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- PDB-4gyo: Crystal Structure of Rap Protein Complexed with Competence and Sp... -

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Basic information

Entry
Database: PDB / ID: 4gyo
TitleCrystal Structure of Rap Protein Complexed with Competence and Sporulation Factor
Components
  • CSF peptide
  • Response regulator aspartate phosphatase J
KeywordsHYDROLASE / Tetratricopeptide repeat
Function / homology
Function and homology information


phosphoprotein phosphatase activity / Hydrolases; Acting on ester bonds
Similarity search - Function
Phosphatase RapC/F inhibitor, PhrC/F / Rap-phr extracellular signalling / : / response regulator aspartate phosphatase H, N terminal / : / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat ...Phosphatase RapC/F inhibitor, PhrC/F / Rap-phr extracellular signalling / : / response regulator aspartate phosphatase H, N terminal / : / 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
Response regulator aspartate phosphatase J / Competence and sporulation factor
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.16 Å
AuthorsParashar, V. / Neiditch, M.B.
CitationJournal: Plos Biol. / Year: 2013
Title: Conformational change-induced repeat domain expansion regulates rap phosphatase quorum-sensing signal receptors.
Authors: Parashar, V. / Jeffrey, P.D. / Neiditch, M.B.
History
DepositionSep 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Response regulator aspartate phosphatase J
B: Response regulator aspartate phosphatase J
C: CSF peptide
D: CSF peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2036
Polymers90,1324
Non-polymers712
Water4,990277
1
A: Response regulator aspartate phosphatase J
D: CSF peptide
hetero molecules

B: Response regulator aspartate phosphatase J
C: CSF peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2036
Polymers90,1324
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area5160 Å2
ΔGint-43 kcal/mol
Surface area31740 Å2
MethodPISA
2
A: Response regulator aspartate phosphatase J
D: CSF peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1013
Polymers45,0662
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-13 kcal/mol
Surface area17050 Å2
MethodPISA
3
B: Response regulator aspartate phosphatase J
C: CSF peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1013
Polymers45,0662
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-13 kcal/mol
Surface area16900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.725, 86.725, 225.805
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-582-

HOH

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Components

#1: Protein Response regulator aspartate phosphatase J


Mass: 44472.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU02820, rapJ, ycdE / Production host: Escherichia coli (E. coli)
References: UniProt: O34327, Hydrolases; Acting on ester bonds
#2: Protein/peptide CSF peptide


Mass: 593.674 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetically produced mature peptide CSF / References: UniProt: Q6DL83*PLUS
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 18 mM Tris (pH 8.0), 133 mM KCl, 4 mM DTT, 294 mM magnesium chloride, 2% benzamidine hydrochloride, 9% PEG 3000, 100 mM sodium cacodylate (pH 6.4), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.16→50 Å / Num. obs: 47237 / Observed criterion σ(I): 4.39
Reflection shellResolution: 2.16→2.2 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.16→39 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 22.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 2125 4.51 %RANDOM
Rwork0.1897 ---
obs0.1913 47142 99.86 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.536 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.9223 Å20 Å2-0 Å2
2--1.9223 Å20 Å2
3----3.8447 Å2
Refinement stepCycle: LAST / Resolution: 2.16→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6102 0 2 277 6381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026270
X-RAY DIFFRACTIONf_angle_d0.488441
X-RAY DIFFRACTIONf_dihedral_angle_d12.0782330
X-RAY DIFFRACTIONf_chiral_restr0.041871
X-RAY DIFFRACTIONf_plane_restr0.0011087
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1597-2.210.26071380.21062923X-RAY DIFFRACTION100
2.21-2.26520.26811390.20852949X-RAY DIFFRACTION100
2.2652-2.32650.26791390.21152963X-RAY DIFFRACTION100
2.3265-2.39490.2481400.20272952X-RAY DIFFRACTION100
2.3949-2.47220.26851400.20012959X-RAY DIFFRACTION100
2.4722-2.56060.25381400.19652966X-RAY DIFFRACTION100
2.5606-2.66310.26461400.20522965X-RAY DIFFRACTION100
2.6631-2.78430.27551410.21652972X-RAY DIFFRACTION100
2.7843-2.93110.23161390.21582977X-RAY DIFFRACTION100
2.9311-3.11470.23971420.20482998X-RAY DIFFRACTION100
3.1147-3.35510.24561420.19863007X-RAY DIFFRACTION100
3.3551-3.69260.20381410.1813013X-RAY DIFFRACTION100
3.6926-4.22660.19271450.16363050X-RAY DIFFRACTION100
4.2266-5.3240.20111450.16143071X-RAY DIFFRACTION99
5.324-47.32260.20381540.19443252X-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)
13.46230.0718-0.01323.4566-0.35264.1055-0.24860.28521.03390.01320.2094-0.9967-0.93040.08180.14650.1552-0.19770.30160.14260.11320.322450.561365.138159.1759
22.7148-0.1712-1.27172.2993-0.46565.23240.16840.28460.4289-0.28220.05990.042-0.7235-0.2691-0.0820.26410.03570.04120.14840.01870.217136.634962.594771.5932
33.4434-0.1707-0.22082.2818-0.3153.7586-0.0272-0.1061-0.31450.0126-0.0472-0.07940.53160.08730.07060.24360.0236-0.00850.0932-0.00140.211341.029443.619782.628
43.284-1.2807-0.14843.09950.9784.5183-0.0625-0.18460.19470.31720.1621-0.2372-0.20950.7511-0.04530.177-0.0108-0.05460.2982-0.03240.280648.917956.245697.5952
54.0840.21130.39571.4437-1.1718.3876-0.2126-0.410.10430.09450.0532-0.1302-0.0029-0.29170.13460.20430.0679-0.02150.2382-0.09560.219132.597558.6373102.7166
64.45180.0963-0.00831.8472-0.74934.88710.19830.2333-0.7279-0.4652-0.40880.97250.5124-0.66820.22540.3267-0.0351-0.21450.3629-0.06220.790372.55445.162575.8653
72.9788-2.1454-1.22034.56584.19336.3710.5589-0.7589-1.80420.5602-0.23950.32091.59820.22980.26290.5424-0.2086-0.04660.38220.22440.828580.121437.999785.1919
83.43121.12441.3853.91231.19733.17340.05160.3217-0.3753-0.36840.05560.16460.2225-0.0563-0.11440.21720.0245-0.01360.1937-0.01440.245592.724953.718180.0583
99.10891.54490.90872.9075-0.21823.6459-0.11560.04940.5817-0.21220.07050.1466-0.1972-0.04310.0240.28910.0487-0.00010.1343-0.02940.280990.112270.244589.8022
102.88690.24241.73512.3215-0.31934.8248-0.0032-0.49250.03960.2249-0.05750.18210.0339-0.58560.04990.20060.04050.10310.268-0.00680.214588.006763.1652106.1187
115.56720.08161.41897.21854.20163.4-0.0488-0.6629-0.73570.898-0.0557-0.30481.0804-0.4194-0.00560.3760.10540.07150.33080.1270.316198.751250.5709110.2662
126.7681.20233.65094.93763.93158.3152-0.464-0.23380.1853-0.03960.24040.1107-0.08410.24370.16190.19750.03960.03340.22770.08570.1732107.861155.4894105.6242
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 6:67)
2X-RAY DIFFRACTION2chain 'A' and (resseq 68:172)
3X-RAY DIFFRACTION3chain 'A' and (resseq 173:252)
4X-RAY DIFFRACTION4chain 'A' and (resseq 253:329)
5X-RAY DIFFRACTION5chain 'A' and (resseq 330:371)
6X-RAY DIFFRACTION6chain 'B' and (resseq 7:67)
7X-RAY DIFFRACTION7chain 'B' and (resseq 68:94)
8X-RAY DIFFRACTION8chain 'B' and (resseq 95:195)
9X-RAY DIFFRACTION9chain 'B' and (resseq 196:233)
10X-RAY DIFFRACTION10chain 'B' and (resseq 234:307)
11X-RAY DIFFRACTION11chain 'B' and (resseq 308:329)
12X-RAY DIFFRACTION12chain 'B' and (resseq 330:371)

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