[English] 日本語
Yorodumi
- PDB-8ahw: Structure of DCS-resistant variant D322N of alanine racemase from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ahw
TitleStructure of DCS-resistant variant D322N of alanine racemase from Mycobacterium tuberculosis
ComponentsAlanine racemase
KeywordsISOMERASE / Enzyme / alanine racemase / peptidoglycan biosynthesis
Function / homology
Function and homology information


alanine racemase / D-alanine biosynthetic process / alanine racemase activity / peptidoglycan biosynthetic process / pyridoxal phosphate binding / cytosol
Similarity search - Function
Alanine racemase, pyridoxal-phosphate attachment site / Alanine racemase pyridoxal-phosphate attachment site. / Alanine racemase / Alanine racemase, C-terminal / Alanine racemase, C-terminal domain / Alanine racemase, C-terminal domain / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel
Similarity search - Domain/homology
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
Authorsde Chiara, C. / Prosser, G. / Ogrodowicz, R.W. / de Carvalho, L.P.S.
Funding support United Kingdom, 5items
OrganizationGrant numberCountry
The Francis Crick InstituteSee list below United Kingdom
Cancer Research UKFC001060 United Kingdom
Medical Research Council (MRC, United Kingdom)FC001060 United Kingdom
Wellcome TrustFC001060 United Kingdom
Wellcome Trust104785/B/14/Z United Kingdom
Citation
Journal: Acs Bio Med Chem Au / Year: 2023
Title: Structure of the d-Cycloserine-Resistant Variant D322N of Alanine Racemase from Mycobacterium tuberculosis .
Authors: de Chiara, C. / Prosser, G.A. / Ogrodowicz, R. / de Carvalho, L.P.S.
#1: Journal: Nat Commun / Year: 2019
Title: Comparative fitness analysis of D-cycloserine resistant mutants reveals both fitness-neutral and high-fitness cost genotypes.
Authors: Evangelopoulos, D. / Prosser, G.A. / Rodgers, A. / Dagg, B.M. / Khatri, B. / Ho, M.M. / Gutierrez, M.G. / Cortes, T. / de Carvalho, L.P.S.
#2: Journal: Nat Chem Biol / Year: 2020
Title: D-Cycloserine destruction by alanine racemase and the limit of irreversible inhibition.
Authors: de Chiara, C. / Homsak, M. / Prosser, G.A. / Douglas, H.L. / Garza-Garcia, A. / Kelly, G. / Purkiss, A.G. / Tate, E.W. / de Carvalho, L.P.S.
#3: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#4: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Liebschner, D. / Afonine, P.V. / Baker, M.L. / Bunkoczi, G. / Chen, V.B. / Croll, T.I. / Hintze, B. / Hung, L.W. / Jain, S. / McCoy, A.J. / Moriarty, N.W. / Oeffner, R.D. / Poon, B.K. / ...Authors: Liebschner, D. / Afonine, P.V. / Baker, M.L. / Bunkoczi, G. / Chen, V.B. / Croll, T.I. / Hintze, B. / Hung, L.W. / Jain, S. / McCoy, A.J. / Moriarty, N.W. / Oeffner, R.D. / Poon, B.K. / Prisant, M.G. / Read, R.J. / Richardson, J.S. / Richardson, D.C. / Sammito, M.D. / Sobolev, O.V. / Stockwell, D.H. / Terwilliger, T.C. / Urzhumtsev, A.G. / Videau, L.L. / Williams, C.J. / Adams, P.D.
History
DepositionJul 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3Feb 14, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alanine racemase
B: Alanine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9588
Polymers82,5562
Non-polymers4026
Water5,062281
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, The enzyme is active as a dimer as the two catalytic bases are provided by the two distinct chains
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint0 kcal/mol
Surface area25780 Å2
Unit cell
Length a, b, c (Å)165.320, 165.320, 57.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein Alanine racemase


Mass: 41278.008 Da / Num. of mol.: 2 / Mutation: D322'N
Source method: isolated from a genetically manipulated source
Details: LLP is PLP (pyridoxal 5'-phosphate) bound as a cofactor to LYS 44 epsilon amino group (-NH2) via an aldimine linkage or Schiff base
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: alr, Rv3423c, MTCY78.06
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P9WQA9, alanine racemase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 100 mM sodium MES buffer pH 6.2, 150 mM CaCl, 9% (v/v) PEG Smear Broad, 2% (v/v) Glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 17, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.58→47.35 Å / Num. obs: 109449 / % possible obs: 100 % / Redundancy: 12.3 % / Biso Wilson estimate: 30.03 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.075 / Net I/σ(I): 21.5
Reflection shellResolution: 1.58→1.63 Å / Rmerge(I) obs: 2.54 / Num. unique obs: 10809 / CC1/2: 0.6

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SCZ

6scz


Resolution: 1.58→47.35 Å / SU ML: 0.2313 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5981
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.234 5503 5.03 %
Rwork0.2266 103896 -
obs0.2277 109449 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.4 Å2
Refinement stepCycle: LAST / Resolution: 1.58→47.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5228 0 26 281 5535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00845351
X-RAY DIFFRACTIONf_angle_d1.03157279
X-RAY DIFFRACTIONf_chiral_restr0.0571854
X-RAY DIFFRACTIONf_plane_restr0.0094955
X-RAY DIFFRACTIONf_dihedral_angle_d8.2761796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.60.42392010.38683386X-RAY DIFFRACTION99.94
1.6-1.620.37621710.36083422X-RAY DIFFRACTION99.97
1.62-1.640.33041750.31053448X-RAY DIFFRACTION99.92
1.64-1.660.34571670.32613435X-RAY DIFFRACTION99.94
1.66-1.680.35431860.3093386X-RAY DIFFRACTION99.94
1.68-1.70.3211770.30093461X-RAY DIFFRACTION100
1.7-1.730.32551790.29363397X-RAY DIFFRACTION99.97
1.73-1.750.32811880.29553450X-RAY DIFFRACTION100
1.75-1.780.32682020.29213352X-RAY DIFFRACTION99.92
1.78-1.810.32331880.29013475X-RAY DIFFRACTION99.95
1.81-1.840.321710.30543423X-RAY DIFFRACTION100
1.84-1.870.32871640.30913455X-RAY DIFFRACTION99.97
1.87-1.910.3641850.32013419X-RAY DIFFRACTION100
1.91-1.950.30111890.29423444X-RAY DIFFRACTION99.94
1.95-1.990.33191770.28473478X-RAY DIFFRACTION100
1.99-2.040.29261820.27133408X-RAY DIFFRACTION100
2.04-2.090.33522020.26113430X-RAY DIFFRACTION99.97
2.09-2.140.29841800.2563453X-RAY DIFFRACTION100
2.14-2.210.28292020.25393438X-RAY DIFFRACTION100
2.21-2.280.30791840.24573442X-RAY DIFFRACTION100
2.28-2.360.2952100.23973439X-RAY DIFFRACTION100
2.36-2.450.26281720.24593471X-RAY DIFFRACTION100
2.45-2.570.26981990.23433450X-RAY DIFFRACTION100
2.57-2.70.25081930.22683477X-RAY DIFFRACTION100
2.7-2.870.24811670.21173538X-RAY DIFFRACTION100
2.87-3.090.23951900.22023483X-RAY DIFFRACTION100
3.09-3.40.23931750.21443541X-RAY DIFFRACTION100
3.4-3.90.20361980.1963539X-RAY DIFFRACTION100
3.9-4.910.1961900.16753580X-RAY DIFFRACTION100
4.91-5.060.20681890.19073776X-RAY DIFFRACTION99.92
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.41518291738-0.02763418459290.4075900769221.575833034180.3293391420751.305612834670.264084230140.244532828987-0.110387751556-0.072771761105-0.222711593210.1718667002370.3333835762630.509181770579-0.02180341822430.3282045503740.230200760421-0.1053700042120.368147539678-0.08211229298690.34316699796127.77021292031.294742508277.92405410636
20.7965277912170.03771249809320.5523896195510.403887570297-0.5350786128941.225410089910.05117406833290.407602933348-0.0401483010167-0.169616503177-0.216980675656-0.186734779173-0.1405854823081.008359982570.06299519792380.217132254083-0.0310226003780.03435986371470.8833087684050.1152626550320.31844996127652.714150619618.941757690512.148206533
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 11 through 384 )AA11 - 3841 - 366
22chain 'B' and (resid 14 through 383 )BB14 - 3831 - 348

+
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