[English] 日本語
Yorodumi
- PDB-7xwu: Ketoreductase CpKR mutant - M1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xwu
TitleKetoreductase CpKR mutant - M1
ComponentsEpimerase domain-containing protein
KeywordsOXIDOREDUCTASE / ketoreductase
Function / homologyoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily / nucleotide binding / Chem-NDP / DI(HYDROXYETHYL)ETHER / NAD-dependent epimerase/dehydratase domain-containing protein
Function and homology information
Biological speciesCandida parapsilosis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChen, C. / Zheng, Y.C. / Pan, J. / Xu, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Key Research and Development Program of China2019YFA09005000 China
CitationJournal: To Be Published
Title: Computational Redesign of a robust Ketoreductase for Asymmetric Synthesis of Enantiopure diltiazem precursor.
Authors: Chen, C. / Zheng, Y.C. / Pan, J. / Xu, J.H.
History
DepositionMay 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Epimerase domain-containing protein
B: Epimerase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,6455
Polymers83,0482
Non-polymers1,5973
Water7,656425
1
A: Epimerase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3763
Polymers41,5241
Non-polymers8522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-1 kcal/mol
Surface area14560 Å2
MethodPISA
2
B: Epimerase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2702
Polymers41,5241
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-2 kcal/mol
Surface area15280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.271, 53.562, 79.565
Angle α, β, γ (deg.)78.750, 81.650, 78.150
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Epimerase domain-containing protein


Mass: 41524.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida parapsilosis (yeast) / Strain: CDC 317 / ATCC MYA-4646 / Gene: CPAR2_100480
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: G8B6C8
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2.02 Å3/Da / Density % sol: 39.13 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 3350, 0.1M Tris

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 43031 / % possible obs: 98.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.028 / Rrim(I) all: 0.053 / Χ2: 0.9 / Net I/σ(I): 11.1 / Num. measured all: 152835
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.033.70.27221120.9280.1640.3181.01796.8
2.03-2.073.70.26221710.870.1580.3071.08897.3
2.07-2.113.60.2121030.9450.1280.2461.03796.9
2.11-2.153.60.1821560.9630.110.2111.03297.5
2.15-2.23.60.14220910.9720.0870.1670.95197.4
2.2-2.253.50.13521480.970.0840.1591.10697.4
2.25-2.313.30.11921410.970.0760.1421.25696.9
2.31-2.373.60.1121230.9710.0670.1291.2797.9
2.37-2.443.70.0921790.9860.0540.1050.85297.9
2.44-2.523.60.07621300.990.0460.0890.84498
2.52-2.613.60.06821660.990.0420.080.74798.1
2.61-2.713.50.05821540.9920.0360.0690.73498.2
2.71-2.843.30.04921560.9930.0310.0580.65798
2.84-2.993.60.04721700.9930.0280.0550.60998.7
2.99-3.173.70.04221760.9940.0250.0490.63998.4
3.17-3.423.60.03821510.9930.0240.0450.60898.9
3.42-3.763.30.03421710.9940.0220.0410.59399
3.76-4.313.70.03521640.9950.0210.0410.59899.2
4.31-5.433.50.03321830.9920.020.0390.7399.4
5.43-503.60.03921860.9930.0230.0451.64799.3

-
Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.17_3644refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KWT

6kwt


Resolution: 2→46.84 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 24.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2382 2189 5.09 %
Rwork0.2016 40820 -
obs0.2035 43009 97.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.15 Å2 / Biso mean: 32.8796 Å2 / Biso min: 4.46 Å2
Refinement stepCycle: final / Resolution: 2→46.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5186 0 103 425 5714
Biso mean--32.31 34.33 -
Num. residues----663
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.040.30491280.2498242092
2.04-2.090.27891280.2409252497
2.09-2.140.32621280.2315257297
2.14-2.20.26791430.2279248997
2.2-2.260.24851190.2225258598
2.26-2.340.25431470.2299253897
2.34-2.420.27941390.2309257498
2.42-2.520.22891280.2238251298
2.52-2.630.28371440.2233257798
2.63-2.770.25771460.2153254498
2.77-2.950.25191300.207260198
2.95-3.170.25351530.2081257299
3.17-3.490.21171310.1974255099
3.49-40.20521450.1752259099
4-5.030.20191280.1694259599
5.04-46.840.21761520.1776257799

+
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://pdbjlvh1.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