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- PDB-6wjo: Crystal structure of wild-type Arginine Repressor from the pathog... -

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Basic information

Entry
Database: PDB / ID: 6wjo
TitleCrystal structure of wild-type Arginine Repressor from the pathogenic bacterium Corynebacterium pseudotuberculosis bound to tyrosine
ComponentsArginine repressor
KeywordsDNA BINDING PROTEIN / enzyme specificity
Function / homology
Function and homology information


L-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
TYROSINE / Arginine repressor
Similarity search - Component
Biological speciesCorynebacterium pseudotuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.693 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: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)18,1827
Polymers17,6782
Non-polymers5045
Water1,54986
1
A: Arginine repressor
B: Arginine repressor
hetero molecules

A: Arginine repressor
B: Arginine repressor
hetero molecules

A: Arginine repressor
B: Arginine repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,54721
Polymers53,0346
Non-polymers1,51315
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Buried area9950 Å2
ΔGint-115 kcal/mol
Surface area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.990, 82.990, 82.990
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
11A-204-

NA

21A-318-

HOH

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Components

#1: Protein Arginine repressor


Mass: 8839.020 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
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: 54.35 %
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 17, 2016
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: 0.46
ReflectionResolution: 1.69→48.22 Å / Num. obs: 21903 / % possible obs: 99.4 % / Redundancy: 11.8 % / Biso Wilson estimate: 32.54 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.074 / Net I/σ(I): 22.97
Reflection shellResolution: 1.69→1.8 Å / Redundancy: 9.1 % / Rmerge(I) obs: 1.131 / Mean I/σ(I) obs: 1.74 / Num. unique obs: 3488 / CC1/2: 0.583 / Rrim(I) all: 1.089 / % possible all: 97.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JVO

5jvo


Resolution: 1.693→20.748 Å / Cross valid method: THROUGHOUT / σ(F): 1.54 / Phase error: 22.3
RfactorNum. reflection% reflection
Rfree0.2115 1083 5.07 %
Rwork0.1813 --
obs0.1859 21368 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 55.67 Å2 / Biso mean: 22.1861 Å2 / Biso min: 7.21 Å2
Refinement stepCycle: final / Resolution: 1.693→20.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1178 0 33 86 1297
Biso mean--18.46 30.38 -
Num. residues----155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071224
X-RAY DIFFRACTIONf_angle_d0.9011651
X-RAY DIFFRACTIONf_chiral_restr0.051189
X-RAY DIFFRACTIONf_plane_restr0.006218
X-RAY DIFFRACTIONf_dihedral_angle_d9.813739
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6961-1.77310.41211580.38042464262293
1.7731-1.86620.31811480.29242461260994
1.8662-1.98260.24021120.20422532264496
1.9826-2.13490.19691320.15672525265795
2.1349-2.34820.21081470.15972501264894
2.3482-2.68440.2131030.15972547265096
2.6844-3.36870.20491430.16272546268995
3.3687-11.73680.16121350.16682639277495
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)
13.643-1.13360.43944.6368-0.08953.17680.01820.1084-0.4949-0.168-0.22-0.15480.5101-0.06830.24190.27690.00590.07640.1871-0.06480.2804-2.23518.723-8.76
23.63022.92770.49685.36950.09972.3226-0.15590.04440.0413-0.06050.10370.2527-0.031-0.13990.06480.09480.01410.01190.1213-0.01770.1714-3.55536.07-8.942
31.5350.0885-0.53460.9384-0.03480.8157-0.06170.0737-0.04860.00670.085-0.11260.21620.0563-0.00680.11710.02490.0030.0944-0.02150.0912-1.17229.448-1.482
44.2334-2.60584.14251.6791-2.48964.102-0.02450.0665-0.0644-0.14480.0883-0.22180.04290.2951-0.08660.1514-0.0372-0.00050.38550.08440.304611.27837.561-8.052
50.7658-0.4520.1464.41510.07940.77440.00270.11840.0831-0.39730.0744-0.00490.04390.1817-0.05070.15330.06610.01730.2243-0.01830.14032.63330.114-13.93
61.38990.1163-0.7991.218-0.16511.99860.07660.4296-0.1651-0.40810.03080.2050.03520.062-0.10010.53-0.0711-0.03180.3535-0.09340.2769-17.37413.814-3.147
71.81830.5554-0.4891.1914-0.29990.9453-0.01140.0522-0.2153-0.11720.0138-0.00210.1836-0.1418-0.01290.1311-0.0233-0.00680.1089-0.00690.1148-17.59718.9838.876
83.1761-1.15740.23443.59480.39712.23620.13450.0655-0.2479-0.2056-0.0317-0.09750.3114-0.1492-0.10520.2136-0.06250.00490.1471-0.00190.2603-25.29910.81410.813
92.51582.4955-1.85993.84341.25218.398-0.0568-0.0685-0.048-0.12630.1318-0.02070.00050.0587-0.07490.1703-0.0298-0.01260.1753-0.0310.0836-1.47828.5325.501
101.3068-0.14440.14560.8990.55180.3814-0.0149-0.00170.0177-0.01320.01220.025-0.0113-0.0275-0.03730.1903-0.03950.07280.18730.07660.1107-17.86228.1846.205
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 82:94 )A82 - 94
2X-RAY DIFFRACTION2( CHAIN A AND RESID 95:108 )A95 - 108
3X-RAY DIFFRACTION3( CHAIN A AND RESID 109:143 )A109 - 143
4X-RAY DIFFRACTION4( CHAIN A AND RESID 144:148 )A144 - 148
5X-RAY DIFFRACTION5( CHAIN A AND RESID 149:160 )A149 - 160
6X-RAY DIFFRACTION6( CHAIN B AND RESID 84:94 )B84 - 94
7X-RAY DIFFRACTION7( CHAIN B AND RESID 95:143 )B95 - 143
8X-RAY DIFFRACTION8( CHAIN B AND RESID 144:159 )B144 - 159
9X-RAY DIFFRACTION9( CHAIN A AND RESID 201:201 )A201
10X-RAY DIFFRACTION10( CHAIN B AND RESID 201:201 )B201

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