[English] 日本語
Yorodumi
- PDB-2cbt: Crystal structure of the neocarzinostatin 4Tes1 mutant bound test... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2cbt
TitleCrystal structure of the neocarzinostatin 4Tes1 mutant bound testosterone hemisuccinate.
ComponentsNEOCARZINOSTATIN
KeywordsANTIBIOTIC / PHAGE-DISPLAY / HAPTEN BINDING / NEOCARZINOSTATIN / ANTIMICROBIAL / DNA-BINDING
Function / homology
Function and homology information


defense response to bacterium / DNA binding
Similarity search - Function
Neocarzinostatin-like / Neocarzinostatin family / Neocarzinostatin family / Neocarzinostatin-like / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
TESTOSTERONE HEMISUCCINATE / Neocarzinostatin
Similarity search - Component
Biological speciesSTREPTOMYCES CARZINOSTATICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDrevelle, A. / Graille, M. / Heyd, B. / Sorel, I. / Ulryck, N. / Pecorari, F. / Desmadril, M. / Van Tilbeurgh, H. / Minard, P.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: Structures of in Vitro Evolved Binding Sites on Neocarzinostatin Scaffold Reveal Unanticipated Evolutionary Pathways.
Authors: Drevelle, A. / Graille, M. / Heyd, B. / Sorel, I. / Ulryck, N. / Pecorari, F. / Desmadril, M. / Van Tilbeurgh, H. / Minard, P.
#1: Journal: Biochemistry / Year: 2003
Title: In Vitro Evolution of the Binding Specificity of Neocarzinostatin, an Enediyne-Binding Chromoprotein.
Authors: Heyd, B. / Pecorari, F. / Collinet, B. / Adjadj, E. / Desmadril, M. / Minard, P.
History
DepositionJan 6, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NEOCARZINOSTATIN
B: NEOCARZINOSTATIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3584
Polymers22,5812
Non-polymers7772
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)52.510, 52.510, 128.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein NEOCARZINOSTATIN / NCS / MITOMALCIN / MMC


Mass: 11290.296 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES CARZINOSTATICUS (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR(DE3)PLYSS / References: UniProt: P0A3R9
#2: Chemical ChemComp-TH2 / TESTOSTERONE HEMISUCCINATE / 4-OXO-4-{[(8ALPHA,9BETA,10ALPHA,13ALPHA,14BETA,17ALPHA)-3-OXOANDROST-4-EN-17-YL]OXY}BUTANOIC ACID


Mass: 388.497 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H32O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 67 TO TRP ENGINEERED RESIDUE IN CHAIN A, GLY 69 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, ASP 67 TO TRP ENGINEERED RESIDUE IN CHAIN A, GLY 69 TO ALA ENGINEERED RESIDUE IN CHAIN A, CYS 71 TO SER ENGINEERED RESIDUE IN CHAIN A, LEU 79 TO TYR ENGINEERED RESIDUE IN CHAIN A, CYS 81 TO SER ENGINEERED RESIDUE IN CHAIN A, PHE 86 TO ILE ENGINEERED RESIDUE IN CHAIN A, PHE 112 TO TRP ENGINEERED RESIDUE IN CHAIN A, GLN 128 TO HIS ENGINEERED RESIDUE IN CHAIN A, GLY 130 TO THR ENGINEERED RESIDUE IN CHAIN A, SER 132 TO ARG ENGINEERED RESIDUE IN CHAIN A, ALA 135 TO LEU ENGINEERED RESIDUE IN CHAIN A, GLY 136 TO SER ENGINEERED RESIDUE IN CHAIN B, ASP 67 TO TRP ENGINEERED RESIDUE IN CHAIN B, GLY 69 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 71 TO SER ENGINEERED RESIDUE IN CHAIN B, LEU 79 TO TYR ENGINEERED RESIDUE IN CHAIN B, CYS 81 TO SER ENGINEERED RESIDUE IN CHAIN B, PHE 86 TO ILE ENGINEERED RESIDUE IN CHAIN B, PHE 112 TO TRP ENGINEERED RESIDUE IN CHAIN B, GLN 128 TO HIS ENGINEERED RESIDUE IN CHAIN B, GLY 130 TO THR ENGINEERED RESIDUE IN CHAIN B, SER 132 TO ARG ENGINEERED RESIDUE IN CHAIN B, ALA 135 TO LEU ENGINEERED RESIDUE IN CHAIN B, GLY 136 TO SER

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43.71 %
Crystal growDetails: 0.9 M SODIUM CITRATE, 0.1 M HEPES PH 7.5 AND 3% ETHANOL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.987
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 9943 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 11 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.3
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 11 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9

-
Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NCO

1nco


Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: TWINNING FRACTION 0.42
Rfactor% reflectionSelection details
Rfree0.344 -RANDOM
obs0.218 98.9 %-
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1578 0 56 30 1664
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d1.508
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

+
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://pdbjlvh1.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