[English] 日本語
Yorodumi
- PDB-5h80: Biotin Carboxylase domain of single-chain bacterial carboxylase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5h80
TitleBiotin Carboxylase domain of single-chain bacterial carboxylase
ComponentsCarboxylaseCarboxylation
KeywordsLIGASE / Multienzymes / protein dynamics / X-ray crystallography / small-angle X-ray scattering / carrier protein
Function / homology
Function and homology information


ligase activity / ATP binding / metal ion binding
Similarity search - Function
Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. ...Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Rossmann fold - #20 / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Dna Ligase; domain 1 / Carbamoyl-phosphate synthase subdomain signature 2. / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHagmann, A. / Hunkeler, M. / Stuttfeld, E. / Maier, T.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation138262 Switzerland
Swiss National Science Foundation159696 Switzerland
Swiss National Science Foundation14523 Switzerland
CitationJournal: Structure / Year: 2016
Title: Hybrid Structure of a Dynamic Single-Chain Carboxylase from Deinococcus radiodurans.
Authors: Hagmann, A. / Hunkeler, M. / Stuttfeld, E. / Maier, T.
History
DepositionDec 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Apr 24, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.3Jan 10, 2024Group: 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: Carboxylase
B: Carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3389
Polymers105,9032
Non-polymers4347
Water14,160786
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint26 kcal/mol
Surface area33290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.100, 138.100, 97.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein Carboxylase / Carboxylation


Mass: 52951.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: DR_A0310 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9RYK2
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 786 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MgCl2 HEPES (pH 7.5) poly(acrylic acid sodium salt) 5,100.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.694
11K, H, -L20.306
ReflectionResolution: 1.7→75.74 Å / Num. obs: 116236 / % possible obs: 99.87 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 15.61
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 1.18 / % possible all: 97.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DZD

2dzd


Resolution: 1.7→75.74 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.475 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.016 / ESU R Free: 0.017 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18441 4740 4.1 %RANDOM
Rwork0.14942 ---
obs0.15084 111463 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.312 Å2
Baniso -1Baniso -2Baniso -3
1--11.26 Å2-0 Å2-0 Å2
2---11.26 Å2-0 Å2
3---22.52 Å2
Refinement stepCycle: LAST / Resolution: 1.7→75.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6463 0 28 786 7277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0196649
X-RAY DIFFRACTIONr_bond_other_d0.0020.026382
X-RAY DIFFRACTIONr_angle_refined_deg2.3711.9549061
X-RAY DIFFRACTIONr_angle_other_deg1.266314565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1075855
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20523.355304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.74115977
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6181559
X-RAY DIFFRACTIONr_chiral_restr0.1680.21041
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0217700
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021555
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6293.1763435
X-RAY DIFFRACTIONr_mcbond_other3.6283.1753434
X-RAY DIFFRACTIONr_mcangle_it4.5394.7494285
X-RAY DIFFRACTIONr_mcangle_other4.5394.754286
X-RAY DIFFRACTIONr_scbond_it4.3563.5443214
X-RAY DIFFRACTIONr_scbond_other4.3553.5443214
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.925.1634777
X-RAY DIFFRACTIONr_long_range_B_refined8.03427.3767955
X-RAY DIFFRACTIONr_long_range_B_other7.80826.477483
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 368 -
Rwork0.291 8109 -
obs--98.31 %

+
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