[English] 日本語
Yorodumi
- PDB-2cbo: Crystal structure of the neocarzinostatin 3Tes24 mutant bound to ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2cbo
TitleCrystal structure of the neocarzinostatin 3Tes24 mutant bound to 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: 1.7 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 / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4894
Polymers11,6161
Non-polymers8733
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)43.984, 43.984, 54.708
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein NEOCARZINOSTATIN / NCS / MITOMALCIN / MMC


Mass: 11615.560 Da / Num. of mol.: 1 / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHAS ANTIBIOTIC ACTIVITY FOR GRAM-POSITIVE BACTERIA AND ANTITUMOR ACTIVITY FOR CERTAIN MOUSE TUMORS ...HAS ANTIBIOTIC ACTIVITY FOR GRAM-POSITIVE BACTERIA AND ANTITUMOR ACTIVITY FOR CERTAIN MOUSE TUMORS 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 TRP ENGINEERED RESIDUE IN CHAIN A, TRP 73 TO ARG ENGINEERED RESIDUE IN CHAIN A, LEU 79 TO TRP ENGINEERED RESIDUE IN CHAIN A, CYS 81 TO TYR ENGINEERED RESIDUE IN CHAIN A, PHE 86 TO ASN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 50 %
Crystal growDetails: 1.6-1.7M (NH4)2SO4, 0.1 M SODIUM CITRATE PH 6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.978
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 10933 / % possible obs: 94.9 % / Observed criterion σ(I): 2 / Redundancy: 1.97 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.3
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.6 / % possible all: 91.7

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NCO

1nco


Resolution: 1.7→18.51 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 187070.78 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22 533 5.3 %RANDOM
Rwork0.193 ---
obs0.193 10099 87.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.2945 Å2 / ksol: 0.388351 e/Å3
Displacement parametersBiso mean: 21.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20 Å20 Å2
2--1.6 Å20 Å2
3----3.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 1.7→18.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms818 0 61 116 995
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.34
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it1.812
X-RAY DIFFRACTIONc_scbond_it1.742
X-RAY DIFFRACTIONc_scangle_it2.362.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.369 83 5.6 %
Rwork0.344 1404 -
obs--77.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2THS.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION4ION.PARAMTHS.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