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- PDB-4i9c: Crystal structure of aspartyl phosphate phosphatase F from B.subt... -

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Basic information

Entry
Database: PDB / ID: 4i9c
TitleCrystal structure of aspartyl phosphate phosphatase F from B.subtilis in complex with its inhibitory peptide
Components
  • PhrF
  • Response regulator aspartate phosphatase F
KeywordsGENE REGULATION / ComA inhibitor / PhrF
Function / homology
Function and homology information


establishment of competence for transformation / metal ion binding / cytoplasm
Similarity search - Function
response regulator aspartate phosphatase H, N terminal / Anaphase-promoting complex, cyclosome, subunit 3 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe ...response regulator aspartate phosphatase H, N terminal / Anaphase-promoting complex, cyclosome, subunit 3 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Regulatory protein RapF
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.1 Å
AuthorsMarina, A. / Gallego, F.
CitationJournal: Plos Biol. / Year: 2013
Title: Structural basis of Rap phosphatase inhibition by Phr peptides
Authors: Gallego del Sol, F. / Marina, A.
History
DepositionDec 5, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Response regulator aspartate phosphatase F
C: PhrF


Theoretical massNumber of molelcules
Total (without water)46,2702
Polymers46,2702
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-3 kcal/mol
Surface area17720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)220.791, 220.791, 220.791
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132

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Components

#1: Protein Response regulator aspartate phosphatase F


Mass: 45664.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU37460, rapF, ywhJ / Plasmid: pproex / Production host: Escherichia coli (E. coli) / Strain (production host): RIL
References: UniProt: P71002, Hydrolases; Acting on ester bonds
#2: Protein/peptide PhrF


Mass: 604.743 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: peptide purchased from Genescript
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.85 Å3/Da / Density % sol: 74.62 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1M ammonium sulphate, 17% glycerol, 0.1M tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1801
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALBA XALOC11.0722
SYNCHROTRONESRF BM1421.07131
Detector
TypeIDDetectorDateDetails
DECTRIS PILATUS 6M1PIXELSep 26, 2012Channel-cut Si(111) + KB focusing mirrors
MARMOSAIC 225 mm CCD2CCDSep 23, 2010
RadiationMonochromator: Si(111) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.07221
21.071311
ReflectionResolution: 3.1→49.37 Å / Num. all: 16988 / Num. obs: 16991 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 22 % / Biso Wilson estimate: 107.9 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.095 / Net I/σ(I): 31.3
Reflection shellResolution: 3.1→3.26 Å / Redundancy: 22.3 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2427 / Rsym value: 0.265 / % possible all: 100

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Processing

Software
NameVersionClassification
xalocbeamlinedata collection
MOLREPphasing
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 3.1→47.07 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.941 / SU B: 27.984 / SU ML: 0.243 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.639 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22686 1332 7.8 %RANDOM
Rwork0.18648 ---
all0.18962 16969 --
obs0.18648 15637 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.074 Å2
Refinement stepCycle: LAST / Resolution: 3.1→47.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3187 0 0 18 3205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.023263
X-RAY DIFFRACTIONr_angle_refined_deg1.7111.9634378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7445375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.22624.101178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.88715612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0571518
X-RAY DIFFRACTIONr_chiral_restr0.1080.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022500
LS refinement shellResolution: 3.1→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 78 -
Rwork0.296 1037 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 8.129 Å / Origin y: 42.168 Å / Origin z: 2.106 Å
111213212223313233
T0.0575 Å20.1019 Å2-0.0255 Å2-0.3038 Å2-0.1018 Å2--0.2581 Å2
L2.6038 °2-0.0256 °2-0.4174 °2-2.588 °2-1.6173 °2--2.3856 °2
S0.0868 Å °0.3829 Å °-0.4364 Å °0.153 Å °0.0893 Å °0.0203 Å °0.0745 Å °0.0588 Å °-0.1761 Å °

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