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- PDB-3tgn: Crystal Structure of the zinc-dependent MarR Family Transcription... -

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Basic information

Entry
Database: PDB / ID: 3tgn
TitleCrystal Structure of the zinc-dependent MarR Family Transcriptional Regulator AdcR in the Zn(II)-bound State
ComponentsAdc operon repressor AdcR
KeywordsTRANSCRIPTION / Helix-turn-Helix / Transcriptional regulator
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / metal ion binding
Similarity search - Function
Helix Hairpins - #1680 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2360 / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / MarR family / ArsR-like helix-turn-helix domain / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Helix Hairpins ...Helix Hairpins - #1680 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2360 / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / MarR family / ArsR-like helix-turn-helix domain / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Helix Hairpins / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Special / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulator AdcR
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsGuerra, A.J. / Dann III, C.E. / Giedroc, D.P.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Crystal Structure of the Zinc-Dependent MarR Family Transcriptional Regulator AdcR in the Zn(II)-Bound State.
Authors: Guerra, A.J. / Dann, C.E. / Giedroc, D.P.
History
DepositionAug 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Database references
Revision 1.2Dec 21, 2011Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adc operon repressor AdcR
B: Adc operon repressor AdcR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5196
Polymers33,2582
Non-polymers2624
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-125 kcal/mol
Surface area14930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.848, 57.621, 85.443
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Adc operon repressor AdcR


Mass: 16628.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: D39 / NCTC 7466 / Gene: adcR, SPD_2000 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q04I02
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.07 Å3/Da / Density % sol: 40.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl, 18 % PEG 10000, 20 % glycerol, 0.1 M NaCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9184 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Apr 23, 2011
Details: Rosenbaum-Rock monochromator 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: SAGITALLY FOCUSED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 19294 / Num. obs: 18718 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2-2.035.60.287199.7
2.03-2.075.70.247197.5
2.07-2.115.60.207199.3
2.11-2.155.70.199197.8
2.15-2.25.70.239198.5
2.2-2.255.70.137198.4
2.25-2.315.70.166197.2
2.31-2.375.70.149198.9
2.37-2.445.70.115197.7
2.44-2.525.70.11196.9
2.52-2.615.70.097197.3
2.61-2.715.70.089197.7
2.71-2.845.70.08197.2
2.84-2.995.80.075196.8
2.99-3.175.70.062196.5
3.17-3.425.70.05196.1
3.42-3.765.70.041195.9
3.76-4.315.70.04195.5
4.31-5.435.70.041194.3
5.43-505.40.046192.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXAutoSolmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXAutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2→47.773 Å / SU ML: 0.56 / σ(F): 0 / Phase error: 22.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2497 1773 10.01 %RANDOM
Rwork0.1847 ---
all0.1912 19294 --
obs0.1912 17718 91.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.694 Å2 / ksol: 0.326 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8093 Å20 Å2-0 Å2
2--0.8533 Å2-0 Å2
3----0.044 Å2
Refinement stepCycle: LAST / Resolution: 2→47.773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2200 0 4 302 2506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042247
X-RAY DIFFRACTIONf_angle_d0.6243050
X-RAY DIFFRACTIONf_dihedral_angle_d11.413809
X-RAY DIFFRACTIONf_chiral_restr0.042373
X-RAY DIFFRACTIONf_plane_restr0.002387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05180.27671340.18761164X-RAY DIFFRACTION89
2.0518-2.11210.27671440.17031231X-RAY DIFFRACTION95
2.1121-2.18030.25291320.18861167X-RAY DIFFRACTION90
2.1803-2.25820.43551260.29121087X-RAY DIFFRACTION83
2.2582-2.34860.31241160.23811085X-RAY DIFFRACTION82
2.3486-2.45550.24871360.1891259X-RAY DIFFRACTION94
2.4555-2.5850.22981380.18481236X-RAY DIFFRACTION94
2.585-2.74690.22951420.18091263X-RAY DIFFRACTION95
2.7469-2.9590.24581380.18741273X-RAY DIFFRACTION96
2.959-3.25670.25851390.18181274X-RAY DIFFRACTION95
3.2567-3.72780.22521400.17241271X-RAY DIFFRACTION94
3.7278-4.6960.20411440.15021287X-RAY DIFFRACTION93
4.696-47.78650.22181440.17841348X-RAY DIFFRACTION93
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)
12.8013-0.5021-1.56670.80880.73881.92420.0394-0.2350.06540.09990.1312-0.0962-0.01560.1658-0.13110.1192-0.0162-0.00090.10910.01710.092914.367131.419452.102
21.37640.3473-0.8070.9344-0.23231.11510.0204-0.2146-0.09420.21040.014-0.0552-0.00550.2068-0.020.1080.0112-0.01180.11830.01390.089528.537323.341132.5759
31.2354-0.6664-0.56032.28690.46341.01650.08710.08960.1508-0.1025-0.0123-0.1521-0.10470.0452-0.04160.1053-0.0099-0.00410.1425-0.00110.108933.702431.753824.4697
44.9101-0.3066-2.91330.48410.29352.186-0.11010.2223-0.52810.0561-0.12950.07950.0234-0.15450.23430.12710.004-0.00550.0925-0.01310.152920.504917.798231.4155
51.6571.68760.48064.0710.61511.709-0.0754-0.05070.1787-0.1182-0.04730.3327-0.2285-0.1530.08590.0993-0.0416-0.00120.1237-0.00870.09583.166230.423841.5568
63.33121.06370.13161.96050.11092.0121-0.1090.09530.0359-0.34680.0220.0152-0.12790.06280.05770.12490.01390.03020.07190.00860.119212.978929.466136.5038
72.23050.69890.48191.85810.6521.7641-0.0380.12350.0486-0.06460.07220.1309-0.15420.3197-0.07690.11280.02890.00660.16960.00890.132725.84944.6653.9679
81.2189-0.65310.30921.84280.16652.2308-0.00070.3809-0.1588-0.0822-0.23770.28830.0723-0.08140.21150.18260.03430.02660.296-0.00740.189936.373741.455763.6263
91.75040.28930.40170.81970.18641.05320.0138-0.17950.04640.0846-0.05310.05410.1029-0.0370.01610.1040.01160.01290.11090.01470.077311.567336.547152.9786
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:18)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 19:49)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 50:98)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 99:125)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 126:145)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 1:19)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 20:50)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 51:98)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 99:146)

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