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- PDB-3vb2: Crystal Structure of the Reduced Form of MarR from E.coli -

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Basic information

Entry
Database: PDB / ID: 3vb2
TitleCrystal Structure of the Reduced Form of MarR from E.coli
ComponentsMultiple antibiotic resistance protein marR
Keywordstranscription regulator / Winged Helix-turn-Helix DNA-binding motif
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: The reduced form of MarR structure
Authors: Lou, H. / Zhu, R. / Hao, Z.
History
DepositionDec 30, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 30, 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 / 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

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)31,9812
Polymers31,9812
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-34 kcal/mol
Surface area13980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.800, 62.800, 173.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUASNASNAA10 - 8910 - 89
21GLUGLUASNASNBB10 - 8910 - 89
12ASPASPPROPROAA118 - 144118 - 144
22ASPASPPROPROBB118 - 144118 - 144

NCS ensembles :
ID
1
2

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Components

#1: Protein Multiple antibiotic resistance protein marR


Mass: 15990.629 Da / Num. of mol.: 2 / Mutation: C47S, C51S, C54S,C80S, C108S, C111S
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.67 Å3/Da / Density % sol: 53.89 % / Mosaicity: 0.76 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 5% Tacsimate,0.1M HEPES, 10% PEG 5000MME, 0.3M NaCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jan 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.6→59.033 Å / Num. all: 10837 / Num. obs: 10837 / % possible obs: 95.9 % / Redundancy: 6 % / Biso Wilson estimate: 59.8 Å2 / Rsym value: 0.099 / Net I/σ(I): 10.9
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
2.6-2.746.20.5340.4931.3971215570.1920.5340.4933.497.6
2.74-2.916.20.3220.2982.5909514680.1150.3220.2985.197.1
2.91-3.116.20.220.2033.7858613960.0790.220.2036.896.9
3.11-3.366.10.1420.1315.5804413080.0510.1420.1319.496.8
3.36-3.686.10.1190.114.8724111940.0430.1190.1112.696.1
3.68-4.1160.0930.0866.8657110920.0340.0930.08615.496.3
4.11-4.755.90.090.0847.156709570.0310.090.08418.194.1
4.75-5.815.30.1040.0966.243498150.0380.1040.09616.893.3
5.81-8.226.10.0660.0618.940766710.0230.0660.0611994.9
8.22-39.5085.10.050.04612.219493790.0190.050.04620.787.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.895 / WRfactor Rfree: 0.3054 / WRfactor Rwork: 0.25 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7764 / SU B: 27.662 / SU ML: 0.281 / SU R Cruickshank DPI: 0.7214 / SU Rfree: 0.3472 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.721 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2834 511 4.8 %RANDOM
Rwork0.2429 ---
obs0.2448 10739 94.83 %-
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: 178.45 Å2 / Biso mean: 77.1884 Å2 / Biso min: 43.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2104 0 0 18 2122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192129
X-RAY DIFFRACTIONr_angle_refined_deg0.6812.0072883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8695267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.63824.93881
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.89615416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0541513
X-RAY DIFFRACTIONr_chiral_restr0.0570.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211506
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Ens-IDNumberRms dev position (Å)
16306.98
22183.33
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 34 -
Rwork0.254 631 -
all-665 -
obs--96.1 %
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)
18.71294.3607-6.50354.5181-3.7886.6254-0.1050.8424-0.3176-0.42550.216-0.17420.3039-0.5782-0.11090.37390.01780.05740.353-0.00840.225219.6598.19611.776
26.5069-0.737-1.47678.5574-0.73898.9205-0.2307-0.6648-0.56460.9321-0.0376-0.31651.08980.66630.26830.45830.01020.03520.3569-0.02310.286434.38119.21212.422
343.187413.483618.851412.18743.52719.7866-0.0408-0.16390.74680.9936-0.0202-1.4313-1.40521.38850.0610.5304-0.2027-0.00540.5753-0.13230.581240.78627.93611.613
433.188616.0228-7.17321.4137-4.02972.03630.7053-1.1441-0.63430.8035-0.65720.4326-0.08930.3056-0.04810.57850.01420.08280.3939-0.06290.227822.51526.3297.538
510.29140.97425.27745.8165-0.300614.2179-0.03320.79070.1491-0.08880.31120.3503-0.43680.4351-0.2780.3513-0.01970.07080.25780.07340.34168.92213.38419.886
65.4306-2.1039-2.02096.84521.59684.27020.07130.08670.4655-0.04790.2453-0.9249-0.09670.1096-0.31660.3041-0.09660.02660.39440.01510.230125.4065.03221.699
718.52186.5009-2.000711.4308-3.950911.95040.10881.35271.3112-1.6050.972-0.6476-0.92840.6348-1.08070.9079-0.26750.54180.7429-0.09210.851634.909-3.5788.745
84.5431-3.4012-2.27093.96961.53621.66150.06970.03240.01860.10370.1967-0.20730.07650.1811-0.26640.4383-0.02490.03670.36130.00390.40720.475-2.25626.01
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 45
2X-RAY DIFFRACTION2A46 - 82
3X-RAY DIFFRACTION3A83 - 99
4X-RAY DIFFRACTION4A100 - 112
5X-RAY DIFFRACTION5A113 - 144
6X-RAY DIFFRACTION6B6 - 58
7X-RAY DIFFRACTION7B59 - 89
8X-RAY DIFFRACTION8B96 - 144

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