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- PDB-9f82: Arbitrium receptor from ATCC13952 phage in complex with GVVRGA peptide -

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Basic information

Entry
Database: PDB / ID: 9f82
TitleArbitrium receptor from ATCC13952 phage in complex with GVVRGA peptide
Components
  • Arbitrium receptor from ATCC13952 phage
  • GLY-VAL-VAL-ARG-GLY-ALA
KeywordsDNA BINDING PROTEIN / Arbitrium receptor / AimR / AimP
Function / homology:
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsGallego del Sol, F. / Marina, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN) Spain
CitationJournal: To Be Published
Title: Arbitrium receptor from ATCC13952 phage
Authors: Gallego del Sol, F. / Marina, A.
History
DepositionMay 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arbitrium receptor from ATCC13952 phage
B: GLY-VAL-VAL-ARG-GLY-ALA
C: Arbitrium receptor from ATCC13952 phage
D: GLY-VAL-VAL-ARG-GLY-ALA
E: Arbitrium receptor from ATCC13952 phage
F: GLY-VAL-VAL-ARG-GLY-ALA
G: Arbitrium receptor from ATCC13952 phage
K: GLY-VAL-VAL-ARG-GLY-ALA


Theoretical massNumber of molelcules
Total (without water)183,4428
Polymers183,4428
Non-polymers00
Water43224
1
A: Arbitrium receptor from ATCC13952 phage
B: GLY-VAL-VAL-ARG-GLY-ALA


Theoretical massNumber of molelcules
Total (without water)45,8612
Polymers45,8612
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-6 kcal/mol
Surface area16670 Å2
MethodPISA
2
C: Arbitrium receptor from ATCC13952 phage
D: GLY-VAL-VAL-ARG-GLY-ALA


Theoretical massNumber of molelcules
Total (without water)45,8612
Polymers45,8612
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-5 kcal/mol
Surface area16560 Å2
MethodPISA
3
E: Arbitrium receptor from ATCC13952 phage
F: GLY-VAL-VAL-ARG-GLY-ALA


Theoretical massNumber of molelcules
Total (without water)45,8612
Polymers45,8612
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-6 kcal/mol
Surface area16330 Å2
MethodPISA
4
G: Arbitrium receptor from ATCC13952 phage
K: GLY-VAL-VAL-ARG-GLY-ALA


Theoretical massNumber of molelcules
Total (without water)45,8612
Polymers45,8612
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-6 kcal/mol
Surface area16360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.343, 82.959, 146.86
Angle α, β, γ (deg.)90, 90.88, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Arbitrium receptor from ATCC13952 phage


Mass: 45301.863 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: KS08_10720
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A7U4KS82
#2: Protein/peptide
GLY-VAL-VAL-ARG-GLY-ALA


Mass: 558.652 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Bacillus subtilis (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.44 Å3/Da / Density % sol: 49.65 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 3000 0.1M CHES pH 9.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.1→146.84 Å / Num. obs: 29584 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.994 / Net I/σ(I): 8.7
Reflection shellResolution: 3.1→3.29 Å / Num. unique obs: 4750 / CC1/2: 0.92

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→146.84 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.895 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27694 1521 -RANDOM
Rwork0.22789 ---
obs0.23053 28034 99.65 %-
Displacement parametersBiso mean: 80.756 Å2
Baniso -1Baniso -2Baniso -3
1--5.59 Å20 Å2-0.59 Å2
2--4.11 Å2-0 Å2
3---1.5 Å2
Refinement stepCycle: LAST / Resolution: 3.1→146.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11464 0 0 24 11488
LS refinement shellResolution: 3.1→3.18 Å /
Rfactor% reflection
Rfree0.364 -
Rwork0.273 -
obs-99.77 %
Refinement TLS params.

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)
15.35930.7505-1.28971.0781-0.49151.8433-0.1195-0.0621-0.0661-0.06210.0594-0.2798-0.0661-0.27980.06010.0801-0.0541-0.00450.1093-0.02410.041518.4468-9.362952.8712
25.4706-1.4635-1.27521.19650.55452.0444-0.02070.0727-0.03390.07270.030.2297-0.03390.2297-0.00940.0740.0052-0.00460.1027-0.01280.043432.4214-9.779190.6895
35.0752-0.66161.03021.2390.0222.01250.07080.0336-0.10170.0336-0.02880.3087-0.10170.3087-0.04210.18810.01020.02110.1388-0.00490.047433.70639.4056125.3383
45.21680.3771.04091.3444-0.18371.40150.3537-0.09930.1063-0.0993-0.166-0.26350.1063-0.2635-0.18770.33190.06520.05750.17670.0390.108817.53559.511717.9146
500000000000000-00.2377000.237700.2377000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A46 - 386
2X-RAY DIFFRACTION2C45 - 386
3X-RAY DIFFRACTION3E46 - 386
4X-RAY DIFFRACTION4G46 - 386

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