[English] 日本語
Yorodumi
- PDB-5wul: Serratia marcescens short-chain dehydrogenase/reductase F98A/F202L -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wul
TitleSerratia marcescens short-chain dehydrogenase/reductase F98A/F202L
ComponentsShort-chain dehydrogenase
KeywordsOXIDOREDUCTASE / Serratia marcescens short-chain dehydrogenase/reductase / SmSDR / F98A/F202L
Function / homologyEnoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / nucleotide binding / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Short-chain dehydrogenase
Function and homology information
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsLiu, J.-S. / Tsou, Y. / Wang, W.-C.
CitationJournal: Sci Rep / Year: 2018
Title: Structure-guided design of Serratia marcescens short-chain dehydrogenase/reductase for stereoselective synthesis of (R)-phenylephrine.
Authors: Liu, J.-S. / Kuan, Y.-C. / Tsou, Y. / Lin, T.-Y. / Hsu, W.-H. / Yang, M.-T. / Lin, J.-Y. / Wang, W.-C.
History
DepositionDec 19, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Short-chain dehydrogenase
B: Short-chain dehydrogenase


Theoretical massNumber of molelcules
Total (without water)59,0872
Polymers59,0872
Non-polymers00
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-10 kcal/mol
Surface area18450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.799, 83.799, 114.253
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-420-

HOH

21B-410-

HOH

-
Components

#1: Protein Short-chain dehydrogenase


Mass: 29543.250 Da / Num. of mol.: 2 / Mutation: F98A/F202L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A192ICX3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 1.7 Å3/Da / Density % sol: 27.53 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7
Details: 50mM HEPES buffer (pH 7.0), 40% (v/v) tacsimate (pH 7.0), 2mM spermine, 2mM hexamine cobalt (III) chloride

-
Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→67.58 Å / Num. obs: 34418 / % possible obs: 99.5 % / Redundancy: 13.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.014 / Rsym value: 0.053 / Net I/σ(I): 44.7
Reflection shellResolution: 1.87→1.94 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZGW

4zgw


Resolution: 1.87→67.58 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.335 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19261 1768 5.2 %RANDOM
Rwork0.14685 ---
obs0.14918 32399 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.12 Å20 Å2
3---0.24 Å2
Refinement stepCycle: 1 / Resolution: 1.87→67.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 0 257 3565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0193349
X-RAY DIFFRACTIONr_bond_other_d0.0020.023276
X-RAY DIFFRACTIONr_angle_refined_deg2.0291.9554531
X-RAY DIFFRACTIONr_angle_other_deg1.10137477
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4235460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61124.046131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.23915516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7261523
X-RAY DIFFRACTIONr_chiral_restr0.1250.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023948
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02751
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_it2.1291.7521852
X-RAY DIFFRACTIONr_mcbond_other2.1291.7521851
X-RAY DIFFRACTIONr_mcangle_it2.9942.6072308
X-RAY DIFFRACTIONr_mcangle_other2.9932.6082309
X-RAY DIFFRACTIONr_scbond_it3.9462.2681497
X-RAY DIFFRACTIONr_scbond_other3.9452.2671498
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0063.2142224
X-RAY DIFFRACTIONr_long_range_B_refined7.20915.3363768
X-RAY DIFFRACTIONr_long_range_B_other7.14815.0463694
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.871→1.92 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 117 -
Rwork0.155 2336 -
obs--98.43 %

+
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