[English] 日本語
Yorodumi
- PDB-7cxu: Crystal structure of CmnK in complex with NAD+ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cxu
TitleCrystal structure of CmnK in complex with NAD+
ComponentsCmnK
KeywordsBIOSYNTHETIC PROTEIN / CmnB / Lyase / capreomycin
Function / homology
Function and homology information


nucleotide binding / cytoplasm
Similarity search - Function
Ornithine cyclodeaminase/mu-crystallin / Ornithine cyclodeaminase, N-terminal / Ornithine cyclodeaminase/mu-crystallin family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / CmnK
Similarity search - Component
Biological speciesSaccharothrix mutabilis subsp. capreolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsChang, C.Y. / Hsu, S.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)107-2113-M-009-021-MY3 Taiwan
CitationJournal: Biochemistry / Year: 2021
Title: Characterization of Enzymes Catalyzing the Formation of the Nonproteinogenic Amino Acid l-Dap in Capreomycin Biosynthesis.
Authors: Hsu, S.H. / Zhang, S. / Huang, S.C. / Wu, T.K. / Xu, Z. / Chang, C.Y.
History
DepositionSep 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CmnK
B: CmnK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0813
Polymers74,4182
Non-polymers6631
Water1,49583
1
B: CmnK
hetero molecules

A: CmnK


Theoretical massNumber of molelcules
Total (without water)75,0813
Polymers74,4182
Non-polymers6631
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Buried area5540 Å2
ΔGint-40 kcal/mol
Surface area25150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.609, 87.124, 146.702
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein CmnK


Mass: 37209.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharothrix mutabilis subsp. capreolus (bacteria)
Gene: cmnK / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A6YEI2
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50 mM MgCl2.6H2O, 30% w/v PEG-550, and 100 mM HEPES

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.9732 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9732 Å / Relative weight: 1
ReflectionResolution: 2.19→30 Å / Num. obs: 34342 / % possible obs: 99.5 % / Redundancy: 4.5 % / CC1/2: 0.75 / Net I/σ(I): 14.05
Reflection shellResolution: 2.19→2.25 Å / Num. unique obs: 3300 / CC1/2: 0.83

-
Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CXS

7cxs


Resolution: 2.19→28.13 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.018 / SU ML: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.342 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 1572 5.1 %RANDOM
Rwork0.2049 ---
obs0.207 29408 90.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.44 Å2 / Biso mean: 33.404 Å2 / Biso min: 13.53 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 2.19→28.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4854 0 44 83 4981
Biso mean--49.1 29.96 -
Num. residues----653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0135005
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174686
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.6356838
X-RAY DIFFRACTIONr_angle_other_deg1.1711.5710746
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6665650
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.66219.844256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12515711
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.341548
X-RAY DIFFRACTIONr_chiral_restr0.1650.2649
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025761
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021126
LS refinement shellResolution: 2.19→2.243 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.314 68 -
Rwork0.239 1304 -
obs--55.39 %

+
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