[English] 日本語
Yorodumi
- PDB-7p97: Structure of 3-phospho-D-glycerate guanylyltransferase with produ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p97
TitleStructure of 3-phospho-D-glycerate guanylyltransferase with product 3-GPPG bound
Components3-phospho-D-glycerate guanylyltransferase
KeywordsTRANSFERASE / F420 synthesis / FbiD / CofC / guanylyltransferase / 3-phospho-glycerate
Function / homology3-phospho-D-glycerate guanylyltransferase / phospholactate guanylyltransferase activity / Phosphoenolpyruvate guanylyltransferase CofC / Guanylyl transferase CofC like / F420-0 metabolic process / Nucleotide-diphospho-sugar transferases / GTP binding / 3-(guanosine-5'-diphospho)-D-glycerate / 3-phospho-D-glycerate guanylyltransferase
Function and homology information
Biological speciesMycetohabitans rhizoxinica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsPalm, G.J. / Berndt, L. / Lammers, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)LA2984-5/1 Germany
German Research Foundation (DFG)LA2984-6/1 Germany
CitationJournal: Mbio / Year: 2022
Title: Diversification by CofC and Control by CofD Govern Biosynthesis and Evolution of Coenzyme F 420 and Its Derivative 3PG-F 420.
Authors: Hasan, M. / Schulze, S. / Berndt, L. / Palm, G.J. / Braga, D. / Richter, I. / Last, D. / Lammers, M. / Lackner, G.
History
DepositionJul 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: 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
AAA: 3-phospho-D-glycerate guanylyltransferase
BBB: 3-phospho-D-glycerate guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,07911
Polymers51,8132
Non-polymers1,2669
Water3,477193
1
AAA: 3-phospho-D-glycerate guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5225
Polymers25,9071
Non-polymers6154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: 3-phospho-D-glycerate guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5576
Polymers25,9071
Non-polymers6515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.090, 57.090, 228.970
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11BBB-305-

CL

21BBB-491-

HOH

-
Components

#1: Protein 3-phospho-D-glycerate guanylyltransferase / 3PG guanylyltransferase


Mass: 25906.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycetohabitans rhizoxinica (strain DSM 19002 / CIP 109453 / HKI 454) (bacteria)
Strain: DSM 19002 / CIP 109453 / HKI 454 / Gene: cofC, RBRH_02550 / Plasmid: pACYCduet / Details (production host): N-terminal His-tag / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: E5ASS2, 3-phospho-D-glycerate guanylyltransferase
#2: Chemical ChemComp-6WI / 3-(guanosine-5'-diphospho)-D-glycerate / 3GPPG / (2~{R})-3-[[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-2-oxidanyl-propanoic acid


Mass: 531.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% PEG 3000, 200 mm MgCl2, 100 mm sodium cacodylate pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 28, 2021 / Details: Si111
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 18963 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.1 % / Biso Wilson estimate: 29.9 Å2 / CC1/2: 0.975 / Rrim(I) all: 0.489 / Rsym value: 0.465 / Net I/σ(I): 5.4
Reflection shellResolution: 2.35→2.49 Å / Redundancy: 10.6 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 31546 / CC1/2: 0.511 / Rrim(I) all: 1.898 / Rsym value: 1.805 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSFeb 5, 2021data reduction
XDSFeb 5, 2021data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6bwg

6bwg


Resolution: 2.35→49.49 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.904 / SU B: 22.024 / SU ML: 0.221 / Cross valid method: FREE R-VALUE / ESU R: 0.35 / ESU R Free: 0.24
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2381 878 4.63 %
Rwork0.1865 18084 -
all0.189 --
obs-18962 99.832 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.473 Å2
Baniso -1Baniso -2Baniso -3
1-0.004 Å20.002 Å20 Å2
2--0.004 Å2-0 Å2
3----0.013 Å2
Refinement stepCycle: LAST / Resolution: 2.35→49.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2945 0 75 194 3214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133091
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172916
X-RAY DIFFRACTIONr_angle_refined_deg1.8221.6664220
X-RAY DIFFRACTIONr_angle_other_deg1.2991.596699
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3215400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.42919.404151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.58515459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.791532
X-RAY DIFFRACTIONr_chiral_restr0.0760.2412
X-RAY DIFFRACTIONr_chiral_restr_other0.0360.24
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023492
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02700
X-RAY DIFFRACTIONr_nbd_refined0.2040.2628
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.22673
X-RAY DIFFRACTIONr_nbtor_refined0.1590.21467
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21570
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2140
X-RAY DIFFRACTIONr_metal_ion_refined0.0530.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1550.212
X-RAY DIFFRACTIONr_nbd_other0.20.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1040.29
X-RAY DIFFRACTIONr_mcbond_it0.691.561594
X-RAY DIFFRACTIONr_mcbond_other0.6781.5591593
X-RAY DIFFRACTIONr_mcangle_it1.1582.3361990
X-RAY DIFFRACTIONr_mcangle_other1.1592.3381991
X-RAY DIFFRACTIONr_scbond_it1.0321.7321497
X-RAY DIFFRACTIONr_scbond_other1.0321.7321498
X-RAY DIFFRACTIONr_scangle_it1.7312.5232228
X-RAY DIFFRACTIONr_scangle_other1.732.5232229
X-RAY DIFFRACTIONr_lrange_it3.10918.5183380
X-RAY DIFFRACTIONr_lrange_other3.09918.5013370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.410.375540.3061302X-RAY DIFFRACTION98.4749
2.41-2.4760.285470.291311X-RAY DIFFRACTION99.9264
2.476-2.5480.285670.2621190X-RAY DIFFRACTION100
2.548-2.6260.361580.2391220X-RAY DIFFRACTION100
2.626-2.7120.258480.2111197X-RAY DIFFRACTION99.9197
2.712-2.8080.269450.2171123X-RAY DIFFRACTION99.9145
2.808-2.9140.302540.2051118X-RAY DIFFRACTION99.9147
2.914-3.0330.278510.2051042X-RAY DIFFRACTION100
3.033-3.1670.28720.2041012X-RAY DIFFRACTION100
3.167-3.3220.262430.193987X-RAY DIFFRACTION99.903
3.322-3.5020.239490.167915X-RAY DIFFRACTION99.8964
3.502-3.7140.195470.144876X-RAY DIFFRACTION99.7838
3.714-3.970.188350.148846X-RAY DIFFRACTION99.8866
3.97-4.2880.191450.142794X-RAY DIFFRACTION100
4.288-4.6970.142490.125708X-RAY DIFFRACTION100
4.697-5.2520.202260.133666X-RAY DIFFRACTION100
5.252-6.0630.229290.177596X-RAY DIFFRACTION100
6.063-7.4250.146170.163521X-RAY DIFFRACTION100
7.425-10.4950.256290.124402X-RAY DIFFRACTION100
10.495-49.490.177130.245260X-RAY DIFFRACTION99.2727
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9297-0.58060.7121.9892-0.39122.15910.01-0.0140.02330.0847-0.08320.0729-0.0184-0.09290.07320.0118-0.00540.00730.0315-0.00540.0091-18.374819.908342.882
22.12470.6149-0.12542.4971-0.56282.6654-0.00730.0091-0.07610.04090.00790.0520.0777-0.0976-0.00060.04570.005-0.00160.0526-0.00790.0064-17.7896-2.839166.2015
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA12 - 214
2X-RAY DIFFRACTION2ALLBBB12 - 206

+
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