[English] 日本語
Yorodumi
- PDB-6kxr: Crystal structure of wild type Alp1U from the biosynthesis of kin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kxr
TitleCrystal structure of wild type Alp1U from the biosynthesis of kinamycins
ComponentsPutative hydrolase
KeywordsHYDROLASE / Hydrolyse epoxide / Cis-vicinal diol
Function / homology
Function and homology information


epoxide hydrolase activity
Similarity search - Function
Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
D-MALATE / Putative hydrolase / Putative hydrolase
Similarity search - Component
Biological speciesStreptomyces ambofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45073679781 Å
AuthorsZhang, L. / Yingli, Z. / De, B.C. / Zhang, C.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China41606193 China
National Natural Science Foundation of China31820103003 China
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Mutation of an atypical oxirane oxyanion hole improves regioselectivity of the alpha / beta-fold epoxide hydrolase Alp1U.
Authors: Zhang, L. / De, B.C. / Zhang, W. / Mandi, A. / Fang, Z. / Yang, C. / Zhu, Y. / Kurtan, T. / Zhang, C.
History
DepositionSep 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative hydrolase
B: Putative hydrolase
C: Putative hydrolase
D: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,3385
Polymers148,2044
Non-polymers1341
Water2,288127
1
A: Putative hydrolase
D: Putative hydrolase


Theoretical massNumber of molelcules
Total (without water)74,1022
Polymers74,1022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-20 kcal/mol
Surface area21310 Å2
MethodPISA
2
B: Putative hydrolase
C: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2363
Polymers74,1022
Non-polymers1341
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-22 kcal/mol
Surface area21380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.09, 101.58, 117.42
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein
Putative hydrolase / / epoxy hydrolase Alp1U


Mass: 37050.914 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces ambofaciens (strain ATCC 23877 / 3486 / DSM 40053 / JCM 4204 / NBRC 12836 / NRRL B-2516) (bacteria)
Gene: SAMT0137, SAMT0138 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q1RQU8, UniProt: A0A0K2AJY3*PLUS, epoxide hydrolase
#2: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 37.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M MMT PH5.0, 25% PEG 1500

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97894 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97894 Å / Relative weight: 1
ReflectionResolution: 2.45073679781→70.19 Å / Num. obs: 43063 / % possible obs: 99.35 % / Redundancy: 2 % / Biso Wilson estimate: 46.6816931705 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.02819 / Net I/σ(I): 13.73
Reflection shellResolution: 2.451→2.538 Å / Rmerge(I) obs: 0.2004 / Num. unique obs: 4255 / CC1/2: 0.846

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
PHENIX1.9_1692+SVNrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45073679781→70.1866527268 Å / SU ML: 0.339490266101 / Cross valid method: FREE R-VALUE / σ(F): 1.3435988873 / Phase error: 24.1668710666
RfactorNum. reflection% reflection
Rfree0.234445837871 2052 4.76621838199 %
Rwork0.168676881612 --
obs0.171747585964 43053 99.3377941855 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.2833727776 Å2
Refinement stepCycle: LAST / Resolution: 2.45073679781→70.1866527268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9097 0 9 127 9233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008184038640999365
X-RAY DIFFRACTIONf_angle_d1.1091975783712747
X-RAY DIFFRACTIONf_chiral_restr0.04312293125631337
X-RAY DIFFRACTIONf_plane_restr0.005088843414341678
X-RAY DIFFRACTIONf_dihedral_angle_d14.56676825243342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45073679781-2.50770.3099316812471230.2189417208212711X-RAY DIFFRACTION99.5433789954
2.5077-2.57050.3068264948291240.2083092047742691X-RAY DIFFRACTION99.4348286824
2.5705-2.640.3154748001341500.2104679825362709X-RAY DIFFRACTION99.3053143453
2.64-2.71770.2830512147531370.2103130366912679X-RAY DIFFRACTION99.4350282486
2.7177-2.80540.2766955569451540.2085805187492682X-RAY DIFFRACTION99.1955229101
2.8054-2.90560.2661525930491210.2091409981142724X-RAY DIFFRACTION99.6846531184
2.9056-3.0220.3274758899961250.2187618498262717X-RAY DIFFRACTION99.3011879804
3.022-3.15950.3174212918811430.2126451402542655X-RAY DIFFRACTION97.5933031043
3.1595-3.32610.2726371027541500.2132384705562722X-RAY DIFFRACTION99.9651931779
3.3261-3.53450.2595212740711510.1892460307772724X-RAY DIFFRACTION99.9652294854
3.5345-3.80740.2371779651191410.1669992829032765X-RAY DIFFRACTION99.8968717772
3.8074-4.19050.184031462281270.137964585982754X-RAY DIFFRACTION99.8959778086
4.1905-4.79670.1937402134951280.1267264898792795X-RAY DIFFRACTION99.795151929
4.7967-6.04280.1815970230371350.1501910727842749X-RAY DIFFRACTION97.7627118644
6.0428-70.18665272680.183872701321430.1354934225752924X-RAY DIFFRACTION99.3521218011

+
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