[English] 日本語
Yorodumi
- PDB-9k8r: Structure of Promiscuous short chain dehydrogenase Spm14 in compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9k8r
TitleStructure of Promiscuous short chain dehydrogenase Spm14 in complex with NADPH
ComponentsSpm14
KeywordsBIOSYNTHETIC PROTEIN / Short chain dehydrogenase / coenzyme / NADPH
Function / homologyNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Function and homology information
Biological speciesSpiromastix sp. SCSIO F190 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsJing, L.Q. / Peng, M. / Chen, Y.Y. / Ju, J.H. / Wu, D.L.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: to be published
Title: Biosynthesis of Spiromarmycin Reveals the Unusual Formation of Benzopyran and the Mechanistic Insight of a Promiscuous Short Chain reductase Spm14
Authors: Jing, L.Q. / Chen, Y.Y. / Peng, M. / Ju, J.H. / Wu, D.L.
History
DepositionOct 24, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spm14
B: Spm14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4865
Polymers61,8772
Non-polymers1,6093
Water00
1
A: Spm14
B: Spm14
hetero molecules

A: Spm14
B: Spm14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,97110
Polymers123,7544
Non-polymers3,2186
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545x,x-y-1,-z1
Buried area25320 Å2
ΔGint-153 kcal/mol
Surface area35360 Å2
MethodPISA
2
A: Spm14
B: Spm14
hetero molecules

A: Spm14
B: Spm14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,97110
Polymers123,7544
Non-polymers3,2186
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-y,-x,-z+1/31
Buried area16340 Å2
ΔGint-76 kcal/mol
Surface area44350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.285, 123.285, 98.611
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

-
Components

#1: Protein Spm14


Mass: 30938.387 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spiromastix sp. SCSIO F190 (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 64.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8
Details: 0.2M Sodium thiocyanate, 20%w/v Polyethylene glycol 3,350

-
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 11, 2021
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.077→50 Å / Num. obs: 16043 / % possible obs: 100 % / Redundancy: 9.9 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.055 / Rrim(I) all: 0.175 / Χ2: 0.924 / Net I/σ(I): 4.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.1-3.1510.21.1017760.7480.9250.3611.1590.893100
3.15-3.21100.9477910.8490.9580.3140.9980.915100
3.21-3.279.90.7018040.8790.9670.2330.7390.927100
3.27-3.349.50.6237980.8990.9730.2120.6580.893100
3.34-3.419.80.4977810.9280.9810.1670.5250.951100
3.41-3.4910.10.458100.940.9850.1480.4740.976100
3.49-3.58100.3667970.9720.9930.1210.3860.957100
3.58-3.689.50.3347960.9630.9910.1140.3530.944100
3.68-3.7810.40.297950.9760.9940.0940.3050.993100
3.78-3.9110.30.2347970.9810.9950.0760.2460.988100
3.91-4.0410.30.2057950.9820.9950.0670.2151.007100
4.04-4.21100.1577900.9890.9970.0520.1650.963100
4.21-4.49.60.1268160.9910.9980.0430.1331.044100
4.4-4.6310.30.1117960.9940.9990.0360.1161.065100
4.63-4.929.70.0978080.9950.9990.0330.1021.019100
4.92-5.310.40.0988060.9930.9980.0320.1030.955100
5.3-5.8310.20.0968110.9930.9980.0310.1010.893100
5.83-6.679.60.088070.9960.9990.0270.0850.808100
6.67-8.49.70.0548220.9980.9990.0180.0580.716100
8.4-508.90.0398470.9980.9990.0130.0420.53599.9

-
Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BMS

4bms


Resolution: 3.1→38.504 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2012 756 4.73 %
Rwork0.1836 --
obs0.1845 15979 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→38.504 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4281 0 104 0 4385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0174484
X-RAY DIFFRACTIONf_angle_d1.3436109
X-RAY DIFFRACTIONf_dihedral_angle_d17.7281588
X-RAY DIFFRACTIONf_chiral_restr0.074693
X-RAY DIFFRACTIONf_plane_restr0.008774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.31450.31461200.26623015X-RAY DIFFRACTION99
3.3145-3.64780.25121520.22183036X-RAY DIFFRACTION100
3.6478-4.17510.21061360.18953049X-RAY DIFFRACTION100
4.1751-5.2580.16921850.15483031X-RAY DIFFRACTION100
5.258-38.5040.1811630.16183092X-RAY DIFFRACTION99

+
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