[English] 日本語
Yorodumi
- PDB-1ixc: Crystal structure of CbnR, a LysR family transcriptional regulator -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ixc
TitleCrystal structure of CbnR, a LysR family transcriptional regulator
ComponentsLysR-type regulatory protein
KeywordsDNA BINDING PROTEIN / Long alpha helix connecting DNA binding and regulatory domains
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / D-Maltodextrin-Binding Protein; domain 2 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / D-Maltodextrin-Binding Protein; domain 2 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
LysR-type regulatory protein
Similarity search - Component
Biological speciesCupriavidus necator (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsMuraoka, S. / Okumura, R. / Ogawa, N. / Miyashita, K. / Senda, T.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal Structure of a Full-length LysR-type Transcriptional Regulator, CbnR: Unusual Combination of Two Subunit Forms and Molecular Bases for Causing and Changing DNA Bend
Authors: Muraoka, S. / Okumura, R. / Ogawa, N. / Nonaka, T. / Miyashita, K. / Senda, T.
History
DepositionJun 18, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LysR-type regulatory protein
B: LysR-type regulatory protein


Theoretical massNumber of molelcules
Total (without water)64,6392
Polymers64,6392
Non-polymers00
Water2,306128
1
A: LysR-type regulatory protein
B: LysR-type regulatory protein

A: LysR-type regulatory protein
B: LysR-type regulatory protein


Theoretical massNumber of molelcules
Total (without water)129,2794
Polymers129,2794
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area11480 Å2
ΔGint-55 kcal/mol
Surface area49230 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.220, 100.856, 87.735
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsTetrameric form of CbnR is generated by the two fold axis: -x, -y, z.

-
Components

#1: Protein LysR-type regulatory protein / CbnR


Mass: 32319.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus necator (bacteria) / Gene: cbnR / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WXC7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Tris/HCl, MgSO4, NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11111
21051
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL40B210.9796, 0.9798, 0.9721, 0.9862
SYNCHROTRONPhoton Factory BL-6A20.978
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDOct 1, 2001
ADSC QUANTUM 42CCDJan 30, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1fixed-exit double crystal monochromatorMADMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.97981
30.97211
40.98621
50.9781
ReflectionResolution: 2.2→35.6 Å / Num. all: 32808 / Num. obs: 32808 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 9.4
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 0.265 / Num. unique all: 4689 / Rsym value: 0.265 / % possible all: 100

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→87.71 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.927 / SU B: 8.424 / SU ML: 0.22 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.291 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24527 1676 5.1 %RANDOM
Rwork0.21763 ---
all0.21907 31092 --
obs0.21907 31080 99.9 %-
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: 16.122 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å20 Å2
2---2.05 Å20 Å2
3---2.97 Å2
Refinement stepCycle: LAST / Resolution: 2.2→87.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4436 0 0 128 4564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0214504
X-RAY DIFFRACTIONr_bond_other_d0.0010.024360
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.9616065
X-RAY DIFFRACTIONr_angle_other_deg0.725310033
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8723557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.42715823
X-RAY DIFFRACTIONr_chiral_restr0.0780.2707
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024902
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02965
X-RAY DIFFRACTIONr_nbd_refined0.3540.31122
X-RAY DIFFRACTIONr_nbd_other0.20.34149
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.5298
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0020.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1090.317
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1960.3107
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4550.514
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.581.52859
X-RAY DIFFRACTIONr_mcangle_it1.08724558
X-RAY DIFFRACTIONr_scbond_it1.52131645
X-RAY DIFFRACTIONr_scangle_it2.5934.51507
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.343 118
Rwork0.252 2237
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)
12.66550.1256-0.54677.3072-1.04714.6531-0.32040.3694-0.0113-1.37730.26980.02720.5823-0.59640.05070.8298-0.29390.06860.34830.01140.048511.8323.9923.505
21.076-1.6265-2.055916.12659.30068.7455-0.42560.15590.0445-0.15820.14910.56330.5314-0.41280.27640.4433-0.14780.04260.3161-0.00140.170410.90729.20319.684
30.94050.392-0.05222.3223-0.46180.59730.0292-0.20510.00880.0947-0.0542-0.0056-0.01680.09990.0250.26450.0060.01040.3654-0.01070.1618-4.18115.71938.046
43.40390.0018-0.8843.6375-0.75027.1280.00510.02420.2353-0.37960.1415-0.8126-0.70610.7981-0.14660.3636-0.18160.09960.3196-0.01780.353626.35443.65119.303
50.24490.2133-1.687117.41575.934.2374-0.1642-0.1435-0.02820.10820.2463-0.74120.5530.1094-0.08220.4386-0.0166-0.03370.2658-0.00370.251920.72226.83421.318
61.08660.4345-0.44493.5621-0.06751.6873-0.05670.0998-0.2211-0.59550.0487-0.4212-0.04260.05730.0080.33130.00870.10930.2779-0.04630.237416.793-20.69417.922
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 581 - 58
2X-RAY DIFFRACTION2AA59 - 8859 - 88
3X-RAY DIFFRACTION3AA89 - 29289 - 292
4X-RAY DIFFRACTION4BB1 - 581 - 58
5X-RAY DIFFRACTION5BB59 - 8859 - 88
6X-RAY DIFFRACTION6BB89 - 28989 - 289

+
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