[English] 日本語
Yorodumi
- PDB-2z4y: S. cerevisiae geranylgeranyl pyrophosphate synthase in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2z4y
TitleS. cerevisiae geranylgeranyl pyrophosphate synthase in complex with magnesium and BPH-252
ComponentsGeranylgeranyl pyrophosphate synthetase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / prenyltransferase / geranylgeranyl pyrophosphate / bisphosphonate / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Cholesterol biosynthesis / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / geranyl diphosphate biosynthetic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / dimethylallyltranstransferase / geranylgeranyl diphosphate synthase activity / (2E,6E)-farnesyl diphosphate synthase / terpenoid biosynthetic process / isoprenoid biosynthetic process ...Cholesterol biosynthesis / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / geranyl diphosphate biosynthetic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / dimethylallyltranstransferase / geranylgeranyl diphosphate synthase activity / (2E,6E)-farnesyl diphosphate synthase / terpenoid biosynthetic process / isoprenoid biosynthetic process / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / protein transport / mitochondrion / metal ion binding
Similarity search - Function
Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(1-HYDROXYNONANE-1,1-DIYL)BIS(PHOSPHONIC ACID) / Geranylgeranyl pyrophosphate synthase BTS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChen, C.K.-M. / Guo, R.T. / Hudock, M. / Cao, R. / Oldfield, E. / Wang, A.H.-J.
CitationJournal: J.Med.Chem. / Year: 2008
Title: Inhibition of geranylgeranyl diphosphate synthase by bisphosphonates: a crystallographic and computational investigation
Authors: Chen, C.K.-M. / Hudock, M.P. / Zhang, Y. / Guo, R.-T. / Cao, R. / No, J.H. / Liang, P.-H. / Ko, T.-P. / Chang, T.-H. / Chang, S.-C. / Song, Y. / Axelson, J. / Kumar, A. / Wang, A.H.-J. / Oldfield, E.
History
DepositionJun 26, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Geranylgeranyl pyrophosphate synthetase
B: Geranylgeranyl pyrophosphate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5356
Polymers78,5982
Non-polymers9374
Water7,044391
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8670 Å2
ΔGint-67 kcal/mol
Surface area23990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.952, 116.208, 126.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Geranylgeranyl pyrophosphate synthetase / GGPP synthetase / GGPPSase / Geranylgeranyl diphosphate synthase / BET2 suppressor protein 1


Mass: 39299.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pET32 Xa/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q12051, heptaprenyl diphosphate synthase, dimethylallyltranstransferase, (2E,6E)-farnesyl diphosphate synthase, geranylgeranyl diphosphate synthase
#2: Chemical ChemComp-252 / (1-HYDROXYNONANE-1,1-DIYL)BIS(PHOSPHONIC ACID)


Mass: 304.214 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H22O7P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.14 Å3/Da / Density % sol: 42.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.08M CH3COONa, 16% PEG 4000, 6-10% glycerol, 6-10% 1,2-propanediol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 23, 2007 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 40284 / Num. obs: 40023 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 29.1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 4.3 / Num. unique all: 3951 / % possible all: 99.7

-
Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DH4

2dh4


Resolution: 2.1→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1942 -RANDOM
Rwork0.181 ---
all-40284 --
obs-38785 96.3 %-
Displacement parametersBiso mean: 38.27 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati sigma a obs: 0.12 Å
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4663 0 55 391 5109
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg1.7
LS refinement shellResolution: 2.1→2.18 Å
RfactorNum. reflection% reflection
Rfree0.256 199 -
Rwork0.197 --
obs-3538 89.5 %

+
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