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- PDB-3vod: Crystal Structure of mutant MarR C80S from E.coli -

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Basic information

Entry
Database: PDB / ID: 3vod
TitleCrystal Structure of mutant MarR C80S from E.coli
ComponentsMultiple antibiotic resistance protein marRMultiple drug resistance
KeywordsTRANSCRIPTION / winged helix-turn-helix DNA binding motif
Function / homology
Function and homology information


cellular response to antibiotic / response to heat / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding
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
Multiple antibiotic resistance protein MarR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsLou, H. / Zhu, R. / Hao, Z.
CitationJournal: Nat.Chem.Biol. / Year: 2014
Title: The multiple antibiotic resistance regulator MarR is a copper sensor in Escherichia coli.
Authors: Hao, Z. / Lou, H. / Zhu, R. / Zhu, J. / Zhang, D. / Zhao, B.S. / Zeng, S. / Chen, X. / Chan, J. / He, C. / Chen, P.R.
History
DepositionJan 21, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Multiple antibiotic resistance protein marR
B: Multiple antibiotic resistance protein marR


Theoretical massNumber of molelcules
Total (without water)32,1422
Polymers32,1422
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-28 kcal/mol
Surface area15310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.162, 62.162, 131.466
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 4 / Auth seq-ID: 11 - 144 / Label seq-ID: 11 - 144

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Multiple antibiotic resistance protein marR / Multiple drug resistance


Mass: 16070.957 Da / Num. of mol.: 2 / Mutation: C80S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1530, cfxB, inaR, JW5248, marR, soxQ / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P27245

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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: 1.98 Å3/Da / Density % sol: 37.74 % / Mosaicity: 0.817 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.03M Citric Acid, 0.07M BIS-TRIS, pH7.6, 24% PEG 3350,0.3M NaCl, 10mM DTT, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorDate: Jul 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 8479 / % possible obs: 99.8 % / Redundancy: 6 % / Rmerge(I) obs: 0.072 / Χ2: 1.904 / Net I/σ(I): 16.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.696.20.3868220.9651100
2.69-2.86.10.2778190.9661100
2.8-2.936.10.2158261.0141100
2.93-3.086.20.1568221.1981100
3.08-3.2860.1048381.361100
3.28-3.536.20.0778281.731100
3.53-3.8860.0688532.2231100
3.88-4.4460.068602.815199.8
4.44-5.595.90.0558683.115199.7
5.59-305.40.0649433.692198.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.6 Å29.06 Å
Translation2.6 Å29.06 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.911 / Occupancy max: 1 / Occupancy min: 1 / SU B: 40.259 / SU ML: 0.358 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.383 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2809 390 4.7 %RANDOM
Rwork0.2557 ---
obs0.2568 8380 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 174.68 Å2 / Biso mean: 80.7712 Å2 / Biso min: 44.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2110 0 0 0 2110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192136
X-RAY DIFFRACTIONr_angle_refined_deg1.0712.0092893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7865269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.00824.81581
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95815419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4341514
X-RAY DIFFRACTIONr_chiral_restr0.0650.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211516
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1042 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.490.5
MEDIUM THERMAL8.362
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.485 28 -
Rwork0.396 488 -
all-516 -
obs--98.47 %
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)
16.50095.1861-3.73665.7906-1.77863.0503-0.0232-0.023-0.5760.55780.099-1.0340.49380.1833-0.07580.4140.0694-0.18260.4532-0.04820.25261.923-19.65521.205
23.76680.74861.45354.2053-1.29922.9594-0.11270.06450.6428-0.0117-0.06120.14970.11330.27540.17390.29950.0251-0.00540.4157-0.01620.1145-14.235-33.05318.617
32.69390.80311.26422.11691.43196.68790.2714-0.3438-0.30390.1015-0.22240.11290.946-0.033-0.0490.46930.0406-0.05340.38040.00480.0588-19.295-41.2718.131
427.54884.94215.61246.69755.898230.522-1.2084-0.78312.1182-0.42430.5157-0.0644-0.7708-0.14960.69270.38950.1082-0.0420.2558-0.25270.3849-17.225-24.67229.327
52.55520.49290.00382.95280.25073.4838-0.0143-0.01470.28530.18680.0064-0.0533-0.0992-0.38850.0080.26960.0269-0.00070.404-0.03870.075-6.509-9.82421.559
65.7926-2.7689-1.038514.688814.004513.8493-1.24121.3793-1.46071.9525-1.41623.17551.5684-0.89282.65740.7371-0.3260.72920.7694-0.31250.9715-13.416-13.96718.403
71.2016-1.7529-0.18892.56680.27660.07720.01420.0732-0.03210.0696-0.09530.0526-0.0081-0.12730.08110.358-0.0915-0.01210.5222-0.02680.11584.523-27.1169.227
85.05610.7959-1.03724.64840.88486.25590.10850.3322-0.33580.4253-0.10420.16580.9018-0.614-0.00430.5016-0.1083-0.00530.31080.07740.07469.846-39.17915.345
93.9577-1.82494.00274.4044-6.34710.8618-0.06770.17640.2497-0.12720.174-0.13710.7254-0.3706-0.10630.5522-0.084-0.10420.42920.00190.1716.944-34.1412.174
102.6252-0.82610.01843.0734-0.00120.00410.04420.09250.2354-0.1386-0.0135-0.1313-0.01850.0201-0.03070.3059-0.0024-0.01950.43690.01460.12232.381-9.86610.813
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 33
2X-RAY DIFFRACTION2A34 - 66
3X-RAY DIFFRACTION3A67 - 106
4X-RAY DIFFRACTION4A107 - 116
5X-RAY DIFFRACTION5A117 - 144
6X-RAY DIFFRACTION6B10 - 16
7X-RAY DIFFRACTION7B17 - 57
8X-RAY DIFFRACTION8B58 - 90
9X-RAY DIFFRACTION9B91 - 114
10X-RAY DIFFRACTION10B115 - 144

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