[English] 日本語
Yorodumi
- PDB-3wwh: Crystal structure of the first R-stereoselective -transaminase id... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wwh
TitleCrystal structure of the first R-stereoselective -transaminase identified from Arthrobacter sp. KNK168 (FERM-BP-5228)
Components(R)-amine transaminase
KeywordsTRANSFERASE / transaminase / amine-pyruvate aminotransferase / PYRIDOXAL-5'-PHOSPHATE / Multi-domain protein (alpha and beta) / Fold class IV PLP-dependent enzyme
Function / homology
Function and homology information


carboxylic acid biosynthetic process / catalytic activity
Similarity search - Function
: / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV / D-amino Acid Aminotransferase; Chain A, domain 1 ...: / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV / D-amino Acid Aminotransferase; Chain A, domain 1 / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / (R)-amine transaminase
Similarity search - Component
Biological speciesArthrobacter sp. KNK168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsGuan, L.J. / Ohtsuka, J. / Okai, M. / Miyakawa, T. / Mase, T. / Zhi, Y. / Ito, N. / Yasohara, Y. / Tanokura, M.
CitationJournal: Sci Rep / Year: 2015
Title: A new target region for changing the substrate specificity of amine transaminases.
Authors: Guan, L.J. / Ohtsuka, J. / Okai, M. / Miyakawa, T. / Mase, T. / Zhi, Y. / Hou, F. / Ito, N. / Iwasaki, A. / Yasohara, Y. / Tanokura, M.
History
DepositionJun 18, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: (R)-amine transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7923
Polymers36,4531
Non-polymers3392
Water5,837324
1
A: (R)-amine transaminase
hetero molecules

A: (R)-amine transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5846
Polymers72,9062
Non-polymers6784
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6290 Å2
ΔGint-27 kcal/mol
Surface area24290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.620, 80.620, 93.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-617-

HOH

21A-804-

HOH

-
Components

#1: Protein (R)-amine transaminase / R-stereoselective -transaminase


Mass: 36452.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter sp. KNK168 (bacteria) / Gene: TAS / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)
References: UniProt: F7J696, beta-alanine-pyruvate transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 0.2 M magnesium chloride, 0.1 M Bis-Tris, 22% (w/v) PEG 3350, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→45 Å / Num. all: 37806 / Num. obs: 37725 / % possible obs: 99.8 % / Observed criterion σ(I): -3
Reflection shellResolution: 1.65→1.75 Å / % possible all: 98.8

-
Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→40.31 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.542 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.019 / ESU R Free: 0.017 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17243 1885 5 %RANDOM
Rwork0.15331 ---
obs0.15426 35839 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.829 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.65→40.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2566 0 21 324 2911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192649
X-RAY DIFFRACTIONr_bond_other_d0.0010.022462
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.9633619
X-RAY DIFFRACTIONr_angle_other_deg0.71135658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.55328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.31623.607122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.61615404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3181520
X-RAY DIFFRACTIONr_chiral_restr0.0680.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213010
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02602
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 1.651→1.694 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.09 123 -
Rwork0.081 2534 -
obs--97.11 %
Refinement TLS params.Method: refined / Origin x: 15.884 Å / Origin y: 5.132 Å / Origin z: 20.591 Å
111213212223313233
T0.1111 Å2-0.0095 Å2-0.002 Å2-0.1376 Å20.0027 Å2--0.004 Å2
L0.1799 °20.0173 °20.0649 °2-0.0944 °20.1122 °2--0.3385 °2
S0.0185 Å °0.0128 Å °-0.0027 Å °0.0075 Å °-0.0189 Å °-0.0146 Å °-0.026 Å °0.0195 Å °0.0003 Å °

+
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