[English] 日本語
Yorodumi
- PDB-6scz: Mycobacterium tuberculosis alanine racemase inhibited by DCS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6scz
TitleMycobacterium tuberculosis alanine racemase inhibited by DCS
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 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 ...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 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-L7N / Chem-OJQ / polyethylene glycol / DI(HYDROXYETHYL)ETHER / Alanine racemase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
Authorsde Chiara, C. / Purkiss, A. / Prosser, G. / Homsak, M. / 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
CitationJournal: 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.
History
DepositionJul 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_symmetry

-
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)89,55652
Polymers82,1022
Non-polymers7,45450
Water9,458525
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The homodimer represents the Biological assembly. The enzyme is only active as a dimer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13740 Å2
ΔGint21 kcal/mol
Surface area25110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.178, 164.178, 57.742
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 on special symmetry positions
IDModelComponents
11A-403-

GOL

21A-405-

CA

31A-641-

HOH

41A-721-

HOH

51A-735-

HOH

61B-762-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Alanine racemase


Mass: 41050.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal GSH is part of the thrombin recognition site
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: alr, Rv3423c, MTCY78.06 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WQA9, alanine racemase

-
Non-polymers , 10 types, 575 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-P4K / polyethylene glycol / 3,6,9,12,15,18,21,24,27,30,33,36,39,42-tetradecaoxatetratetracontan-1-ol


Mass: 662.804 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C30H62O15
#8: Chemical ChemComp-L7N / (~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylidene-[(4~{R})-3-oxidanylidene-1,2-oxazolidin-4-yl]azanium


Mass: 332.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N3O7P / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-OJQ / [2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methyl-(3-oxidanyl-1,2-oxazol-4-yl)azanium


Mass: 332.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N3O7P
#10: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 100 mM sodium MES buffer pH 6.2, 150 mM CaCl, 10% (v/v) PEG Smear Broad, 3% (v/v) Glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.57→164.18 Å / Num. obs: 109883 / % possible obs: 100 % / Redundancy: 12.41 % / Biso Wilson estimate: 22.06 Å2 / CC1/2: 0.9986 / Rmerge(I) obs: 0.1262 / Net I/σ(I): 9.93
Reflection shellResolution: 1.57→1.6 Å / Rmerge(I) obs: 0.471 / Num. unique obs: 5434

-
Processing

Software
NameVersionClassification
PHENIXdev_3765refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XFC

1xfc


Resolution: 1.57→82.09 Å / SU ML: 0.181 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.9704
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1897 5447 4.96 %
Rwork0.1504 104436 -
obs0.1524 109883 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.94 Å2
Refinement stepCycle: LAST / Resolution: 1.57→82.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5454 0 322 525 6301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076097
X-RAY DIFFRACTIONf_angle_d0.87118248
X-RAY DIFFRACTIONf_chiral_restr0.0521931
X-RAY DIFFRACTIONf_plane_restr0.0061062
X-RAY DIFFRACTIONf_dihedral_angle_d11.09111017
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.590.32061640.28713401X-RAY DIFFRACTION99.3
1.59-1.610.33632010.25933443X-RAY DIFFRACTION99.73
1.61-1.630.29021930.24873401X-RAY DIFFRACTION99.75
1.63-1.650.32541880.23643443X-RAY DIFFRACTION99.86
1.65-1.670.28631730.21653421X-RAY DIFFRACTION99.78
1.67-1.690.25871710.20123462X-RAY DIFFRACTION99.89
1.69-1.720.23911830.1933428X-RAY DIFFRACTION99.89
1.72-1.740.25671880.18383452X-RAY DIFFRACTION99.73
1.74-1.770.24091750.17633404X-RAY DIFFRACTION99.89
1.77-1.80.22271730.17193476X-RAY DIFFRACTION99.95
1.8-1.830.25281630.17383458X-RAY DIFFRACTION99.83
1.83-1.860.21981680.16163468X-RAY DIFFRACTION99.92
1.86-1.90.21311750.15743440X-RAY DIFFRACTION99.89
1.9-1.940.19531990.14133456X-RAY DIFFRACTION100
1.94-1.980.19871880.13893451X-RAY DIFFRACTION99.92
1.98-2.020.20581730.13743459X-RAY DIFFRACTION99.97
2.02-2.070.19171820.13653473X-RAY DIFFRACTION99.97
2.07-2.130.18651740.13183479X-RAY DIFFRACTION100
2.13-2.190.19711700.12833467X-RAY DIFFRACTION99.92
2.19-2.260.18121890.12743460X-RAY DIFFRACTION99.97
2.26-2.350.17161880.13053481X-RAY DIFFRACTION99.92
2.35-2.440.15961730.1253488X-RAY DIFFRACTION99.97
2.44-2.550.18252000.12963469X-RAY DIFFRACTION99.97
2.55-2.680.1771870.13263498X-RAY DIFFRACTION100
2.68-2.850.16691740.13023532X-RAY DIFFRACTION100
2.85-3.070.17421950.14023510X-RAY DIFFRACTION100
3.07-3.380.16631750.14393551X-RAY DIFFRACTION100
3.38-3.870.16241910.14023574X-RAY DIFFRACTION100
3.87-4.880.15681950.13273590X-RAY DIFFRACTION100
4.88-82.090.22321790.19713801X-RAY DIFFRACTION99.85

+
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