[English] 日本語
Yorodumi
- PDB-3c3e: Crystal structure of 2-phospho-(S)-lactate transferase from Metha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3c3e
TitleCrystal structure of 2-phospho-(S)-lactate transferase from Methanosarcina mazei in complex with Fo and GDP. Northeast Structural Genomics Consortium target MaR46
Components2-phospho-L-lactate transferase
KeywordsTRANSFERASE / alpha-beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Magnesium
Function / homology
Function and homology information


2-phospho-L-lactate transferase / LPPG:FO 2-phospho-L-lactate transferase activity / F420-0 metabolic process / magnesium ion binding
Similarity search - Function
CofD-like domain / CofD-like domains / Phosphoenolpyruvate transferase/2-phospho-L-lactate transferase / 2-phospho-L-lactate transferase CofD / CofD-like domain superfamily / 2-phospho-L-lactate transferase CofD / Helicase, Ruva Protein; domain 3 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...CofD-like domain / CofD-like domains / Phosphoenolpyruvate transferase/2-phospho-L-lactate transferase / 2-phospho-L-lactate transferase CofD / CofD-like domain superfamily / 2-phospho-L-lactate transferase CofD / Helicase, Ruva Protein; domain 3 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-FO1 / GUANOSINE-5'-DIPHOSPHATE / 2-phospho-L-lactate transferase
Similarity search - Component
Biological speciesMethanosarcina mazei Go1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsForouhar, F. / Abashidze, M. / Xu, H. / Grochowski, L.L. / Seetharaman, J. / Hussain, M. / Kuzin, A.P. / Chen, Y. / Zhou, W. / Xiao, R. ...Forouhar, F. / Abashidze, M. / Xu, H. / Grochowski, L.L. / Seetharaman, J. / Hussain, M. / Kuzin, A.P. / Chen, Y. / Zhou, W. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Galinier, A. / White, R.H. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Molecular insights into the biosynthesis of the f420 coenzyme.
Authors: Forouhar, F. / Abashidze, M. / Xu, H. / Grochowski, L.L. / Seetharaman, J. / Hussain, M. / Kuzin, A. / Chen, Y. / Zhou, W. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Galinier, A. / White, R.H. / Tong, L.
History
DepositionJan 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2-phospho-L-lactate transferase
B: 2-phospho-L-lactate transferase
C: 2-phospho-L-lactate transferase
D: 2-phospho-L-lactate transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,57912
Polymers139,3534
Non-polymers3,2268
Water68538
1
A: 2-phospho-L-lactate transferase
B: 2-phospho-L-lactate transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2906
Polymers69,6772
Non-polymers1,6134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
MethodPISA
2
C: 2-phospho-L-lactate transferase
D: 2-phospho-L-lactate transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2906
Polymers69,6772
Non-polymers1,6134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.544, 186.544, 67.790
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
Components

#1: Protein
2-phospho-L-lactate transferase / LPPG:FO / 2-phospho-(S)-lactate transferase


Mass: 34838.324 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei Go1 (archaea) / Species: Methanosarcina mazei / Strain: Go1 / DSM 3647 / Goe1 / JCM 11883 / OCM 88 / Gene: cofD, MM_1874 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic
References: UniProt: Q8PVT6, Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups
#2: Chemical
ChemComp-FO1 / 1-deoxy-1-(8-hydroxy-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-D-ribitol / 7,8-didemethyl-8-hydroxy-5-deazariboflavin


Mass: 363.322 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H17N3O7
#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.89 Å3/Da / Density % sol: 74.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM Fo, 5 mM GDP, 5 mM MgCl2, 5 mM DTT. Reservoir solution: 100 mM HEPES pH 6.8, 0.5% PEG 8000, 1.35 M Ammonium sulfate, VAPOR ...Details: Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM Fo, 5 mM GDP, 5 mM MgCl2, 5 mM DTT. Reservoir solution: 100 mM HEPES pH 6.8, 0.5% PEG 8000, 1.35 M Ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 11, 2005 / Details: Mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 3→28.69 Å / Num. all: 49264 / Num. obs: 49264 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 84.9 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.073 / Net I/σ(I): 12.13
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.345 / % possible all: 90.3

-
Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3C3D

3c3d


Resolution: 3→28.69 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 294429.51 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3958 10 %RANDOM
Rwork0.206 ---
obs0.206 39441 74.7 %-
all-49264 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.2239 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 84.9 Å2
Baniso -1Baniso -2Baniso -3
1--18.32 Å20 Å20 Å2
2---18.32 Å20 Å2
3---36.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.62 Å
Refinement stepCycle: LAST / Resolution: 3→28.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9444 0 180 38 9662
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.11 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.337 234 9.6 %
Rwork0.334 2192 -
obs--45.7 %

+
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