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- PDB-6wjp: Crystal structure of Arginine Repressor P115Q mutant from the pat... -

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Basic information

Entry
Database: PDB / ID: 6wjp
TitleCrystal structure of Arginine Repressor P115Q mutant from the pathogenic bacterium Corynebacterium pseudotuberculosis bound to arginine
ComponentsArginine repressor
KeywordsDNA BINDING PROTEIN / enzyme specificity
Function / homology
Function and homology information


arginine biosynthetic process / arginine binding / protein complex oligomerization / DNA-binding transcription factor activity / DNA binding / cytoplasm
Similarity search - Function
Arginine repressor / Arginine repressor, C-terminal / Arginine repressor, DNA-binding domain / Arginine repressor, C-terminal domain superfamily / Arginine repressor, DNA binding domain / Arginine repressor, C-terminal domain / Gyrase A; domain 2 - #40 / Gyrase A; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...Arginine repressor / Arginine repressor, C-terminal / Arginine repressor, DNA-binding domain / Arginine repressor, C-terminal domain superfamily / Arginine repressor, DNA binding domain / Arginine repressor, C-terminal domain / Gyrase A; domain 2 - #40 / Gyrase A; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ARGININE / Arginine repressor
Similarity search - Component
Biological speciesCorynebacterium pseudotuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.701 Å
AuthorsNascimento, A.F.Z. / Hernandez-Gonzalez, J.E. / de Morais, M.A.B. / Murakami, M.T. / Carareto, C.M.A. / Arni, R.K. / Mariutti, R.B.
Funding support Brazil, 9items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)307338/2014-2 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)309940/2019-2 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)303455/2017-9 Brazil
Sao Paulo Research Foundation (FAPESP)2016/19995-0 Brazil
Sao Paulo Research Foundation (FAPESP)2018/10736-8 Brazil
Sao Paulo Research Foundation (FAPESP)2018/07977-3 Brazil
Sao Paulo Research Foundation (FAPESP)2015/13765-0 Brazil
Sao Paulo Research Foundation (FAPESP)2015/18868-2 Brazil
Sao Paulo Research Foundation (FAPESP)2016/24587-9 Brazil
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2020
Title: A single P115Q mutation modulates specificity in the Corynebacterium pseudotuberculosis arginine repressor.
Authors: Mariutti, R.B. / Hernandez-Gonzalez, J.E. / Nascimento, A.F.Z. / de Morais, M.A.B. / Murakami, M.T. / Carareto, C.M.A. / Arni, R.K.
History
DepositionApr 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arginine repressor
B: Arginine repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5627
Polymers17,9382
Non-polymers6245
Water99155
1
B: Arginine repressor
hetero molecules

B: Arginine repressor
hetero molecules

B: Arginine repressor
hetero molecules

A: Arginine repressor
hetero molecules

A: Arginine repressor
hetero molecules

A: Arginine repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,68621
Polymers53,8156
Non-polymers1,87115
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation11_555y+1/2,-z+1/2,-x1
Buried area11270 Å2
ΔGint-9 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.341, 83.341, 83.341
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11B-203-

TRS

21B-203-

TRS

31A-321-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Arginine repressor


Mass: 8969.165 Da / Num. of mol.: 2 / Mutation: P115Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium pseudotuberculosis (strain C231) (bacteria)
Strain: C231 / Gene: argR, CpC231_0953 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D9QA55

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Non-polymers , 5 types, 60 molecules

#2: Chemical ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.0 M Sodium Formate, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 25, 2017
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
Reflection twinOperator: l,-k,h / Fraction: 0.49
ReflectionResolution: 1.7→37.271 Å / Num. obs: 21469 / % possible obs: 99.9 % / Redundancy: 35.1 % / Biso Wilson estimate: 40.21 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.056 / Net I/σ(I): 48.98
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 19.4 % / Rmerge(I) obs: 2.587 / Mean I/σ(I) obs: 1.15 / Num. unique obs: 3400 / CC1/2: 0.369 / Rrim(I) all: 2.656 / % possible all: 99.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JVO

5jvo


Resolution: 1.701→37.271 Å / Cross valid method: THROUGHOUT / σ(F): 14.16 / Phase error: 20.24
RfactorNum. reflection% reflection
Rfree0.1972 1073 5 %
Rwork0.1733 --
obs0.1805 21457 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 80.84 Å2 / Biso mean: 36.8252 Å2 / Biso min: 18.91 Å2
Refinement stepCycle: final / Resolution: 1.701→37.271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1211 0 42 55 1308
Biso mean--31.16 40.43 -
Num. residues----159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081262
X-RAY DIFFRACTIONf_angle_d0.9361693
X-RAY DIFFRACTIONf_chiral_restr0.048194
X-RAY DIFFRACTIONf_plane_restr0.005224
X-RAY DIFFRACTIONf_dihedral_angle_d10.01766
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 95 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.7019-1.77940.34311330.33692529
1.7794-1.87320.29371310.26042485
1.8732-1.99050.23681330.22922530
1.9905-2.14420.19821340.20612534
2.1442-2.35990.22191330.1962534
2.3599-2.70130.24151340.18982538
2.7013-3.4030.1851350.17672566
3.403-37.2710.19171400.15182656
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)
13.59390.69070.53721.26950.69891.499-0.13190.11270.3659-0.02280.0137-0.0249-0.23610.14410.10070.43970.05840.00650.48540.04760.44092.562-22.77612.297
21.4567-0.73610.42131.966-0.59941.36660.02520.23070.1476-0.1895-0.0514-0.0464-0.06540.16920.02360.223-0.0040.0090.28610.02740.1956-11.393-21.34516.7
35.5584-0.2608-0.61931.13240.19952.00810.15370.4706-0.0932-0.40020.0389-0.12580.04180.2021-0.14310.44190.00450.01040.3995-0.01360.3062-9.675-18.2436.519
40.0561-0.21950.02271.2625-0.14440.0193-0.0186-0.3719-0.20780.42520.00990.26240.1542-0.31470.01720.4374-0.06680.01320.58390.0390.4501-6.9282.9624.649
52.24570.71941.39081.54391.09432.06760.0271-0.3310.06280.0584-0.08160.14640.1342-0.39110.04430.2321-0.01530.03470.29670.00810.2438-2.8834.91812.711
61.14260.52030.37772.90970.38350.81740.0606-0.0796-0.14820.1172-0.04080.11920.147-0.0527-0.01330.2236-0.02760.01270.25830.0270.2275-1.635-2.328.784
70.7534-0.9342-2.051.16992.58785.7347-0.0542-0.3207-0.11090.269-0.080.16910.2288-0.38230.13660.3088-0.07330.03140.43080.02130.3875-12.376-1.13813.168
88.8962-8.55396.36132.0003-6.264.5599-0.03770.08670.13050.0824-0.0203-0.1514-0.02780.07630.07280.2254-0.03970.00050.2436-0.01990.2486-7.522-22.46326.291
94.57323.51344.04862.96783.93266.10470.1524-0.1210.02310.1643-0.072-0.09250.2379-0.209-0.06570.28960.0019-0.01290.31450.00010.2077.3252.85914.658
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 81:94 )A81 - 94
2X-RAY DIFFRACTION2( CHAIN A AND RESID 95:148 )A95 - 148
3X-RAY DIFFRACTION3( CHAIN A AND RESID 149:160 )A149 - 160
4X-RAY DIFFRACTION4( CHAIN B AND RESID 82:94 )B82 - 94
5X-RAY DIFFRACTION5( CHAIN B AND RESID 95:124 )B95 - 124
6X-RAY DIFFRACTION6( CHAIN B AND RESID 125:148 )B125 - 148
7X-RAY DIFFRACTION7( CHAIN B AND RESID 149:160 )B149 - 160
8X-RAY DIFFRACTION8( CHAIN A AND RESID 201:201 )A201
9X-RAY DIFFRACTION9( CHAIN B AND RESID 201:201 )B201

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