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- PDB-5jls: Crystal Structure of Adhesin competence repressor (AdcR) from Str... -

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Basic information

Entry
Database: PDB / ID: 5jls
TitleCrystal Structure of Adhesin competence repressor (AdcR) from Streptococcus pyogenes (C-terminally His tagged)
ComponentsAdhesin competence repressor
KeywordsTRANSCRIPTION / Metal-sensing transcription regulator / DNA binding protein
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / zinc ion binding
Similarity search - Function
: / : / MarR family / ArsR-like helix-turn-helix domain / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Putative repressor protein
Similarity search - Component
Biological speciesStreptococcus pyogenes serotype M3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsDo, H. / Kumaraswami, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI109096-01A1 United States
CitationJournal: To Be Published
Title: Crystal structure of Adhesin competence repressor (AdcR) from Streptococcus pyogenes
Authors: Do, H. / Kumaraswami, M.
History
DepositionApr 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 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: Adhesin competence repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6912
Polymers17,6251
Non-polymers651
Water1629
1
A: Adhesin competence repressor
hetero molecules

A: Adhesin competence repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3814
Polymers35,2502
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5580 Å2
ΔGint-115 kcal/mol
Surface area15220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.560, 105.560, 36.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Adhesin competence repressor / AdcR


Mass: 17625.096 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M3 (bacteria)
Gene: adcR, SpyM3_0069 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2USX5
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.91 Å3/Da / Density % sol: 57.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M imidazole, pH 7.0, 10% PEG3350, 5 mM magnesium chloride, 5 mM nickel chloride, 5 mM cobalt chloride, 14% PEG400 as additive
PH range: 6.5-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 22, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115 Å / Relative weight: 1
ReflectionResolution: 2.7→47.2 Å / Num. obs: 6084 / % possible obs: 99.5 % / Redundancy: 8.9 % / Rsym value: 0.052 / Net I/σ(I): 21
Reflection shellHighest resolution: 2.7 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
SCALAdata scaling
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.924 / SU B: 10.859 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R: 0.477 / ESU R Free: 0.332 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27821 327 5.4 %RANDOM
Rwork0.20009 ---
obs0.20429 5722 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 101.409 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å2-0 Å2
2--0.02 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1061 0 1 9 1071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191071
X-RAY DIFFRACTIONr_bond_other_d0.0020.021082
X-RAY DIFFRACTIONr_angle_refined_deg1.8441.9721445
X-RAY DIFFRACTIONr_angle_other_deg1.10732490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5535132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.83226.45848
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.86715213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.376153
X-RAY DIFFRACTIONr_chiral_restr0.1120.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021180
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02221
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it9.2149.537534
X-RAY DIFFRACTIONr_mcbond_other9.2219.534533
X-RAY DIFFRACTIONr_mcangle_it12.23814.258664
X-RAY DIFFRACTIONr_mcangle_other12.24614.269665
X-RAY DIFFRACTIONr_scbond_it9.66510.629537
X-RAY DIFFRACTIONr_scbond_other9.65710.635538
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.48315.502782
X-RAY DIFFRACTIONr_long_range_B_refined17.8674.4721191
X-RAY DIFFRACTIONr_long_range_B_other17.86174.481191
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.702→2.772 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 20 -
Rwork0.238 424 -
obs--100 %

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