[English] 日本語
Yorodumi
- PDB-4jba: Crystal Structure of the Oxidized Form of MarR from E.coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jba
TitleCrystal Structure of the Oxidized Form of MarR from E.coli
ComponentsMultiple antibiotic resistance protein MarRMultiple drug resistance
KeywordsTRANSCRIPTION REGULATOR / disulfide bonds / DNA / TRANSCRIPTION REGULATION
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 ...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: 2.5 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
DepositionFeb 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,0132
Polymers32,0132
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-33 kcal/mol
Surface area14070 Å2
MethodPISA
2
A: Multiple antibiotic resistance protein MarR
B: Multiple antibiotic resistance protein MarR

A: Multiple antibiotic resistance protein MarR
B: Multiple antibiotic resistance protein MarR


Theoretical massNumber of molelcules
Total (without water)64,0274
Polymers64,0274
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area11600 Å2
ΔGint-80 kcal/mol
Surface area26110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.270, 62.270, 161.880
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A7 - 91
2111B7 - 91
1121A96 - 144
2121B96 - 144

NCS ensembles :
ID
1
2

-
Components

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


Mass: 16006.695 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
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.54 %
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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 5, 2011
RadiationMonochromator: Monochromator crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.5→53.96 Å / Num. all: 13187 / Num. obs: 13130 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rsym value: 0.094 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.647.80.78111448918680.78199.9
2.64-2.87.70.4751.61391818020.475100
2.8-2.997.70.2792.71301516900.279100
2.99-3.237.60.1524.61189415630.152100
3.23-3.547.60.16.21109914700.1100
3.54-3.957.50.0727.3999013330.072100
3.95-4.567.30.0816.5874711910.081100
4.56-5.597.10.0866.5721110180.086100
5.59-7.916.60.073754078180.07399.9
7.91-44.8795.70.071824784340.07190.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å44.88 Å
Translation3 Å44.88 Å

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASER2.3.0phasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 1 / SU B: 30.359 / SU ML: 0.294 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.442 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2636 642 4.9 %RANDOM
Rwork0.2408 ---
obs0.2419 13130 99.36 %-
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: 193.62 Å2 / Biso mean: 86.6287 Å2 / Biso min: 37.23 Å2
Baniso -1Baniso -2Baniso -3
1-2.26 Å21.13 Å20 Å2
2--2.26 Å20 Å2
3----3.39 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2104 0 0 3 2107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022131
X-RAY DIFFRACTIONr_angle_refined_deg0.5952.0072886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2845266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.48525.06281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.31615411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6061512
X-RAY DIFFRACTIONr_chiral_restr0.0470.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211508
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)
16727.33
23744.04
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.47 42 -
Rwork0.392 790 -
all-832 -
obs--100 %
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)
10.30360.2414-0.1711.2207-1.21281.3878-0.1831-0.33680.0999-0.49440.0713-0.20080.3948-0.31040.11180.70050.09980.0540.6053-0.10820.1937-21.926-15.265517.3155
22.28583.9622-1.41268.12150.15216.5152-0.39690.2404-0.0419-0.34760.7375-0.37230.78080.4588-0.34060.65170.1030.10220.6066-0.4190.5303-15.18910.09757.9232
30.2417-0.94880.032132.2763-20.673115.0436-0.40420.14720.24860.73031.1839-0.2541-0.1232-1.4177-0.77980.8635-0.0329-0.06450.5240.19490.4052-33.2448-7.911813.2783
42.73831.3892-0.61363.173-0.6170.70650.1888-0.21440.07390.07340.06750.05830.0952-0.1137-0.25630.51180.03860.02360.47750.0180.2331-28.5483-17.708531.6243
58.9445-2.3347-2.60020.9908-0.28223.3790.6196-0.13610.4721-0.15140.07820.0074-0.521-0.163-0.69770.68140.07140.27270.4150.01990.2904-20.1821-9.859127.9842
60.63270.71451.1624.19220.49493.31260.187-0.20980.0423-0.55360.2549-0.38760.2409-0.3951-0.44190.6202-0.03190.32120.5799-0.03140.483-6.4198-21.544315.5381
73.0045-1.351-1.00250.8245-0.2453.09280.31350.19050.1599-0.08570.069-0.0113-0.1766-0.0134-0.38260.6599-0.00270.20430.5938-0.04920.1955-1.7124-23.54489.2208
81.2045-0.6133-1.52760.66140.23922.86270.1008-0.3516-0.0078-0.18250.19560.12870.01450.2473-0.29640.5810.01620.01230.51040.00060.2618-15.9767-21.210534.5884
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 57
2X-RAY DIFFRACTION2A58 - 101
3X-RAY DIFFRACTION3A102 - 120
4X-RAY DIFFRACTION4A121 - 144
5X-RAY DIFFRACTION5B6 - 30
6X-RAY DIFFRACTION6B31 - 65
7X-RAY DIFFRACTION7B66 - 112
8X-RAY DIFFRACTION8B113 - 144

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more