[English] 日本語
Yorodumi
- PDB-4ogu: The effects of Lysine 200 and Phenylalanine 239 Farnesyl Pyrophos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ogu
TitleThe effects of Lysine 200 and Phenylalanine 239 Farnesyl Pyrophosphate Synthase (FPPS) mutations on the catalytic activity, crystal structure and inhibition by nitrogen containing bisphosphonates
ComponentsFarnesyl pyrophosphate synthase
KeywordsTRANSFERASE / All Alpha-Helical / Prenyltransferase / Isoprene Biosynthesis / Lipid Biosynthesis / Steroid Biosynthesis / Isoprenoid Pathway / Cholesterol Synthesis
Function / homology
Function and homology information


geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / Cholesterol biosynthesis / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / peroxisome ...geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / Cholesterol biosynthesis / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / peroxisome / mitochondrial matrix / RNA binding / nucleoplasm / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Farnesyl pyrophosphate synthase-like / 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
PAMIDRONATE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTsoumpra, M.K. / Barnett, B.L. / Muniz, J.R.C. / Walter, R.L. / Ebetino, F.H. / von Delft, F. / Russell, R.G.G. / Oppermann, U. / Dunford, J.E.
CitationJournal: To be Published
Title: The effects of Lysine 200 and Phenylalanine 239 Farnesyl Pyrophosphate Synthase (FPPS) mutations on the catalytic activity, crystal structure and inhibition by nitrogen containing bisphosphonates
Authors: Tsoumpra, M.K. / Barnett, B.L. / Muniz, J.R.C. / Walter, R.L. / Ebetino, F.H. / von Delft, F. / Russell, R.G.G. / Oppermann, U. / Dunford, J.E.
History
DepositionJan 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Sep 20, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6536
Polymers43,0991
Non-polymers5545
Water1,964109
1
A: Farnesyl pyrophosphate synthase
hetero molecules

A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,30612
Polymers86,1982
Non-polymers1,10810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7040 Å2
ΔGint-75 kcal/mol
Surface area26140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.210, 111.210, 67.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-607-

HOH

-
Components

#1: Protein Farnesyl pyrophosphate synthase / FPP synthase / FPS / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / ...FPP synthase / FPS / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl diphosphate synthase / Geranyltranstransferase


Mass: 43098.914 Da / Num. of mol.: 1 / Fragment: UNP residues 67-419 / Mutation: F239A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FDPS, FPS, KIAA1293 / Plasmid: PET 11 Derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE)
References: UniProt: P14324, (2E,6E)-farnesyl diphosphate synthase, dimethylallyltranstransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE


Mass: 246.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O7P2
#4: Chemical ChemComp-210 / PAMIDRONATE / (3-AMINO-1-HYDROXY-1-PHOSPHONO-PROPYL)PHOSPHONIC ACID


Mass: 235.069 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H11NO7P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M NH4Cl, PEG 6000, 10% Ethylene Glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2009
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.1→51.12 Å / Num. all: 25182 / Num. obs: 25116 / % possible obs: 99.9 % / Observed criterion σ(F): 2.7 / Observed criterion σ(I): 2.7 / Redundancy: 10.6 % / Biso Wilson estimate: 41.24 Å2 / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 11.6
Reflection shellResolution: 2.1→2.21 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CP6

3cp6


Resolution: 2.1→24.4 Å / Cor.coef. Fo:Fc: 0.9512 / Cor.coef. Fo:Fc free: 0.9331 / SU R Cruickshank DPI: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2311 1284 5.11 %RANDOM
Rwork0.1973 ---
all0.199 25182 --
obs0.199 25116 99.83 %-
Displacement parametersBiso mean: 60.21 Å2
Baniso -1Baniso -2Baniso -3
1-1.5758 Å20 Å20 Å2
2--1.5758 Å20 Å2
3----3.1516 Å2
Refine analyzeLuzzati coordinate error obs: 0.355 Å
Refinement stepCycle: LAST / Resolution: 2.1→24.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2636 0 30 109 2775
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012769HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.963776HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1293SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes67HARMONIC2
X-RAY DIFFRACTIONt_gen_planes402HARMONIC5
X-RAY DIFFRACTIONt_it2769HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.63
X-RAY DIFFRACTIONt_other_torsion2.81
X-RAY DIFFRACTIONt_chiral_improper_torsion359SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3474SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.19 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2748 138 4.97 %
Rwork0.233 2638 -
all0.2351 2776 -
obs--99.83 %
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)
12.00681.51040.53343.8177-0.63671.03370.05-0.0877-0.01110.0341-0.1280.1506-0.1297-0.34250.078-0.30320.1520.152-0.0909-0.09050.2375-0.451230.44398.4617
22.31371.65110.09260.6002-0.45424.6370.0015-0.19580.02950.2307-0.05450.10890.0935-0.09670.0529-0.22270.09110.1011-0.1946-0.03690.30416.00825.769115.9039
35.1811-1.92181.5270.65360.92462.61430.01370.0135-0.06380.2207-0.02720.1954-0.0083-0.48060.0135-0.3040.10040.06060.03830.00290.304-5.30526.08470.1502
43.0634-0.05460.73552.78460.83152.238-0.0177-0.3966-0.12260.12340.01220.1183-0.1424-0.37840.0055-0.3040.07290.0474-0.2608-0.00710.303711.235125.37054.0537
53.21730.2622-0.77451.978-1.56542.6717-0.01210.319-0.1208-0.30160.01570.25080.1755-0.0598-0.0037-0.3040.0627-0.0448-0.1615-0.03580.30415.072424.51-13.862
64.13720.46950.12311.89820.28331.0633-0.04670.53720.2931-0.40660.0260.1989-0.1716-0.01190.0207-0.3040.0457-0.0513-0.1391-0.01070.30412.114334.8176-16.2734
74.0158-0.60650.00912.32230.33271.26880.18160.25180.4017-0.4163-0.3370.3262-0.2527-0.10780.1554-0.3040.0918-0.0893-0.1343-0.05750.3042.942437.9296-18.917
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|8 - 28}A8 - 28
2X-RAY DIFFRACTION2{A|29 - 52}A29 - 52
3X-RAY DIFFRACTION3{A|53 - 78}A53 - 78
4X-RAY DIFFRACTION4{A|79 - 152}A79 - 152
5X-RAY DIFFRACTION5{A|153 - 206}A153 - 206
6X-RAY DIFFRACTION6{A|207 - 294}A207 - 294
7X-RAY DIFFRACTION7{A|295 - 350}A295 - 350

+
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