[English] 日本語
Yorodumi
- PDB-2qww: Crystal structure of multiple antibiotic-resistance repressor (Ma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qww
TitleCrystal structure of multiple antibiotic-resistance repressor (MarR) (YP_013417.1) from Listeria monocytogenes 4b F2365 at 2.07 A resolution
ComponentsTranscriptional regulator, MarR family
KeywordsTRANSCRIPTION / YP_013417.1 / multiple antibiotic-resistance repressor (MarR) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / DNA-binding / Transcription regulation
Function / homologyWinged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / :
Function and homology information
Biological speciesListeria monocytogenes str. 4b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.07 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of multiple antibiotic-resistance repressor (MarR) (YP_013417.1) from Listeria monocytogenes 4b F2365 at 2.07 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 300 BIOMOLECULE: 1, 2, 3, 4 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY ... BIOMOLECULE: 1, 2, 3, 4 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 8 CHAINS. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcriptional regulator, MarR family
B: Transcriptional regulator, MarR family
C: Transcriptional regulator, MarR family
D: Transcriptional regulator, MarR family
E: Transcriptional regulator, MarR family
F: Transcriptional regulator, MarR family
G: Transcriptional regulator, MarR family
H: Transcriptional regulator, MarR family


Theoretical massNumber of molelcules
Total (without water)137,2408
Polymers137,2408
Non-polymers00
Water5,999333
1
A: Transcriptional regulator, MarR family
B: Transcriptional regulator, MarR family


Theoretical massNumber of molelcules
Total (without water)34,3102
Polymers34,3102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
MethodPISA
2
C: Transcriptional regulator, MarR family
D: Transcriptional regulator, MarR family


Theoretical massNumber of molelcules
Total (without water)34,3102
Polymers34,3102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
MethodPISA
3
E: Transcriptional regulator, MarR family
F: Transcriptional regulator, MarR family


Theoretical massNumber of molelcules
Total (without water)34,3102
Polymers34,3102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
MethodPISA
4
G: Transcriptional regulator, MarR family
H: Transcriptional regulator, MarR family


Theoretical massNumber of molelcules
Total (without water)34,3102
Polymers34,3102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.250, 159.700, 90.270
Angle α, β, γ (deg.)90.000, 103.260, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ASNASNSERSER5AA5 - 1526 - 153
2GLYGLYLYSLYS3BB3 - 1514 - 152
3THRTHRLYSLYS6CC6 - 1517 - 152
4THRTHRSERSER6DD6 - 1527 - 153
5GLYGLYLYSLYS3EE3 - 1514 - 152
6THRTHRLYSLYS6FF6 - 1517 - 152
7ASNASNLYSLYS5GG5 - 1516 - 152
8VALVALLYSLYS2HH2 - 1513 - 152
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE

-
Components

#1: Protein
Transcriptional regulator, MarR family


Mass: 17154.953 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes str. 4b (bacteria)
Species: Listeria monocytogenes / Strain: F2365 / Gene: YP_013417.1, LMOf2365_0814 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q722C0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: NANODROP, 29.545% PEG 4000, 0.2M Ammonium acetate, 0.1M Citric acid pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162, 0.97939, 0.97918
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 15, 2007 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979391
30.979181
ReflectionResolution: 2.07→46.984 Å / Num. obs: 79209 / % possible obs: 93.7 % / Biso Wilson estimate: 33.42 Å2 / Rmerge(I) obs: 0.149 / Net I/σ(I): 7.65
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allDiffraction-ID% possible all
2.07-2.140.5712.1165346323182.5
2.14-2.230.462.5206537632190.5
2.23-2.330.3763.1197297298191.7
2.33-2.450.2853.8201607416193.9
2.45-2.610.2564.3215887940194.6
2.61-2.810.195.5208567636195.3
2.81-3.090.2587.4271577694196.1
3.09-3.530.24311.4434977834197.8
3.53-46.9840.11616.5443227970198.1

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.07→46.984 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.882 / SU B: 13.641 / SU ML: 0.181 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.211
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.293 3967 5 %RANDOM
Rwork0.239 ---
all0.242 ---
obs0.242 79173 98.11 %-
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 mean: 37.773 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å20.53 Å2
2---1.67 Å20 Å2
3---2.85 Å2
Refinement stepCycle: LAST / Resolution: 2.07→46.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8349 0 0 333 8682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228474
X-RAY DIFFRACTIONr_bond_other_d0.0020.028214
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.98611485
X-RAY DIFFRACTIONr_angle_other_deg0.789318963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.87451139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.96425.956272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.919151563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.8651527
X-RAY DIFFRACTIONr_chiral_restr0.070.21486
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029247
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021476
X-RAY DIFFRACTIONr_nbd_refined0.1930.32066
X-RAY DIFFRACTIONr_nbd_other0.1360.38195
X-RAY DIFFRACTIONr_nbtor_refined0.1750.54419
X-RAY DIFFRACTIONr_nbtor_other0.0850.55239
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.5528
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0040.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.314
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1420.373
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.240.531
X-RAY DIFFRACTIONr_mcbond_it1.52335854
X-RAY DIFFRACTIONr_mcbond_other0.47632343
X-RAY DIFFRACTIONr_mcangle_it2.28858997
X-RAY DIFFRACTIONr_scbond_it4.18483035
X-RAY DIFFRACTIONr_scangle_it5.724112477
Refine LS restraints NCS

Ens-ID: 1 / Number: 1787 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.440.5
2BMEDIUM POSITIONAL0.680.5
3CMEDIUM POSITIONAL0.450.5
4DMEDIUM POSITIONAL0.390.5
5EMEDIUM POSITIONAL0.660.5
6FMEDIUM POSITIONAL0.810.5
7GMEDIUM POSITIONAL0.470.5
8HMEDIUM POSITIONAL0.570.5
1AMEDIUM THERMAL0.622
2BMEDIUM THERMAL0.662
3CMEDIUM THERMAL0.622
4DMEDIUM THERMAL0.632
5EMEDIUM THERMAL0.662
6FMEDIUM THERMAL0.662
7GMEDIUM THERMAL0.642
8HMEDIUM THERMAL0.672
LS refinement shellResolution: 2.07→2.124 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 286 -
Rwork0.299 5162 -
obs-5448 91.62 %
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)
10.66590.129-0.28950.7255-0.28090.5862-0.04760.0360.0750.01890.04080.04130.0032-0.00770.0067-0.1797-0.00010.0039-0.1281-0.0018-0.2182-23.9451-14.30470.0986
20.33120.2230.34550.7650.36950.4761-0.0138-0.01780.02330.03370.02060.0684-0.0289-0.0171-0.0068-0.18250.00220.0315-0.1040.0005-0.1719-0.054811.8807-1.3766
30.38140.01780.38081.1908-0.01460.4354-0.030.0284-0.0437-0.07540.0229-0.02810.0320.01550.0071-0.167-0.00710.0304-0.10210.0131-0.2396-14.147553.1571-44.4953
40.41110.279-0.20740.82550.02860.1528-0.04870.00330.2168-0.01080.0243-0.0236-0.0268-0.02370.0245-0.1478-0.0002-0.0128-0.11750.011-0.150710.287726.3726-45.0725
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA5 - 896 - 90
21AA92 - 15293 - 153
31BB3 - 1514 - 152
42CC6 - 887 - 89
52CC97 - 15198 - 152
62DD6 - 877 - 88
72DD96 - 15297 - 153
83EE3 - 884 - 89
93EE95 - 15196 - 152
103FF6 - 887 - 89
113FF96 - 15197 - 152
124GG5 - 876 - 88
134GG95 - 15196 - 152
144HH2 - 883 - 89
154HH96 - 15197 - 152

+
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