8233
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8233 Å / Relative weight: 1
ReflectionResolution: 3→49.12 Å / Num. obs: 2672 / % possible obs: 100 % / Observed criterion σ(I): 7.9 / Redundancy: 38.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 27.2
Reflection shellResolution: 3→3.16 Å / Redundancy: 38.7 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 7.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M05

3m05


Resolution: 3→49.18 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.884 / SU B: 52.048 / SU ML: 0.401 / Cross valid method: THROUGHOUT / ESU R: 1.714 / ESU R Free: 0.437 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. DISORDERED REGIONS BETWEEN T33 AND N41 AND BETWEEN R67 AND V93 WERE NOT MODELLED
RfactorNum. reflection% reflectionSelection details
Rfree0.29267 134 5 %RANDOM
Rwork0.24575 ---
obs0.24849 2536 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 82.885 Å2
Baniso -1Baniso -2Baniso -3
1--2.47 Å2-1.23 Å20 Å2
2---2.47 Å20 Å2
3---8.01 Å2
Refinement stepCycle: LAST / Resolution: 3→49.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms605 0 0 0 605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.019610
X-RAY DIFFRACTIONr_bond_other_d0.0020.02590
X-RAY DIFFRACTIONr_angle_refined_deg1.0731.928823
X-RAY DIFFRACTIONr_angle_other_deg0.70731344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.863575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52725.80631
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.4915106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.604153
X-RAY DIFFRACTIONr_chiral_restr0.0540.2100
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02700
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02143
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_it2.6825.228309
X-RAY DIFFRACTIONr_mcbond_other2.6745.227308
X-RAY DIFFRACTIONr_mcangle_it4.3637.818381
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6025.626301
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 9 -
Rwork0.335 174 -
obs--97.86 %
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)
111.35123.8788-1.62256.9049-8.408511.29770.19120.35520.39120.6050.11820.2979-0.7443-0.0829-0.30940.327-0.0485-0.19780.1371-0.0330.26721.758624.473528.371
214.52654.1677-5.94075.73961.52814.7498-0.60530.4287-0.5061-0.78280.16320.2029-0.1234-0.06650.44210.44350.0997-0.01840.4319-0.04420.20562.350415.080117.2475
31.5885-5.04532.943117.2793-10.94577.57450.21710.0898-0.4707-0.8510.18071.17030.5806-0.2715-0.39780.3394-0.1161-0.14860.459-0.03120.3067-3.872121.404521.3108
415.24217.4254-15.9128.7316-6.199234.6769-0.83931.5280.3263-0.93530.91460.00640.0708-0.4558-0.07530.2513-0.0566-0.16890.2946-0.02720.2813.37926.520618.5745
512.8359-2.38-3.32314.87152.15067.63-0.2839-0.2174-0.39120.17970.06620.18920.65210.18840.21770.2598-0.0287-0.06320.0426-0.04380.23663.640115.714929.1063
69.9798-1.0732-4.46613.06851.69342.8692-0.15430.55760.27740.17370.24350.02230.46840.0685-0.08920.3470.1241-0.01430.25690.06880.02690.410124.935728.8443
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 9
2X-RAY DIFFRACTION2A10 - 23
3X-RAY DIFFRACTION3A24 - 30
4X-RAY DIFFRACTION4A31 - 47
5X-RAY DIFFRACTION5A48 - 66
6X-RAY DIFFRACTION6A67 - 109

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