[English] 日本語
Yorodumi
- PDB-7a8y: X-ray crystal structure of Aspartate alpha-decarboxylase in compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7a8y
TitleX-ray crystal structure of Aspartate alpha-decarboxylase in complex with D-Serine
Components(Aspartate 1-decarboxylase) x 2
KeywordsLYASE / Decarboxylase
Function / homology
Function and homology information


alanine biosynthetic process / aspartate 1-decarboxylase / aspartate 1-decarboxylase activity / pantothenate biosynthetic process / cytoplasm
Similarity search - Function
Aspartate decarboxylase / Aspartate decarboxylase / Aspartate decarboxylase-like domain superfamily
Similarity search - Domain/homology
D-SERINE / PYRUVIC ACID / SERINE / Aspartate 1-decarboxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsYorke, B.A. / Raskar, T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust110296/B/15/Z United Kingdom
CitationJournal: Phys Chem Chem Phys / Year: 2022
Title: Structure and diffusive dynamics of aspartate alpha-decarboxylase (ADC) liganded with D-serine in aqueous solution.
Authors: Raskar, T. / Niebling, S. / Devos, J.M. / Yorke, B.A. / Hartlein, M. / Huse, N. / Forsyth, V.T. / Seydel, T. / Pearson, A.R.
History
DepositionAug 31, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Data collection / Database references / Derived calculations
Category: atom_type / citation ...atom_type / citation / citation_author / diffrn_source
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.ptnr2_label_atom_id
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Aspartate 1-decarboxylase
BBB: Aspartate 1-decarboxylase
DDD: Aspartate 1-decarboxylase
EaE: Aspartate 1-decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,21011
Polymers26,5524
Non-polymers6597
Water3,747208
1
AAA: Aspartate 1-decarboxylase
BBB: Aspartate 1-decarboxylase
DDD: Aspartate 1-decarboxylase
EaE: Aspartate 1-decarboxylase
hetero molecules

AAA: Aspartate 1-decarboxylase
BBB: Aspartate 1-decarboxylase
DDD: Aspartate 1-decarboxylase
EaE: Aspartate 1-decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,42122
Polymers53,1048
Non-polymers1,31714
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area23650 Å2
ΔGint-114 kcal/mol
Surface area17730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.300, 71.300, 216.650
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

-
Components

-
Protein/peptide / Protein , 2 types, 4 molecules AAADDDBBBEaE

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


Mass: 3056.588 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Modification at residue 25: Serine and pyrovoyl residues are present with partial occupancies.
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: panD, BON96_17415, D9J78_12565, FKO60_12525, G5697_15675
Production host: Escherichia coli (E. coli) / References: UniProt: A0A4Y8GT61, aspartate 1-decarboxylase
#2: Protein Aspartate 1-decarboxylase / / Aspartate alpha-decarboxylase


Mass: 10219.350 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Some of the terminal residues are not modeled due to missing density
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: panD, BON96_17415, D9J78_12565, FKO60_12525, G5697_15675
Production host: Escherichia coli (E. coli) / References: UniProt: A0A4Y8GT61, aspartate 1-decarboxylase

-
Non-polymers , 5 types, 215 molecules

#3: Chemical ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DSN / D-SERINE / Serine


Type: D-peptide linking / Mass: 105.093 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-SER / SERINE / Serine


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5
Details: 1.8 M ammonium sulphate, 100 mM sodium citrate pH 4.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.75→46.98 Å / Num. obs: 33922 / % possible obs: 99.99 % / Redundancy: 2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.02384 / Net I/σ(I): 21.5
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.1564 / Mean I/σ(I) obs: 5.25 / Num. unique obs: 3301 / CC1/2: 0.93

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AW8

1aw8


Resolution: 1.75→46.975 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.187 / WRfactor Rwork: 0.165 / SU B: 1.67 / SU ML: 0.054 / Average fsc free: 0.9557 / Average fsc work: 0.9597 / Cross valid method: FREE R-VALUE / ESU R: 0.092 / ESU R Free: 0.088
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1905 1702 5.017 %
Rwork0.1705 32220 -
all0.171 --
obs-33922 99.988 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.673 Å2
Baniso -1Baniso -2Baniso -3
1-0.257 Å20.129 Å20 Å2
2--0.257 Å2-0 Å2
3----0.835 Å2
Refinement stepCycle: LAST / Resolution: 1.75→46.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1828 0 40 208 2076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0131997
X-RAY DIFFRACTIONr_bond_other_d0.0040.0171838
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.6392712
X-RAY DIFFRACTIONr_angle_other_deg1.2441.5874243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg16.8255.227264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.11321.887106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.10615320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.6981515
X-RAY DIFFRACTIONr_chiral_restr0.0530.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022416
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02429
X-RAY DIFFRACTIONr_nbd_refined0.2080.2352
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.21676
X-RAY DIFFRACTIONr_nbtor_refined0.1480.2927
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2828
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2150
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1580.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2250.227
X-RAY DIFFRACTIONr_nbd_other0.2460.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1510.221
X-RAY DIFFRACTIONr_mcbond_it1.1112.0821011
X-RAY DIFFRACTIONr_mcbond_other1.1112.0821011
X-RAY DIFFRACTIONr_mcangle_it1.9393.0831264
X-RAY DIFFRACTIONr_mcangle_other1.9393.0841265
X-RAY DIFFRACTIONr_scbond_it1.3172.244985
X-RAY DIFFRACTIONr_scbond_other1.3172.245986
X-RAY DIFFRACTIONr_scangle_it2.1583.3011441
X-RAY DIFFRACTIONr_scangle_other2.1573.3021442
X-RAY DIFFRACTIONr_lrange_it5.32225.3142185
X-RAY DIFFRACTIONr_lrange_other5.32125.3212186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.7950.2361120.2122352X-RAY DIFFRACTION100
1.795-1.8450.21270.1992237X-RAY DIFFRACTION99.9577
1.845-1.8980.211100.1922199X-RAY DIFFRACTION100
1.898-1.9560.1921060.1862153X-RAY DIFFRACTION100
1.956-2.020.1861170.1672089X-RAY DIFFRACTION100
2.02-2.0910.181950.1672037X-RAY DIFFRACTION100
2.091-2.170.189950.1671955X-RAY DIFFRACTION100
2.17-2.2590.1821040.161880X-RAY DIFFRACTION100
2.259-2.3590.1441120.1591798X-RAY DIFFRACTION100
2.359-2.4740.2041030.1631735X-RAY DIFFRACTION100
2.474-2.6070.181710.1671663X-RAY DIFFRACTION100
2.607-2.7650.143780.1581593X-RAY DIFFRACTION100
2.765-2.9560.19760.1591494X-RAY DIFFRACTION100
2.956-3.1920.203800.1661381X-RAY DIFFRACTION100
3.192-3.4960.155650.1621305X-RAY DIFFRACTION100
3.496-3.9070.205630.1521185X-RAY DIFFRACTION100
3.907-4.5080.147620.1371056X-RAY DIFFRACTION100
4.508-5.5140.237580.171910X-RAY DIFFRACTION100
5.514-7.7670.275430.231737X-RAY DIFFRACTION100
7.767-9.50.288250.234462X-RAY DIFFRACTION99.3878

+
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