[English] 日本語
Yorodumi
- PDB-2c45: NATIVE PRECURSOR OF PYRUVOYL DEPENDENT ASPARTATE DECARBOXYLASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2c45
TitleNATIVE PRECURSOR OF PYRUVOYL DEPENDENT ASPARTATE DECARBOXYLASE
ComponentsAspartate 1-decarboxylase
KeywordsLYASE / DOUBLE-PSI BETA BARREL / CARBOXYLASE / ZYMOGEN / PANTOTHENATE BIOSYNTHESIS / DECARBOXYLASE / PYRUVATE
Function / homology
Function and homology information


alanine biosynthetic process / aspartate 1-decarboxylase / aspartate 1-decarboxylase activity / pantothenate biosynthetic process / peptidoglycan-based cell wall / cytosol
Similarity search - Function
Aspartate decarboxylase / Aspartate decarboxylase / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / Aspartate decarboxylase-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Aspartate 1-decarboxylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsGopalan, G. / Chopra, S. / Ranganathan, A. / Swaminathan, K.
Citation
Journal: Proteins / Year: 2006
Title: Crystal structure of uncleaved L-aspartate-alpha-decarboxylase from Mycobacterium tuberculosis.
Authors: Gopalan, G. / Chopra, S. / Ranganathan, A. / Swaminathan, K.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: Crystal Structure of Aspartate Decarboxylase at 2.2A Resolution Provides Evidence for an Ester in Protein Self-Processing
Authors: Albert, A. / Dhanaraj, V. / Genschel, U. / Khan, G. / Ramjee, M.K. / Pulido, R. / Sibanda, B.L. / von Delft, F. / Witty, M. / Blundell, T.L. / Smith, A.G. / Abell, C.
#2: Journal: Embo J. / Year: 2003
Title: Structural Constraints on Protein Self-Processing in L-Aspartate-Alpha-Decarboxylase
Authors: Schmitzberger, F. / Kilkenny, M.L. / Lobley, C.M. / Webb, M.E. / Vinkovic, M. / Matak-Vinkovic, D. / Witty, M. / Chirgadze, D.Y. / Smith, A.G. / Abell, C. / Blundell, T.L.
#3: Journal: J.Mol.Biol. / Year: 2004
Title: Crystal Structure of the Schiff Base Intermediate Prior to Decarboxylation in the Catalytic Cycle of Aspartate Alpha-Decarboxylase
Authors: Lee, B.I. / Suh, S.W.
History
DepositionOct 15, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Dec 12, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / struct_ref / struct_ref_seq
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.pdbx_description / _entity.src_method / _entity_name_com.name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.5May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.6Dec 13, 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: Aspartate 1-decarboxylase
B: Aspartate 1-decarboxylase
C: Aspartate 1-decarboxylase
D: Aspartate 1-decarboxylase
E: Aspartate 1-decarboxylase
F: Aspartate 1-decarboxylase
G: Aspartate 1-decarboxylase
H: Aspartate 1-decarboxylase


Theoretical massNumber of molelcules
Total (without water)119,2088
Polymers119,2088
Non-polymers00
Water88349
1
A: Aspartate 1-decarboxylase
B: Aspartate 1-decarboxylase
C: Aspartate 1-decarboxylase
D: Aspartate 1-decarboxylase


Theoretical massNumber of molelcules
Total (without water)59,6044
Polymers59,6044
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: Aspartate 1-decarboxylase
F: Aspartate 1-decarboxylase
G: Aspartate 1-decarboxylase
H: Aspartate 1-decarboxylase


Theoretical massNumber of molelcules
Total (without water)59,6044
Polymers59,6044
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)150.100, 150.100, 60.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

-
Components

#1: Protein
Aspartate 1-decarboxylase / / Aspartate alpha-decarboxylase


Mass: 14900.986 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: panD, Rv3601c, MTCY07H7B.21 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WIL3, aspartate 1-decarboxylase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 3.7 Å3/Da / Density % sol: 66.5 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: SODIUM CACODYLATE (PH 6.5), 1.5 M MAGNESIUM SULPHATE AND 20% PEG2000, HANGING DROP, TEMPERATURE 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.1
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. obs: 30363 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 1.1 Å2 / Rmerge(I) obs: 0.12
Reflection shellResolution: 2.99→3.1 Å / Redundancy: 2.6 % / % possible all: 96

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PPY

1ppy


Resolution: 2.99→7.99 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 105724.32 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THERE ARE EIGHT MOLECULES IN THE ASYMMETRIC UNIT, FORMING TWO TETRAMERS. HEMIHEDRAL TWINNING WITH TWIN FRACTION 0.437 AND TWIN OPERATOR H,-H-K,-L. RESTRAINED NCS MODE WAS USED FOR REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.308 1959 8.6 %RANDOM
Rwork0.265 ---
obs0.265 22764 78.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.9342 Å2 / ksol: 0.39434 e/Å3
Displacement parametersBiso mean: 38.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.31 Å26.82 Å20 Å2
2--2.31 Å20 Å2
3----4.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.66 Å0.59 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.75 Å
Refinement stepCycle: LAST / Resolution: 2.99→7.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6832 0 0 49 6881
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.99→3.12 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.317 118 8.9 %
Rwork0.282 1202 -
obs--36.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.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