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- PDB-3voe: Crystal Structure of wild type MarR (apo form) from E.coli -

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Basic information

Entry
Database: PDB / ID: 3voe
TitleCrystal Structure of wild type MarR (apo form) from E.coli
ComponentsMultiple antibiotic resistance protein marR
KeywordsTRANSCRIPTION / winged helix-turn-helix DNA binding domain
Function / homology
Function and homology information


response to stress / 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: To be Published
Title: MarR structures
Authors: Lou, H. / Zhu, R. / Hao, Z.
History
DepositionJan 21, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)32,1742
Polymers32,1742
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-30 kcal/mol
Surface area15240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.960, 61.960, 131.740
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


Mass: 16087.023 Da / Num. of mol.: 2
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: 1.96 Å3/Da / Density % sol: 37.4 % / Mosaicity: 1.32 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.03M Citric Acid, 0.07M BIS-TRIS, pH7.6, 18-20% 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: Jun 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→56.068 Å / Num. all: 8461 / Num. obs: 8461 / % possible obs: 99.9 % / Redundancy: 7.9 % / Rsym value: 0.07 / Net I/σ(I): 16.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.6-2.748.10.6880.6441.2969011930.2390.6880.6442.7100
2.74-2.9180.4670.4371.8907811280.1630.4670.4374.1100
2.91-3.1180.2620.2443.2860810800.0920.2620.2447.1100
3.11-3.367.90.1360.1276.178889980.0480.1360.12712.8100
3.36-3.687.80.0880.0838.973399420.0310.0880.08318.7100
3.68-4.117.80.0620.05812.465618430.0220.0620.05824.2100
4.11-4.757.90.050.04711.560727650.0180.050.04731.4100
4.75-5.817.90.0840.0797.652106620.0290.0840.07929.4100
5.81-8.227.60.0350.03218.740075290.0120.0350.03229.6100
8.22-35.8286.60.0230.02127.721153210.0090.0230.02137.497.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å29.08 Å
Translation3 Å29.08 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→40 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.2902 / WRfactor Rwork: 0.2413 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7514 / SU B: 39.26 / SU ML: 0.358 / SU R Cruickshank DPI: 0.3463 / SU Rfree: 0.4126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.413 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2902 823 9.8 %RANDOM
Rwork0.2413 ---
obs0.246 8400 99.67 %-
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: 214.16 Å2 / Biso mean: 69.5021 Å2 / Biso min: 32.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2110 0 0 0 2110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192136
X-RAY DIFFRACTIONr_angle_refined_deg0.5252.012893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8055269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.79424.81581
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.06115419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6741514
X-RAY DIFFRACTIONr_chiral_restr0.0370.2359
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 POSITIONAL0.50.5
MEDIUM THERMAL9.492
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.479 49 -
Rwork0.369 458 -
all-507 -
obs--99.8 %
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)
13.9682-4.1582-1.03385.40242.90863.47910.0032-0.4844-0.76830.06120.11990.60790.1845-0.5707-0.12310.2819-0.04370.00630.30770.11870.2695-19.5836-2.0969-11.7303
23.2224-0.409-0.6112.0414-1.56233.1802-0.0580.05470.1902-0.0052-0.1163-0.44190.2276-0.05250.17430.26840.01170.01570.23040.00580.2019-32.965114.0244-14.3029
32.57-0.0123-0.21230.7332-1.54813.3541-0.1832-0.04430.00670.06770.21-0.0098-0.1535-0.5072-0.02680.2653-0.0041-0.0260.31640.03380.1331-41.168319.0254-14.8056
46.0242-10.64530.918421.3495-7.03616.1120.04160.405900.6664-1.0539-0.8295-0.21910.79231.01240.439-0.157-0.40520.38170.07750.444-24.580616.9806-3.5772
52.8755-0.1580.33851.44760.16773.80230.1049-0.2187-0.0641-0.0127-0.0185-0.193-0.1920.1177-0.08640.2914-0.0206-0.02590.2497-0.0230.1561-9.76876.3295-11.3138
61.62850.62660.13950.26830.00430.1101-0.093-0.03870.10140.01370.02640.0231-0.1236-0.04230.06670.33680.0556-0.00320.2846-0.00970.2054-25.0869-1.9951-22.3369
73.6984-0.0509-1.23293.95061.96646.27-0.1593-0.06480.2142-0.03530.10340.2234-0.3428-0.13080.05590.23110.09260.06370.36140.0280.0817-38.4354-8.0529-18.5204
88.99129.6052-11.728511.3951-10.204220.08710.67120.53260.64710.84560.20170.6774-0.6823-1.2496-0.87290.10860.04790.0811.31330.20440.0856-43.774-18.8461-9.4377
98.42123.2472-7.22995.643-6.15668.9482-0.17150.1662-0.3358-0.2113-0.038-0.31370.1157-0.24390.20950.35690.07260.05850.37760.05690.266-29.4524-16.6386-26.9149
103.14920.88350.25121.82150.26720.33-0.00060.1115-0.1374-0.08020.1244-0.14720.15880.144-0.12380.2983-0.00020.01710.25180.00470.1995-9.7819-2.5268-22.1008
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 - 57
7X-RAY DIFFRACTION7B58 - 85
8X-RAY DIFFRACTION8B86 - 97
9X-RAY DIFFRACTION9B98 - 114
10X-RAY DIFFRACTION10B115 - 144

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