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- PDB-3zt9: The bacterial stressosome: a modular system that has been adapted... -

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Basic information

Entry
Database: PDB / ID: 3zt9
TitleThe bacterial stressosome: a modular system that has been adapted to control secondary messenger signaling
ComponentsSERINE PHOSPHATASE
KeywordsHYDROLASE / SIGNAL TRANSDUCTION / PROTEIN PROTEIN INTERACTION / RSBS
Function / homology
Function and homology information


catalytic activity / metal ion binding
Similarity search - Function
Phosphatase RsbX / Stage II sporulation protein E (SpoIIE) / Sigma factor PP2C-like phosphatases / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / Serine phosphatase
Similarity search - Component
Biological speciesMOORELLA THERMOACETICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsQuin, M.B. / Berrisford, J.M. / Newman, J.A. / Basle, A. / Lewis, R.J. / Marles-Wright, J.
CitationJournal: Structure / Year: 2012
Title: The Bacterial Stressosome: A Modular System that Has Been Adapted to Control Secondary Messenger Signaling.
Authors: Quin, M.B. / Berrisford, J.M. / Newman, J.A. / Basle, A. / Lewis, R.J. / Marles-Wright, J.
History
DepositionJul 6, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Atomic model / Derived calculations / Refinement description
Revision 2.0Oct 24, 2018Group: Atomic model / Data collection / Refinement description
Category: atom_site / diffrn_source / software
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _diffrn_source.pdbx_wavelength_list / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SERINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0695
Polymers20,7981
Non-polymers2714
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.000, 46.920, 87.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SERINE PHOSPHATASE / MTX / TYPE 2C PROTEIN PHOSPHATASE


Mass: 20798.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MOORELLA THERMOACETICA (bacteria) / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834
References: UniProt: Q2RIF7, protein-serine/threonine phosphatase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growpH: 5.5
Details: 1 UL PROTEIN, 1 UL CRYSTALLANT, 1 ML WELL, 14 % PEG 3350, 0.2 M NACL, 0.1 M BIS-TRIS PH 5.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 / Wavelength: 0.98 Å
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 25, 2010
RadiationMonochromator: SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→29.48 Å / Num. obs: 19966 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 19.27 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.5
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.75→29.476 Å / SU ML: 0.19 / σ(F): 1.39 / Phase error: 15.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1886 922 5.1 %
Rwork0.152 --
obs0.1538 18067 99.81 %
Solvent computationShrinkage radii: 0.29 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.216 Å2 / ksol: 0.451 e/Å3
Displacement parametersBiso mean: 29 Å2
Baniso -1Baniso -2Baniso -3
1--0.1288 Å20 Å20 Å2
2--0.3124 Å20 Å2
3----0.1836 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1451 0 10 150 1611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161518
X-RAY DIFFRACTIONf_angle_d1.52077
X-RAY DIFFRACTIONf_dihedral_angle_d13.276561
X-RAY DIFFRACTIONf_chiral_restr0.106235
X-RAY DIFFRACTIONf_plane_restr0.006265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.84230.19061330.17572386X-RAY DIFFRACTION100
1.8423-1.95770.19591340.16042404X-RAY DIFFRACTION100
1.9577-2.10880.1951280.14332436X-RAY DIFFRACTION100
2.1088-2.3210.19031290.14152419X-RAY DIFFRACTION100
2.321-2.65660.19071420.14462438X-RAY DIFFRACTION100
2.6566-3.34630.21591220.14512481X-RAY DIFFRACTION100
3.3463-29.48050.16931340.15922581X-RAY DIFFRACTION99
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)
10.3955-0.1159-0.07110.45750.21651.87110.06660.1437-0.04070.04180.0650.1951-0.1073-0.68460.0280.102-0.02-0.01180.19490.0230.179315.29265.443475.5633
21.1194-0.1373-0.2591.6468-0.07431.011900.05180.024-0.24030.08180.36040.4777-0.2265-0.05720.1494-0.04570.00310.16020.00220.133823.21910.627269.3771
31.59530.2647-1.40960.881202.2007-0.0773-0.0021-0.1233-0.10730.0034-0.05210.32270.16980.01620.1454-0.0012-0.0130.13630.00390.137727.48140.824673.7145
40.89360.14060.19950.67950.41190.6386-0.07510.067-0.2764-0.07120.2098-0.06380.5330.17180.08660.2160.03060.0020.1357-0.03520.171729.3619-6.303269.6253
51.9723-0.8184-2.30710.5881.32915.5778-0.24460.2422-0.4930.1862-0.0712-0.00620.7729-0.5744-0.12530.32950.1205-0.02330.0865-0.00990.189433.4149-8.925680.0634
60.6299-0.02350.01730.5585-0.18571.5972-0.0821-0.1333-0.1870.02730.106-0.02040.53790.1510.22040.16760.0032-0.01840.1334-0.00210.173728.0714-0.988582.8895
70.2892-0.20450.18340.62470.12160.58160.0303-0.08720.13690.08420.0641-0.1739-0.02270.0595-0.03130.11820.0053-0.00480.1671-0.02520.170528.83510.338884.7537
80.53470.59530.30950.8747-0.11831.18120.10580.0081-0.11950.05910.0508-0.13670.12530.27190.06420.12010.0392-0.02930.1716-0.03340.155331.24213.026883.7603
90.7644-0.28750.03190.95420.36810.1677-0.0897-0.24550.21570.12290.1187-0.1051-0.04350.0154-0.01490.14960.01460.00030.17520.00060.138919.756515.919376.8858
101.04890.6551-0.00961.60280.79490.55050.280.2897-0.0277-0.0473-0.18150.16110.1602-0.1452-0.14190.17880.0431-0.02040.16160.03980.169916.499713.632970.3287
110.9256-0.2137-0.15050.1113-0.1680.6130.2435-0.05310.2668-0.03160.0230.0538-0.35190.1148-0.09580.151-0.00160.02860.1440.00570.159824.115110.222969.6103
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:11)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 12:30)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 31:42)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 43:60)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 61:76)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 77:101)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 102:120)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 121:148)
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 149:168)
10X-RAY DIFFRACTION10CHAIN A AND (RESSEQ 169:180)
11X-RAY DIFFRACTION11CHAIN A AND (RESSEQ 181:193)

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