[English] 日本語
Yorodumi
- PDB-5m4b: Alpha-amino epsilon-caprolactam racemase D210A mutant in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5m4b
TitleAlpha-amino epsilon-caprolactam racemase D210A mutant in complex with PLP and geminal diamine intermediate
ComponentsAminotransferase class-III
KeywordsISOMERASE / PLP / racemase
Function / homology
Function and homology information


transaminase activity / pyridoxal phosphate binding
Similarity search - Function
: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-7F7 / Aminotransferase class-III
Similarity search - Component
Biological speciesRhizobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsFrese, A. / Sutton, P.W. / Turkenburg, J.P. / Grogan, G.
CitationJournal: Acs Catalysis / Year: 2017
Title: Snapshots of the Catalytic Cycle of the Industrial Enzyme alpha-Amino-epsilon-Caprolactam Racemase (ACLR) Observed Using X-ray Crystallography
Authors: Frese, A. / Sutton, P.W. / Turkenburg, J.P. / Grogan, G.
History
DepositionOct 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name
Revision 1.2Jan 17, 2024Group: 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aminotransferase class-III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4223
Polymers46,0021
Non-polymers4192
Water6,503361
1
A: Aminotransferase class-III
hetero molecules

A: Aminotransferase class-III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8436
Polymers92,0052
Non-polymers8394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area8250 Å2
ΔGint-48 kcal/mol
Surface area27950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.210, 79.111, 58.971
Angle α, β, γ (deg.)90.00, 112.82, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Aminotransferase class-III / Alpha-amino epsilon-caprolactam racemase


Mass: 46002.309 Da / Num. of mol.: 1 / Mutation: D210A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobacter (bacteria) / Gene: RHSP_08934 / Production host: Escherichia coli (E. coli)
References: UniProt: N6UXY4, 2-aminohexano-6-lactam racemase
#2: Chemical ChemComp-7F7 / [6-methyl-5-oxidanyl-4-[(~{E})-[(3~{R})-2-oxidanylideneazepan-3-yl]iminomethyl]pyridin-3-yl]methyl dihydrogen phosphate


Mass: 357.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N3O6P
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.95 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M MgCl2, 25 % PEG 3350, 0.1 mM HEPES (pH 7.0).

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.5→45.79 Å / Num. obs: 57829 / % possible obs: 99.2 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.028 / Net I/σ(I): 26.1
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.22

-
Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZUK

2zuk


Resolution: 1.5→45.79 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.065 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.065 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.168 2859 4.9 %RANDOM
Rwork0.14 ---
obs0.141 54969 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20.25 Å2
2---0.59 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.5→45.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 0 28 362 3586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0193291
X-RAY DIFFRACTIONr_bond_other_d0.0030.023166
X-RAY DIFFRACTIONr_angle_refined_deg2.361.984472
X-RAY DIFFRACTIONr_angle_other_deg1.5223.0017253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1325439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.89122.823124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74515490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6581525
X-RAY DIFFRACTIONr_chiral_restr0.2020.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213792
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02729
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_it1.721.4721759
X-RAY DIFFRACTIONr_mcbond_other1.7211.4721758
X-RAY DIFFRACTIONr_mcangle_it2.3782.2052194
X-RAY DIFFRACTIONr_mcangle_other2.3782.2062195
X-RAY DIFFRACTIONr_scbond_it2.8371.7021532
X-RAY DIFFRACTIONr_scbond_other2.8361.7031532
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0382.4682278
X-RAY DIFFRACTIONr_long_range_B_refined5.11819.8833755
X-RAY DIFFRACTIONr_long_range_B_other5.11719.8893756
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 230 -
Rwork0.18 4057 -
obs--99.81 %

+
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