[English] 日本語
Yorodumi
- PDB-5npu: Inferred ancestral pyruvate decarboxylase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5npu
TitleInferred ancestral pyruvate decarboxylase
ComponentsANC27
KeywordsLYASE / PYRUVATE DECARBOXYLASE / Ancestral Sequence Reconstruction
Function / homologyThiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / DI(HYDROXYETHYL)ETHER / THIAMINE DIPHOSPHATE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsBuddrus, L. / Crennell, S.J. / Leak, D.J. / Danson, M.J. / Andrews, E.S.V. / Arcus, V.L.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Crystal structure of an inferred ancestral bacterial pyruvate decarboxylase.
Authors: Buddrus, L. / Andrews, E.S.V. / Leak, D.J. / Danson, M.J. / Arcus, V.L. / Crennell, S.J.
History
DepositionApr 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 28, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / pdbx_entity_src_syn / Item: _entity.src_method
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ANC27
B: ANC27
C: ANC27
D: ANC27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,70813
Polymers242,8044
Non-polymers1,9059
Water181
1
A: ANC27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1513
Polymers60,7011
Non-polymers4502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ANC27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1513
Polymers60,7011
Non-polymers4502
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ANC27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2574
Polymers60,7011
Non-polymers5563
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ANC27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1513
Polymers60,7011
Non-polymers4502
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.330, 108.330, 322.651
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein
ANC27


Mass: 60700.902 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.15 M sodium citrate pH 5.5, 14%(w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 26, 2016 / Details: FOCUSSING MIRRORS (TWO
RadiationMonochromator: SI111 DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.5→93.82 Å / Num. obs: 28526 / % possible obs: 99.5 % / Redundancy: 4.4 % / Biso Wilson estimate: 53.8 Å2 / CC1/2: 0.965 / Rmerge(I) obs: 0.241 / Net I/σ(I): 5.6
Reflection shellResolution: 3.5→3.71 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.965 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4512 / CC1/2: 0.422 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2wvg

2wvg


Resolution: 3.5→81.1 Å / SU ML: 0.7 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 36.18
RfactorNum. reflection% reflectionSelection details
Rfree0.3186 1358 4.78 %RANDOM
Rwork0.246 ---
obs0.2496 28437 99.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.5→81.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16540 0 115 1 16656
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00717043
X-RAY DIFFRACTIONf_angle_d0.75223204
X-RAY DIFFRACTIONf_dihedral_angle_d13.52610044
X-RAY DIFFRACTIONf_chiral_restr0.0452616
X-RAY DIFFRACTIONf_plane_restr0.0063019
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.62510.44821220.36712690X-RAY DIFFRACTION100
3.6251-3.77020.38271280.32722662X-RAY DIFFRACTION100
3.7702-3.94180.3851240.31432657X-RAY DIFFRACTION100
3.9418-4.14960.3886960.2912756X-RAY DIFFRACTION100
4.1496-4.40960.3491710.24962608X-RAY DIFFRACTION100
4.4096-4.750.31211390.22922698X-RAY DIFFRACTION100
4.75-5.2280.2851470.22712702X-RAY DIFFRACTION100
5.228-5.98430.31271470.22542703X-RAY DIFFRACTION99
5.9843-7.53870.29391550.20392699X-RAY DIFFRACTION98
7.5387-81.12190.22781290.17762904X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -1.4663 Å / Origin y: -51.0351 Å / Origin z: -27.8581 Å
111213212223313233
T0.6996 Å2-0.2799 Å2-0.2799 Å2-0.203 Å2-0.2803 Å2--0.5308 Å2
L0.5092 °2-0.1139 °2-0.7681 °2-0.3 °2-0.7587 °2--1.1769 °2
S0.1727 Å °0.1052 Å °-0.0947 Å °-0.0798 Å °-0.0519 Å °0.2747 Å °0.5378 Å °-0.1941 Å °0.0359 Å °
Refinement TLS groupSelection details: all

+
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