[English] 日本語
Yorodumi
- PDB-1ihf: INTEGRATION HOST FACTOR/DNA COMPLEX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ihf
TitleINTEGRATION HOST FACTOR/DNA COMPLEX
Components
  • (PROTEIN (INTEGRATION HOST FACTOR ...) x 2
  • DNA (35-MER)
  • DNA (5'-D(*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*C P*AP*CP*C)-3')
  • DNA (5'-D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP*CP*AP*TP*T)-3')
KeywordsTRANSCRIPTION/DNA / COMPLEX (TRANSCRIPTION REGULATION-DNA) / TRANSCRIPTION FACTOR / BETA RIBBON MOTIF / DNA BENDING PROTEIN / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


IHF-DNA complex / DNA-binding transcription activator activity / protein-DNA complex / structural constituent of chromatin / regulation of translation / chromosome / DNA recombination / DNA replication / transcription cis-regulatory region binding / DNA-templated transcription ...IHF-DNA complex / DNA-binding transcription activator activity / protein-DNA complex / structural constituent of chromatin / regulation of translation / chromosome / DNA recombination / DNA replication / transcription cis-regulatory region binding / DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / cytosol
Similarity search - Function
Integration host factor, alpha subunit / Integration host factor, beta subunit / HU Protein; Chain A / IHF-like DNA-binding proteins / Histone-like DNA-binding protein, conserved site / Bacterial histone-like DNA-binding proteins signature. / Histone-like DNA-binding protein / Bacterial DNA-binding protein / bacterial (prokaryotic) histone like domain / Integration host factor (IHF)-like DNA-binding domain superfamily ...Integration host factor, alpha subunit / Integration host factor, beta subunit / HU Protein; Chain A / IHF-like DNA-binding proteins / Histone-like DNA-binding protein, conserved site / Bacterial histone-like DNA-binding proteins signature. / Histone-like DNA-binding protein / Bacterial DNA-binding protein / bacterial (prokaryotic) histone like domain / Integration host factor (IHF)-like DNA-binding domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Integration host factor subunit alpha / Integration host factor subunit beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsRice, P.A. / Yang, S.-W. / Mizuuchi, K. / Nash, H.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1996
Title: Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn.
Authors: Rice, P.A. / Yang, S. / Mizuuchi, K. / Nash, H.A.
History
DepositionAug 21, 1996Processing site: NDB
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 2, 2012Group: Derived calculations / Refinement description
Revision 1.4May 9, 2012Group: Refinement description
Revision 1.5May 1, 2019Group: Data collection / Refinement description / Category: software
Revision 1.6Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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
C: DNA (35-MER)
D: DNA (5'-D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP*CP*AP*TP*T)-3')
E: DNA (5'-D(*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*C P*AP*CP*C)-3')
A: PROTEIN (INTEGRATION HOST FACTOR (ALPHA) (IHF))
B: PROTEIN (INTEGRATION HOST FACTOR (BETA) (IHF))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,21920
Polymers43,5335
Non-polymers1,68615
Water6,936385
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.360, 59.920, 180.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
DNA chain , 3 types, 3 molecules CDE

#1: DNA chain DNA (35-MER)


Mass: 10801.969 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP*CP*AP*TP*T)-3')


Mass: 4611.039 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*C P*AP*CP*C)-3') / IHF ALPHA CHAIN


Mass: 6074.938 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
PROTEIN (INTEGRATION HOST FACTOR ... , 2 types, 2 molecules AB

#4: Protein PROTEIN (INTEGRATION HOST FACTOR (ALPHA) (IHF)) / IHF BETA CHAIN


Mass: 11373.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A6X7
#5: Protein PROTEIN (INTEGRATION HOST FACTOR (BETA) (IHF))


Mass: 10671.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A6Y1

-
Non-polymers , 2 types, 400 molecules

#6: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cd
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsBASE NUMBERING CORRESPONDS TO STANDARD LAMBDA ATT SITE COORDINATES. BASES 19 - 47 ARE THOSE FOUND ...BASE NUMBERING CORRESPONDS TO STANDARD LAMBDA ATT SITE COORDINATES. BASES 19 - 47 ARE THOSE FOUND IN THE LAMBDA ATT SITE. THE TOP STRAND (CHAINS D AND E) WAS SYNTHESIZED AS TWO OLIGONUCLEOTIDES, RESULTING IN A NICK BETWEEN BASES 29 AND 30. THE BOTTOM STRAND (CHAIN C) WAS SYNTHESIZED AS A SINGLE 35 MER AND HAS BEEN ASSIGNED NEGATIVE RESIDUE NUMBERS SUCH THAT BASES WITH THE SAME ABSOLUTE VALUE ARE PAIRED. THE CRYSTALS PACK TO FORM A PSEUDO-CONTINUOUS HELIX, WITH THE OVERHANGING BASE 15 OF THE TOP STRAND PAIRED TO THE OVERHANGING BASE -50 OF A 21 NEIGHBORING COMPLEX'S BOTTOM STRAND.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 58 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.4 / Details: pH 7.40, VAPOR DIFFUSION, HANGING DROP / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2BIS-TRIS-PROPANE_HCL11
3NACL11
4PEG 400011
5KCL11
6SPERMINE11
7GLYCEROL11
8CDCL211
9NA AZIDE11
Crystal
*PLUS
Density % sol: 58 %
Crystal grow
*PLUS
pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
123 mg/mlprotein1drop
21.5 mMDNA1drop
320 mMTris-HCl1drop
450 mM1dropNaCl
520-23 %PEG40001reservoir
650 mM1reservoirKCl
71 mMspermine1reservoir
85-15 %glycerol1reservoir
915 mM1reservoirCdCl2
100.3 %1reservoirNaN3
1150 mMTris-HCl1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 14, 1996 / Details: DOUBLE FOCUSSING MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→15 Å / Num. obs: 22925 / % possible obs: 85.2 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Rmerge(I) obs: 0.063
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 15 Å / Observed criterion σ(I): -3 / Redundancy: 8.2 %

-
Processing

Software
NameVersionClassification
MLPHAREphasing
RAVEmodel building
X-PLOR3.816refinement
HKL(DENZO)data reduction
SCALEPACKdata scaling
RAVEphasing
RefinementResolution: 2.5→15 Å / Cross valid method: R-FREE / σ(F): 0
Details: DIFFRACTION IS ANISOTROPIC. FALLS BELOW 2 ALONG X AT 2.5 ANGSTROM, ALONG Y AT 3.0 ANGSTROM, AND ALONG Z IS STILL >2 AT 2.2 ANGSTROM. THE COMPLETENESS OF THE DATA WITHIN AN ELLIPSOID WITH ...Details: DIFFRACTION IS ANISOTROPIC. FALLS BELOW 2 ALONG X AT 2.5 ANGSTROM, ALONG Y AT 3.0 ANGSTROM, AND ALONG Z IS STILL >2 AT 2.2 ANGSTROM. THE COMPLETENESS OF THE DATA WITHIN AN ELLIPSOID WITH THESE PRINCIPLE AXES IS 98.0%. THIS EXPLAINS THE LOW VALUE OF THE COMPLETENESS IN THE HIGHEST RESOLUTION BIN. THE REPORTED OVERALL RESOLUTION OF 2.5 ANGSTROM IS AN AVERAGE VALUE. DNA PARAMETERS FROM PARKINSON, G., VOJTECHOVSKY, J., CLOWNEY, L., BRUNGER, A.T. AND BERMAN, H.M. (1996) ACTA CRYST. D52, 57-64. NON-WATSON-CRICK BASE PAIRING: T C 28 REVERSE WATSON-CRICK BASE PAIR. T C 29 HOOGSTEEN BASE PAIR.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1046 5 %RANDOM
Rwork0.192 ---
all0.255 ---
obs-21918 81.5 %-
Displacement parametersBiso mean: 44.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.684 Å20 Å20 Å2
2--23.18 Å20 Å2
3----17.7 Å2
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1511 1426 15 385 3337
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.18
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.2→2.3 Å
RfactorNum. reflection% reflection
Rfree0.426 49 5 %
Rwork0.382 888 -
obs--29 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1DNA-RNA.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION2PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION3PARAM19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1, 3.816 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 15 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 44.8 Å2
LS refinement shell
*PLUS
% reflection Rfree: 5 %

+
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