[English] 日本語
Yorodumi
- PDB-1zt9: E. coli trp repressor, tetragonal crystal form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zt9
TitleE. coli trp repressor, tetragonal crystal form
ComponentsTrp operon repressor
KeywordsTRANSCRIPTION / helix-turn-helix / DNA-binding protein / protein-protein interaction / L-tryptophan binding protein / bound sulfate anions
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
TrpR-like / Trp repressor, bacterial / Trp repressor / TrpR-like superfamily / Trp repressor protein / Trp repressor/replication initiator / Trp Operon Repressor; Chain A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
TRYPTOPHAN / Trp operon repressor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLawson, C.L. / Chin, A.S. / Benoff, B. / Yung, B.H.
Citation
Journal: To be Published
Title: Two association modes for E. coli trp repressor dimer-dimer interactions
Authors: Lawson, C.L. / Chin, A.S. / Benoff, B. / Yung, B.H.
#1: Journal: J.Biol.Chem. / Year: 1983
Title: Functional inferences from crystals of Escherichia coli trp repressor
Authors: Joachimiak, A. / Schevitz, R.W. / Kelley, R.L. / Yanofsky, C. / Sigler, P.B.
History
DepositionMay 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
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.end_auth_comp_id / _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: Trp operon repressor
B: Trp operon repressor
D: Trp operon repressor
E: Trp operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,54116
Polymers48,9564
Non-polymers1,58512
Water10,052558
1
A: Trp operon repressor
B: Trp operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2718
Polymers24,4782
Non-polymers7936
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-85 kcal/mol
Surface area11470 Å2
MethodPISA
2
D: Trp operon repressor
E: Trp operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2718
Polymers24,4782
Non-polymers7936
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-102 kcal/mol
Surface area11450 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13440 Å2
ΔGint-207 kcal/mol
Surface area20550 Å2
MethodPISA
4
B: Trp operon repressor
hetero molecules

D: Trp operon repressor
hetero molecules

A: Trp operon repressor
E: Trp operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,54116
Polymers48,9564
Non-polymers1,58512
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation4_575y,-x+2,z+1/41
crystal symmetry operation4_565y,-x+1,z+1/41
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-126 kcal/mol
Surface area27160 Å2
MethodPISA
5
E: Trp operon repressor
hetero molecules

B: Trp operon repressor
hetero molecules

A: Trp operon repressor
D: Trp operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,54116
Polymers48,9564
Non-polymers1,58512
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation3_654-y+1,x,z-1/41
crystal symmetry operation4_575y,-x+2,z+1/41
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-122 kcal/mol
Surface area28750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.348, 81.348, 72.687
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31D
41E
51A
61B
71D
81E
91A
101B
111D
121E
131A
141B
151D
161E
171A
181B
191D
201E
211A
221B
231D
241E
251A
261B
271D
281E
291A
301B
311D
321E
331A
341B
351D
361E

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUARGARG5AA13 - 1512 - 14
21GLUGLUARGARG5BB13 - 1512 - 14
31GLUGLUARGARG5DC13 - 1512 - 14
41GLUGLUARGARG5ED13 - 1512 - 14
52GLNGLNTRPTRP5AA17 - 1916 - 18
62GLNGLNTRPTRP5BB17 - 1916 - 18
72GLNGLNTRPTRP5DC17 - 1916 - 18
82GLNGLNTRPTRP5ED17 - 1916 - 18
93LEULEUVALVAL5AA75 - 9474 - 93
103LEULEUVALVAL5BB75 - 9474 - 93
113LEULEUVALVAL5DC75 - 9474 - 93
123LEULEUVALVAL5ED75 - 9474 - 93
134SERSERALAALA5AA5 - 124 - 11
144SERSERALAALA5BB5 - 124 - 11
154SERSERALAALA5DC5 - 124 - 11
164SERSERALAALA5ED5 - 124 - 11
175LEULEULEULEU5AA43 - 6242 - 61
185LEULEULEULEU5BB43 - 6242 - 61
195LEULEULEULEU5DC43 - 6242 - 61
205LEULEULEULEU5ED43 - 6242 - 61
216GLYGLYASNASN5AA64 - 7363 - 72
226GLYGLYASNASN5BB64 - 7363 - 72
236GLYGLYASNASN5DC64 - 7363 - 72
246GLYGLYASNASN5ED64 - 7363 - 72
257PHEPHELEULEU4AA22 - 4121 - 40
267PHEPHELEULEU4BB22 - 4121 - 40
277PHEPHELEULEU4DC22 - 4121 - 40
287PHEPHELEULEU4ED22 - 4121 - 40
298LEULEUGLUGLU4AA96 - 10295 - 101
308LEULEUGLUGLU4BB96 - 10295 - 101
318LEULEUGLUGLU4DC96 - 10295 - 101
328LEULEUGLUGLU4ED96 - 10295 - 101
339LEULEULEULEU4AA104 - 105103 - 104
349LEULEULEULEU4BB104 - 105103 - 104
359LEULEULEULEU4DC104 - 105103 - 104
369LEULEULEULEU4ED104 - 105103 - 104

-
Components

#1: Protein
Trp operon repressor


Mass: 12238.934 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trpR, rtrY / Plasmid: pET13atrpR / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A881
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 558 / 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: 3.1 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 294 K / pH: 5.6
Details: 2.8 M ammonium sulfate plus 50 mM sodium, potassium phosphate buffer, 5 mM L-tryptophan, VAPOR DIFFUSION, HANGING DROP, temperature 294K, pH 5.60

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 19, 2003 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 31825 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.063
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.169

-
Phasing

Phasing MRR rigid body: 34.9 / Cor.coef. Fo:Fc: 72.4 / Cor.coef. Io to Ic: 26.4

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefmac_5.1.24refinement
PDB_EXTRACT1.601data extraction
CBASSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WRP, BIOLOGICAL UNIT

2wrp
PDB Unreleased entry


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.405 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.173 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS WERE ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1636 5.1 %RANDOM
Rwork0.164 ---
obs0.167 30166 99 %-
all-30461 --
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: 19.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3248 0 100 558 3906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0213396
X-RAY DIFFRACTIONr_bond_other_d0.0020.023168
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.9874592
X-RAY DIFFRACTIONr_angle_other_deg0.80237332
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6735400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0690.2520
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023688
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02656
X-RAY DIFFRACTIONr_nbd_refined0.2080.2796
X-RAY DIFFRACTIONr_nbd_other0.2360.23671
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.080.21929
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2367
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.230.2110
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.254
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.94822036
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.28333248
X-RAY DIFFRACTIONr_scbond_it4.33121360
X-RAY DIFFRACTIONr_scangle_it6.14931344
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A868medium positional0.440.5
2B868medium positional0.390.5
3D868medium positional0.360.5
4E868medium positional0.360.5
1A582loose positional0.595
2B582loose positional0.455
3D582loose positional0.545
4E582loose positional0.495
1A868medium thermal1.152
2B868medium thermal1.092
3D868medium thermal1.022
4E868medium thermal1.312
1A582loose thermal3.1710
2B582loose thermal2.7810
3D582loose thermal2.2710
4E582loose thermal3.8910
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.252 128
Rwork0.162 2167

+
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