[English] 日本語
Yorodumi
- PDB-2cg4: Structure of E.coli AsnC -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 2cg4
TitleStructure of E.coli AsnC
ComponentsREGULATORY PROTEIN ASNC
KeywordsTRANSCRIPTION / ASNC / DNA BINDING / FFRP / LRP FAMILY / DNA-BINDING / TRANSCRIPTION REGULATION
Function / homology
Function and homology information


amino acid binding / response to amino acid / sequence-specific DNA binding / negative regulation of transcription, DNA-templated / DNA-binding transcription factor activity / positive regulation of transcription, DNA-templated
Winged helix-turn-helix DNA-binding / Transcription regulator AsnC/Lrp, ligand binding domain / AsnC-type HTH domain profile. / AsnC-type HTH domain signature. / Lrp/AsnC ligand binding domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Transcription regulator AsnC-type / Transcription regulator HTH, AsnC-type, conserved site / ArsR-like helix-turn-helix domain ...Winged helix-turn-helix DNA-binding / Transcription regulator AsnC/Lrp, ligand binding domain / AsnC-type HTH domain profile. / AsnC-type HTH domain signature. / Lrp/AsnC ligand binding domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Transcription regulator AsnC-type / Transcription regulator HTH, AsnC-type, conserved site / ArsR-like helix-turn-helix domain / Dimeric alpha-beta barrel / AsnC-type HTH domain
Regulatory protein AsnC
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsThaw, P. / Sedelnikova, S.E. / Muranova, T. / Wiese, S. / Ayora, S. / Alonso, J.C. / Brinkman, A.B. / Akerboom, J. / van der Oost, J. / Rafferty, J.B.
CitationJournal: Nucleic Acids Res. / Year: 2006
Title: Structural Insight Into Gene Transcriptional Regulation and Effector Binding by the Lrp/Asnc Family.
Authors: Thaw, P. / Sedelnikova, S.E. / Muranova, T. / Wiese, S. / Ayora, S. / Alonso, J.C. / Brinkman, A.B. / Akerboom, J. / Van Der Oost, J. / Rafferty, J.B.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 27, 2006 / Release: Apr 4, 2006
RevisionDateData content typeGroupProviderType
1.0Apr 4, 2006Structure modelrepositoryInitial release
1.1May 8, 2011Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: REGULATORY PROTEIN ASNC
B: REGULATORY PROTEIN ASNC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2465
Polymers33,9572
Non-polymers2893
Water2,432135
1
A: REGULATORY PROTEIN ASNC
B: REGULATORY PROTEIN ASNC
hetero molecules

A: REGULATORY PROTEIN ASNC
B: REGULATORY PROTEIN ASNC
hetero molecules

A: REGULATORY PROTEIN ASNC
B: REGULATORY PROTEIN ASNC
hetero molecules

A: REGULATORY PROTEIN ASNC
B: REGULATORY PROTEIN ASNC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,98420
Polymers135,8308
Non-polymers1,15412
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation2_555-x,-y,z1
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)103.117, 103.117, 52.401
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 4 / Auth seq-ID: 70 - 150

Dom-IDAuth asym-ID
1A
2B

-
Components

#1: Protein/peptide REGULATORY PROTEIN ASNC


Mass: 16978.705 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: B834(DE3) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P0ACI6
#2: Chemical ChemComp-ASN / ASPARAGINE


Mass: 132.118 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8N2O3 / Asparagine
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Magnesium
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O / Water
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLY 37 TO GLU ENGINEERED RESIDUE IN CHAIN B, GLY 37 TO GLU

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.1 Å3/Da / Density % sol: 69.3 %
Crystal growpH: 8.7
Details: 2.2M MAGNESIUM CHLORIDE, O.1M BICINE PH 8.7, 5MM L-ASPARAGINE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 21843 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 0 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.8
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 0 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.7 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: LOW RES ASNC FROM SELENO MET EXPERIMENT

Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.879 / SU B: 8.448 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1103 5.1 %RANDOM
Rwork0.229 ---
Obs0.232 20542 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.33 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å20 Å20 Å2
2---1.75 Å20 Å2
3---3.49 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2300 0 19 135 2454
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0070.0222350
r_bond_other_d
r_angle_refined_deg0.9711.9793180
r_angle_other_deg
r_dihedral_angle_1_deg8.6175296
r_dihedral_angle_2_deg41.224.68194
r_dihedral_angle_3_deg21.49315428
r_dihedral_angle_4_deg17.9011512
r_chiral_restr0.0670.2382
r_gen_planes_refined0.0030.021706
r_gen_planes_other
r_nbd_refined0.2640.21108
r_nbd_other
r_nbtor_refined0.320.21599
r_nbtor_other
r_xyhbond_nbd_refined0.1810.2154
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined0.3380.269
r_symmetry_vdw_other
r_symmetry_hbond_refined0.2470.213
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it1.031.51513
r_mcbond_other
r_mcangle_it1.86922410
r_mcangle_other
r_scbond_it2.8293908
r_scbond_other
r_scangle_it4.5554.5770
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 642 / Refinement-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.120.5
medium thermal0.722
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.429 77
Rwork0.312 1531

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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