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- PDB-3nqo: Crystal structure of a MarR family transcriptional regulator (CD1... -

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Basic information

Entry
Database: PDB / ID: 3nqo
TitleCrystal structure of a MarR family transcriptional regulator (CD1569) from Clostridium difficile 630 at 2.20 A resolution
ComponentsMarR-family transcriptional regulator
KeywordsTRANSCRIPTION / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / 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, MarR family
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a MarR family transcriptional regulator (CD1569) from Clostridium difficile 630 at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_ref_seq_dif.details / _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: MarR-family transcriptional regulator
B: MarR-family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,09510
Polymers44,9172
Non-polymers1,1788
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10100 Å2
ΔGint-69 kcal/mol
Surface area17750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.739, 72.672, 76.072
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A3
2114B3
1212A4 - 164
2212B4 - 164
1316A170 - 188
2316B170 - 188
DetailsCRYSTAL PACKING AND SIZE EXCLUSION CHROMATOGRAPHY COUPLED WITH STATIC LIGHT SCATTERING ANALYSES SUPPORT THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein MarR-family transcriptional regulator


Mass: 22458.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD1569 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q186C2
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT (1-188) WAS EXPRESSED WITH THE PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT (1-188) WAS EXPRESSED WITH THE PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.15 Å3/Da / Density % sol: 42.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.47
Details: 47.0000% polyethylene glycol 200, 0.1M HEPES pH 7.47, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97911
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 12, 2010 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.2→29.672 Å / Num. obs: 20101 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 42.65 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 12.61
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.2-2.280.6811.811021357993.1
2.28-2.370.5052.511870370599.8
2.37-2.480.3813.312421386899.6
2.48-2.610.274.612055374899.6
2.61-2.770.1946.111933371299.8
2.77-2.980.1358.611959371299.9
2.98-3.280.08113.212383383499.7
3.28-3.760.0462112374382299.5
3.76-4.720.02930.612082374399.5
4.72-29.6720.0333.712033378097.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0110refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.2→29.672 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 10.926 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.287 / ESU R Free: 0.211
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 4. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 5. RESIDUES 160-164 OF CHAIN A AND 155-163 OF CHAIN B WERE NOT MODELED DUE TO POOR ELECTRON DENSITY IN THOSE REGIONS. 6. SODIUM (NA) FROM THE PROTEIN BUFFER, AND GLYCEROL (GOL) AND POLYETHYLENE GLYCOL (PG4) FROM THE CRYSTALLIZATION/ CRYOPROTECTANT SOLUTIONS HAVE BEEN MODELED INTO THE SOLVENT STRUCTURE. 7. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD SERVER.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1021 5.1 %RANDOM
Rwork0.197 ---
obs0.199 20052 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 138.76 Å2 / Biso mean: 48.924 Å2 / Biso min: 19.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2---0.82 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2824 0 60 63 2947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222969
X-RAY DIFFRACTIONr_bond_other_d0.0030.022009
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.9693994
X-RAY DIFFRACTIONr_angle_other_deg1.05734933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2555369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21725.324139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15315535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3121513
X-RAY DIFFRACTIONr_chiral_restr0.0650.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023242
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02573
X-RAY DIFFRACTIONr_mcbond_it0.7551.51803
X-RAY DIFFRACTIONr_mcbond_other0.21.5733
X-RAY DIFFRACTIONr_mcangle_it1.42222916
X-RAY DIFFRACTIONr_scbond_it2.59531166
X-RAY DIFFRACTIONr_scangle_it4.0884.51071
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
885TIGHT POSITIONAL0.160.05
1017MEDIUM POSITIONAL0.390.5
237LOOSE POSITIONAL1.115
885TIGHT THERMAL1.120.5
1017MEDIUM THERMAL1.472
237LOOSE THERMAL2.4610
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 61 -
Rwork0.273 1318 -
all-1379 -
obs--95.63 %
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)
114.61547.72510.194513.6158-2.821810.6187-0.00820.1067-0.64130.1362-0.2673-1.44180.09530.87560.27560.08320.0032-0.01570.11690.06080.19792.43635.64853.687
24.0852.0945-0.94873.8109-0.79671.28770.03550.13260.7952-0.00930.21721.0556-0.2105-0.3201-0.25260.13190.0262-0.0440.11260.08490.35156.75230.03661.492
31.95340.59140.24364.0224-0.49911.4330.1473-0.2441-0.020.327-0.0759-0.116-0.07350.0143-0.07140.1402-0.03360.01310.0696-0.00410.052874.40627.13269.255
46.583114.6446-11.829939.1131-21.987215.36231.00370.13590.71882.55430.08862.1444-1.494-0.3622-1.09230.5251-0.12820.30870.2447-0.07740.524962.13129.35677.266
55.56740.8967-1.32513.30711.863212.4146-0.0462-0.2171-0.88340.6128-0.3687-0.02830.78240.38040.41480.193-0.0123-0.00030.11160.07360.181267.7439.59376.08
61.05920.4852-0.42381.599-0.67843.5490.05020.0437-0.04110.07750.0840.1547-0.0036-0.0726-0.13420.076-0.0062-0.04350.04740.00430.12371.88930.34358.385
71.78821.55350.80483.03950.55144.5275-0.04340.3463-0.312-0.3720.1542-0.01520.6075-0.0527-0.11080.1923-0.0026-0.04930.1001-0.08110.114875.88126.43640.136
84.54482.3927-0.17838.012-0.27322.35790.01270.0622-0.28760.4876-0.0207-0.48640.11390.20320.0080.1028-0.0041-0.0170.10760.03490.074283.13826.28663.535
911.401519.8538-9.472931.219-14.72397.6399-1.4482-0.013-1.0711-2.90460.0779-1.46231.52110.51851.37030.7310.04830.16270.27110.10650.597887.21429.15948.44
106.3823-2.2564-1.548910.03420.69472.99380.0656-0.36970.36370.5481-0.1558-0.2481-0.44820.21230.09010.1928-0.0706-0.0270.0941-0.02070.0788.08948.68456.024
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 15
2X-RAY DIFFRACTION2A16 - 115
3X-RAY DIFFRACTION3A116 - 149
4X-RAY DIFFRACTION4A150 - 168
5X-RAY DIFFRACTION5A169 - 188
6X-RAY DIFFRACTION6B3 - 52
7X-RAY DIFFRACTION7B53 - 126
8X-RAY DIFFRACTION8B127 - 147
9X-RAY DIFFRACTION9B148 - 172
10X-RAY DIFFRACTION10B173 - 188

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