[English] 日本語
Yorodumi
- PDB-9emu: RosC-8-demethyl-8-amino-FMN - Phosphate complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9emu
TitleRosC-8-demethyl-8-amino-FMN - Phosphate complex
ComponentsPhosphoglycerate mutase
KeywordsHYDROLASE / RosC / phosphatase / roseoflavin / riboflavin / antibiotics / Streptomyces davaonensis
Function / homology
Function and homology information


phosphatase activity / cytoplasm
Similarity search - Function
: / Phosphoglycerate mutase family / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Chem-RS3 / Phosphoglycerate mutase
Similarity search - Component
Biological speciesStreptomyces davaonensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsErmler, U. / Mack, M. / Demmer, U.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Mol.Biol. / Year: 2024
Title: The Phosphatase RosC from Streptomyces davaonensis is Used for Roseoflavin Biosynthesis and has Evolved to Largely Prevent Dephosphorylation of the Important Cofactor Riboflavin-5'-phosphate.
Authors: Joshi, T. / Demmer, U. / Schneider, C. / Glaser, T. / Warkentin, E. / Ermler, U. / Mack, M.
History
DepositionMar 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphoglycerate mutase
B: Phosphoglycerate mutase
C: Phosphoglycerate mutase
D: Phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,48329
Polymers101,9154
Non-polymers3,56725
Water6,918384
1
A: Phosphoglycerate mutase
B: Phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,60313
Polymers50,9582
Non-polymers1,64511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint-59 kcal/mol
Surface area17990 Å2
2
C: Phosphoglycerate mutase
D: Phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,87916
Polymers50,9582
Non-polymers1,92214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8180 Å2
ΔGint-58 kcal/mol
Surface area18670 Å2
Unit cell
Length a, b, c (Å)51.850, 51.900, 81.820
Angle α, β, γ (deg.)73.46, 81.72, 70.52
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Phosphoglycerate mutase


Mass: 25478.873 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces davaonensis (bacteria) / Gene: BN159_8033
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: K4R812
#2: Chemical
ChemComp-RS3 / 1-deoxy-1-[8-(dimethylamino)-7-methyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl]-D-ribitol / Roseoflavin


Mass: 405.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H23N5O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 1.95 Å3/Da / Density % sol: 36.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.7 / Details: PEG 1500, TBG, pH 5.5, KH2PO4 pH 7.4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 138597 / % possible obs: 91.4 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.063 / Net I/σ(I): 15.7
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.4-1.50.76205620.7160.9061
1.5-1.70.412366020.9080.4821
1.7-20.133313900.9820.1581
2-2.40.059210420.9930.071
2.4-30.039140890.9960.0471
3-3.80.03175750.9970.0371
3.8-4.60.02931600.9950.0351
4.6-5.90.02721890.9970.0321
5.9-80.02211870.9990.0261
8-120.0215820.9980.0251
12-500.0242190.9980.0291

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→34.82 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 20.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.203 4022 2.9 %
Rwork0.1638 --
obs0.1649 138577 91.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→34.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6749 0 230 384 7363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.868
X-RAY DIFFRACTIONf_dihedral_angle_d11.6312681
X-RAY DIFFRACTIONf_chiral_restr0.0781104
X-RAY DIFFRACTIONf_plane_restr0.011292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.3152720.26212703X-RAY DIFFRACTION53
1.42-1.430.3071920.22783042X-RAY DIFFRACTION60
1.43-1.450.25941080.20593396X-RAY DIFFRACTION68
1.45-1.470.29681160.19434181X-RAY DIFFRACTION82
1.47-1.490.24991580.17544664X-RAY DIFFRACTION92
1.49-1.510.22991270.16314782X-RAY DIFFRACTION94
1.51-1.540.23641660.16014769X-RAY DIFFRACTION94
1.54-1.560.21551320.15694779X-RAY DIFFRACTION94
1.56-1.580.22721310.15414825X-RAY DIFFRACTION95
1.58-1.610.22441560.14844818X-RAY DIFFRACTION95
1.61-1.640.23021420.15124789X-RAY DIFFRACTION95
1.64-1.670.22491460.14654950X-RAY DIFFRACTION95
1.67-1.710.22951510.15084771X-RAY DIFFRACTION95
1.71-1.740.1741270.15124851X-RAY DIFFRACTION95
1.74-1.780.22291490.15294880X-RAY DIFFRACTION96
1.78-1.830.20291410.15274821X-RAY DIFFRACTION96
1.83-1.880.20631460.15464898X-RAY DIFFRACTION96
1.88-1.930.18841570.15234872X-RAY DIFFRACTION96
1.93-20.16811450.15184946X-RAY DIFFRACTION97
2-2.070.18381540.1484894X-RAY DIFFRACTION96
2.07-2.150.19391330.15494876X-RAY DIFFRACTION96
2.15-2.250.21811530.1554842X-RAY DIFFRACTION96
2.25-2.370.21621420.16334894X-RAY DIFFRACTION96
2.37-2.520.181390.16824804X-RAY DIFFRACTION95
2.52-2.710.21711410.17254870X-RAY DIFFRACTION96
2.71-2.980.19911550.1764889X-RAY DIFFRACTION97
2.98-3.410.19651490.17094939X-RAY DIFFRACTION97
3.41-4.30.20471470.16094898X-RAY DIFFRACTION96
4.3-34.820.17961470.17014912X-RAY DIFFRACTION97

+
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