[English] 日本語
Yorodumi
- PDB-4d7z: E. coli L-aspartate-alpha-decarboxylase mutant N72Q to a resoluti... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4d7z
TitleE. coli L-aspartate-alpha-decarboxylase mutant N72Q to a resolution of 1.9 Angstroms
Components
  • ASPARTATE 1-DECARBOXYLASE ALPHA CHAIN
  • ASPARTATE 1-DECARBOXYLASE BETA CHAIN
KeywordsLYASE / PROTEIN DERIVED COFACTOR / PANTOTHENATE SYNTHESIS / PYRUVOYL COFACTOR / BETA-ALANINE
Function / homology
Function and homology information


alanine biosynthetic process / aspartate 1-decarboxylase / aspartate 1-decarboxylase activity / pantothenate biosynthetic process / protein autoprocessing / 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
DI(HYDROXYETHYL)ETHER / THIOCYANATE ION / Aspartate 1-decarboxylase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBravo, J.P.K. / Monteiro, D.C.F. / Webb, M.E. / Pearson, A.R.
CitationJournal: To be Published
Title: The Structure of the E. Coli L-Aspartate-Alpha-Decarboxylase Mutant N72Q to a Resolution of 1.9 Angstroms
Authors: Bravo, J.P.K. / Monteiro, D.C.F. / Webb, M.E. / Pearson, A.R.
History
DepositionDec 2, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_label_atom_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ASPARTATE 1-DECARBOXYLASE BETA CHAIN
B: ASPARTATE 1-DECARBOXYLASE ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3385
Polymers15,1162
Non-polymers2223
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-16.1 kcal/mol
Surface area7400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.350, 71.350, 112.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11B-2008-

HOH

21B-2010-

HOH

31B-2052-

HOH

-
Components

#1: Protein/peptide ASPARTATE 1-DECARBOXYLASE BETA CHAIN


Mass: 4770.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PRCETA-ADC(N72Q) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DELTA PAND, DELTA PANZ, DE3 / References: UniProt: P0A790, aspartate 1-decarboxylase
#2: Protein ASPARTATE 1-DECARBOXYLASE ALPHA CHAIN


Mass: 10345.524 Da / Num. of mol.: 1 / Fragment: RESIDUES 25-119 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: RESIDUE 25 IS A COVALENTLY LINKED PYRUVOYL COFACTOR, DERIVED FROM POSTTRANSLATIONAL MODIFICATION OF THE ZYMOGEN.
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PRCETA-ADC(N72Q) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DELTA PAND, DELTA PANZ, DE3 / References: UniProt: P0A790, aspartate 1-decarboxylase
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAIN A CORRESPONDS TO RESIDUES 1-24 OF THE PAND (ZYMOGEN) SEQUENCE. FORMED AFTER BACKBONE CLEAVAGE ...CHAIN A CORRESPONDS TO RESIDUES 1-24 OF THE PAND (ZYMOGEN) SEQUENCE. FORMED AFTER BACKBONE CLEAVAGE AS PART OF ENZYME MATURATION. THIS SEQUENCE INCLUDES THE N-TERMINAL PURIFICATION TAG (17 RESIDUES) CHAIN B CORRESPONDS TO RESIDUES 25-119 OF THE PAND ( ZYMOGEN) SEQUENCE. FORMED AFTER BACKBONE CLEAVAGE AS PART OF ENZYME MATURATION. RESIDUE 25 IS A POSTTRANSLATIONALLY FORMED PYRUVOYL COFACTOR. ALSO CONTAINS MUTATION N72Q.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.4 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.8
Details: ADC.PANZ COMPLEX WAS PREPARED IN A 10: 11 RATIO AT A FINAL CONCENTRATION OF 5.7 MG/ML WITH A 2-FOLD MOLAR EXCESS (RELATIVE TO PANZ) OF ACETYLCOA IN 0.05 M TRIS-HCL PH 7.69, 0.1 M NACL, 0.1 ...Details: ADC.PANZ COMPLEX WAS PREPARED IN A 10: 11 RATIO AT A FINAL CONCENTRATION OF 5.7 MG/ML WITH A 2-FOLD MOLAR EXCESS (RELATIVE TO PANZ) OF ACETYLCOA IN 0.05 M TRIS-HCL PH 7.69, 0.1 M NACL, 0.1 MM DTT. THIS WAS MIXED IN A 1:1 RATIO WITH RESERVOIR SOLUTION (0.2 M POTASSIUM THIOCYANATE, 0.1 M BIS- TRIS PROPANE PH 6.8, 20 % W/V PEG 3350) AND CRYSTALLIZED BY HANGING DROP VAOUR DIFFUSION (4 UL DROPLET OVER A 1 ML RESERVOIR).

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Sep 2, 2014 / Details: VARIMAX
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→23.26 Å / Num. obs: 11805 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 10.3 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.9
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.6 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AW8

1aw8


Resolution: 1.9→60.22 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.122 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY SIDE CHAIN OF RESIDUE Y22 IS NOT MODELLED BEYOND C-BETA DUE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY SIDE CHAIN OF RESIDUE Y22 IS NOT MODELLED BEYOND C-BETA DUE TO LACK OF CLEAR DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.24418 552 4.7 %RANDOM
Rwork0.18622 ---
obs0.18894 11235 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.788 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20 Å2
2--0.6 Å20 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 1.9→60.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms942 0 13 122 1077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.019981
X-RAY DIFFRACTIONr_bond_other_d0.0010.02960
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.9351319
X-RAY DIFFRACTIONr_angle_other_deg0.8263.0022169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6365124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.23223.33345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5115163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.197159
X-RAY DIFFRACTIONr_chiral_restr0.0960.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021113
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02228
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_it2.0392.194495
X-RAY DIFFRACTIONr_mcbond_other2.0292.181492
X-RAY DIFFRACTIONr_mcangle_it2.9683.25615
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2442.574486
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 50 -
Rwork0.285 798 -
obs--100 %

+
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