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- PDB-3cjn: Crystal structure of transcriptional regulator, MarR family, from... -

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Basic information

Entry
Database: PDB / ID: 3cjn
TitleCrystal structure of transcriptional regulator, MarR family, from Silicibacter pomeroyi
ComponentsTranscriptional regulator, MarR family
KeywordsTRANSCRIPTION REGULATOR / Transcriptional regulator / MarR family / Silicibacter pomeroyi / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / DNA-binding / Transcription regulation
Function / homology
Function and homology information


response to stress / DNA-binding transcription factor activity
Similarity search - Function
: / 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
PHOSPHATE ION / Transcriptional regulator, MarR family
Similarity search - Component
Biological speciesSilicibacter pomeroyi DSS-3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsChang, C. / Volkart, L. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of MarR family transcriptional regulator from Silicibacter pomeroyi.
Authors: Chang, C. / Volkart, L. / Freeman, L. / Joachimiak, A.
History
DepositionMar 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.pdbx_leaving_atom_flag / _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: Transcriptional regulator, MarR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5712
Polymers18,4761
Non-polymers951
Water2,558142
1
A: Transcriptional regulator, MarR family
hetero molecules

A: Transcriptional regulator, MarR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1424
Polymers36,9522
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5900 Å2
ΔGint-43.6 kcal/mol
Surface area13690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.976, 87.976, 43.197
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-286-

HOH

21A-342-

HOH

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Components

#1: Protein Transcriptional regulator, MarR family


Mass: 18475.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter pomeroyi DSS-3 (bacteria) / Species: Silicibacter pomeroyi / Strain: DSS-3 / DSM 15171 / Gene: SPO1458 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star / References: UniProt: Q5LTF6
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 Succinic acid pH 7.0, 12 % PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2007
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 12944 / Num. obs: 12941 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 21 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 77.2
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 21.8 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 14.5 / Num. unique all: 1263 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→43.98 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.913 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22257 624 4.9 %RANDOM
Rwork0.17912 ---
all0.18119 12819 --
obs0.18119 12819 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.927 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å20 Å2
2---0.75 Å20 Å2
3---1.5 Å2
Refinement stepCycle: LAST / Resolution: 1.95→43.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1133 0 5 142 1280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221172
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.9811583
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1265148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.83521.92352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96515209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3921515
X-RAY DIFFRACTIONr_chiral_restr0.0980.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02880
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.2535
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2821
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2106
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.264
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8571.5764
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.32921169
X-RAY DIFFRACTIONr_scbond_it2.0063463
X-RAY DIFFRACTIONr_scangle_it2.8814.5414
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→1.997 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 36 -
Rwork0.191 864 -
obs-900 96.26 %
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)
15.6368-0.0487-6.43191.9477-0.92811.1979-0.13280.0160.22560.11540.12420.0041-0.1113-0.2850.0086-0.0855-0.0044-0.0521-0.07660.0107-0.074328.794120.893722.8327
25.17251.2373-2.36142.36640.26873.9984-0.09370.06540.0642-0.190.06650.0912-0.1485-0.15110.0272-0.1113-0.0056-0.0357-0.08540.0271-0.03296.219230.332230.0672
317.30690.9291-4.9080.0608-0.3922.8986-0.2421-0.54490.72570.07990.3126-0.07070.20590.1366-0.07050.02260.0297-0.06660.0206-0.02810.005424.77628.566337.7967
48.7764-0.94855.0472.02070.1594.66720.05490.27120.3255-0.1319-0.0419-0.52770.03360.2562-0.013-0.0573-0.0096-0.0208-0.16550.02320.016427.473137.846821.0356
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA12 - 4615 - 49
2X-RAY DIFFRACTION2AA47 - 11250 - 115
3X-RAY DIFFRACTION3AA113 - 135116 - 138
4X-RAY DIFFRACTION4AA136 - 159139 - 162

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