[English] 日本語
Yorodumi
- PDB-1zre: 4 crystal structures of CAP-DNA with all base-pair substitutions ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zre
Title4 crystal structures of CAP-DNA with all base-pair substitutions at position 6, CAP-[6G;17C]ICAP38 DNA
Components
  • 5'-D(*AP*TP*TP*TP*CP*GP*AP*AP*AP*AP*AP*TP*GP*GP*GP*AP*T)-3'
  • 5'-D(*CP*TP*AP*GP*AP*TP*CP*CP*CP*AP*TP*TP*TP*TP*TP*CP*GP*AP*AP*AP*T)-3'
  • Catabolite gene activator
KeywordsGENE REGULATION/DNA / PROTEIN-DNA COMPLEX / CAP / CAP-DNA / CATABOLITE GENE ACTIVATOR PROTEIN / CAMP RECEPTOR PROTEIN / CRP / GENE REGULATION-DNA COMPLEX
Function / homology
Function and homology information


carbon catabolite repression of transcription / DNA binding, bending / minor groove of adenine-thymine-rich DNA binding / cAMP binding / protein-DNA complex / sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / positive regulation of DNA-templated transcription ...carbon catabolite repression of transcription / DNA binding, bending / minor groove of adenine-thymine-rich DNA binding / cAMP binding / protein-DNA complex / sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / positive regulation of DNA-templated transcription / identical protein binding / cytosol
Similarity search - Function
Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain ...Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Jelly Rolls / Winged helix-like DNA-binding domain superfamily / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / DNA / DNA (> 10) / DNA-binding transcriptional dual regulator CRP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBerman, H.M. / Napoli, A.A.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps.
Authors: Napoli, A.A. / Lawson, C.L. / Ebright, R.H. / Berman, H.M.
History
DepositionMay 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 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
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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
W: 5'-D(*AP*TP*TP*TP*CP*GP*AP*AP*AP*AP*AP*TP*GP*GP*GP*AP*T)-3'
X: 5'-D(*CP*TP*AP*GP*AP*TP*CP*CP*CP*AP*TP*TP*TP*TP*TP*CP*GP*AP*AP*AP*T)-3'
Y: 5'-D(*AP*TP*TP*TP*CP*GP*AP*AP*AP*AP*AP*TP*GP*GP*GP*AP*T)-3'
Z: 5'-D(*CP*TP*AP*GP*AP*TP*CP*CP*CP*AP*TP*TP*TP*TP*TP*CP*GP*AP*AP*AP*T)-3'
A: Catabolite gene activator
B: Catabolite gene activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0348
Polymers70,3766
Non-polymers6582
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.352, 75.566, 179.979
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

-
Components

#1: DNA chain 5'-D(*AP*TP*TP*TP*CP*GP*AP*AP*AP*AP*AP*TP*GP*GP*GP*AP*T)-3'


Mass: 5274.459 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*TP*AP*GP*AP*TP*CP*CP*CP*AP*TP*TP*TP*TP*TP*CP*GP*AP*AP*AP*T)-3'


Mass: 6372.146 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein Catabolite gene activator / cAMP receptor protein / cAMP-regulatory protein


Mass: 23541.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: crp, cap, csm / Plasmid: pAKCRP1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0ACJ8
#4: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP / Cyclic adenosine monophosphate


Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 3.14 Å3/Da / Density % sol: 60.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 2mM cAMP, 0.1M MES, 0.2M NaCl, 0.05M MgCl2, 5% PEG 8000, 15% Dioxane, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1cAMP11
2MES11
3NaClSodium chloride11
4MgCl211
5PEG 800011
6Dioxane1,4-Dioxane11
7H2O11
8cAMP12
9MES12
10NaClSodium chloride12
11MgCl212
12PEG 800012
13H2O12

-
Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 24, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→38.66 Å / Num. all: 21551 / Num. obs: 21500 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.09 / Χ2: 1.325
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. measured obsΧ2
2.8-2.992.45.60.48119601.792
2.9-3.021006.70.41821341.714
3.02-3.1599.86.60.2921581.604
3.15-3.3299.96.50.20521401.471
3.32-3.5399.86.30.14621521.314
3.53-3.899.860.11121771.092
3.8-4.1899.55.90.08721621.154
4.18-4.7999.55.80.07522001.011
4.79-6.0399.86.20.07322091.001
6.03-5095.46.10.05622591.106

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.601data extraction
CBASSdata collection
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZRC

1zrc


Resolution: 2.8→38.66 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2095 9.9 %RANDOM
Rwork0.233 ---
all0.285 21312 --
obs0.285 21159 99.3 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 47.888 Å2 / ksol: 0.345806 e/Å3
Displacement parametersBiso mean: 73.94 Å2
Baniso -1Baniso -2Baniso -3
1--17.12 Å20 Å20 Å2
2--13.44 Å20 Å2
3---3.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.8→38.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3160 1546 44 62 4812
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.99
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree error% reflection obs (%)
2.8-2.930.39727110.40.32523330.02499.6
2.93-3.080.3926810.30.3123270.02499.8
3.08-3.270.3282539.60.25523760.02199.7
3.27-3.530.301261100.24123450.01999.7
3.53-3.880.2882549.60.2324010.01899.7
3.88-4.440.24827210.20.20723830.01599.4
4.44-5.590.2662629.70.22524300.01699.7
5.59-38.660.2592549.30.2224690.01696.3
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3CNS_TOPPAR:dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION4cmp.parcmp_top.top
X-RAY DIFFRACTION5CNS_TOPPAR:water_rep.paramwater.top

+
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