[English] 日本語
Yorodumi
- PDB-3nnr: Crystal structure of a TetR-family transcriptional regulator (Maq... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3nnr
TitleCrystal structure of a TetR-family transcriptional regulator (Maqu_3571) from MARINOBACTER AQUAEOLEI VT8 at 2.49 A resolution
ComponentsTranscriptional regulator, TetR family
KeywordsTRANSCRIPTION / TETR-FAMILY TRANSCRIPTIONAL REGULATOR / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Bacterial transcriptional repressor TetR / Bacterial transcriptional repressor / Tetracycline Repressor, domain 2 / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Unknown ligand / Transcriptional regulator, TetR family
Similarity search - Component
Biological speciesMarinobacter aquaeolei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.49 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a TetR-family transcriptional regulator (Maqu_3571) from MARINOBACTER AQUAEOLEI VT8 at 2.49 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 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 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcriptional regulator, TetR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0954
Polymers26,9031
Non-polymers1923
Water25214
1
A: Transcriptional regulator, TetR family
hetero molecules

A: Transcriptional regulator, TetR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1908
Polymers53,8062
Non-polymers3846
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5720 Å2
ΔGint-74 kcal/mol
Surface area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.745, 58.745, 172.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsCRYSTAL PACKING ANALYSIS SUGGEST THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

-
Components

#1: Protein Transcriptional regulator, TetR family


Mass: 26902.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinobacter aquaeolei (bacteria) / Strain: ATCC 700491 / DSM 11845 / VT8 / Gene: Maqu_3571 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A1U6M1
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS PROTEIN WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS PROTEIN WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.57 %
Crystal growTemperature: 293 K / pH: 9.5
Details: 0.2000M lithium sulfate, 1.0500M potassium sodium tartrate, 0.1M CHES pH 9.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97934,0.97922
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 14, 2010 / Details: FLAT COLLIMATING MIRROR, TOROID FOCUSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979341
30.979221
ReflectionResolution: 2.49→29.93 Å / Num. obs: 11338 / % possible obs: 100 % / Redundancy: 9.1 % / Biso Wilson estimate: 68.12 Å2 / Rsym value: 0.074 / Net I/σ(I): 16.9
Reflection shellHighest resolution: 2.49 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 2.1 / Rsym value: 1.187 / % possible all: 100

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0110refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.3.15data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
autoSHARPphasing
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.49→29.93 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 20.893 / SU ML: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.265
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.SULFATE (SO4) FROM THE CRYSTALLIZATION SOLUTION HAS BEEN MODELED IN THE SOLVENT STRUCTURE. 6.AN UNIDENTIFIED LIGAND (UNL) HAS BEEN MODELED AT A PUTATIVE FUNCTIONAL SITE BASED ON COMPARISON TO THE HOMOLOG STRUCTURE WITH PDB ID 3G1L.
RfactorNum. reflection% reflectionSelection details
Rfree0.26 538 4.8 %RANDOM
Rwork0.23 ---
obs0.232 11278 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 72.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20 Å2
2--0.5 Å20 Å2
3----1.01 Å2
Refinement stepCycle: LAST / Resolution: 2.49→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1687 0 18 14 1719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221766
X-RAY DIFFRACTIONr_bond_other_d0.0020.021205
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.972403
X-RAY DIFFRACTIONr_angle_other_deg1.2832920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6445209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.48423.40791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33815306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1961514
X-RAY DIFFRACTIONr_chiral_restr0.0930.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211936
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02383
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.79231029
X-RAY DIFFRACTIONr_mcbond_other0.4013405
X-RAY DIFFRACTIONr_mcangle_it3.28151671
X-RAY DIFFRACTIONr_scbond_it5.9848737
X-RAY DIFFRACTIONr_scangle_it8.36611728
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.49→2.55 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 35 -
Rwork0.309 787 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 4.3488 Å / Origin y: -2.7976 Å / Origin z: 11.3117 Å
111213212223313233
T0.3022 Å20.0668 Å2-0.0824 Å2-0.4738 Å20.0932 Å2--0.0993 Å2
L4.4727 °22.7366 °2-0.8207 °2-4.3132 °2-1.0378 °2--2.1601 °2
S-0.2304 Å °-0.0233 Å °0.0627 Å °0.1709 Å °-0.073 Å °-0.3304 Å °-0.2514 Å °0.1878 Å °0.3033 Å °

+
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://pdbjlvh1.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