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

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Basic information

Entry
Database: PDB / ID: 5jlu
TitleCrystal Structure of Adhesin competence repressor (AdcR) from Streptococcus pyogenes
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.3Sep 27, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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)16,9022
Polymers16,8361
Non-polymers651
Water66737
1
A: Adhesin competence repressor
hetero molecules

A: Adhesin competence repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8034
Polymers33,6722
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area5610 Å2
ΔGint-117 kcal/mol
Surface area15910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.460, 105.460, 36.700
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: 16836.217 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.: 37 / 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: 3.3 Å3/Da / Density % sol: 62.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1 M sodium/phosphate phosphate, pH 7.2, 30% PEG200
PH range: 6.8-7.5

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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: Jan 24, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115 Å / Relative weight: 1
ReflectionResolution: 2.2→29.25 Å / Num. obs: 10996 / % possible obs: 99.7 % / Redundancy: 11.5 % / Rsym value: 0.07 / Net I/σ(I): 17.8
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 3.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5JLS

5jls


Resolution: 2.2→26.36 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.067 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.038 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24241 598 5.5 %RANDOM
Rwork0.20146 ---
obs0.20358 10356 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 53.757 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å2-0 Å2-0 Å2
2---0.44 Å2-0 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.2→26.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1086 0 1 37 1124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191097
X-RAY DIFFRACTIONr_bond_other_d0.0030.021103
X-RAY DIFFRACTIONr_angle_refined_deg1.9831.9671481
X-RAY DIFFRACTIONr_angle_other_deg1.07432538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8285135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.39326.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.0215216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.944153
X-RAY DIFFRACTIONr_chiral_restr0.1140.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021211
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02228
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_it5.3684.922546
X-RAY DIFFRACTIONr_mcbond_other5.3714.914545
X-RAY DIFFRACTIONr_mcangle_it7.0587.307679
X-RAY DIFFRACTIONr_mcangle_other7.0527.318680
X-RAY DIFFRACTIONr_scbond_it6.6715.681550
X-RAY DIFFRACTIONr_scbond_other6.6655.689551
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.918.207803
X-RAY DIFFRACTIONr_long_range_B_refined11.4238.8241238
X-RAY DIFFRACTIONr_long_range_B_other11.43238.7731227
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 51 -
Rwork0.181 740 -
obs--99.62 %

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