[English] 日本語
Yorodumi
- PDB-4qxs: Crystal structure of human FPPS in complex with WC01088 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qxs
TitleCrystal structure of human FPPS in complex with WC01088
ComponentsFarnesyl pyrophosphate synthaseDimethylallyltranstransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / Cholesterol biosynthesis / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / RNA binding ...geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / Cholesterol biosynthesis / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / 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
PHOSPHATE ION / Chem-WC1 / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsPark, J. / Zielinski, M. / Weiling, C. / Tsantrizos, Y.S. / Berghuis, A.M.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2015
Title: Probing the molecular and structural elements of ligands binding to the active site versus an allosteric pocket of the human farnesyl pyrophosphate synthase.
Authors: Gritzalis, D. / Park, J. / Chiu, W. / Cho, H. / Lin, Y.S. / De Schutter, J.W. / Lacbay, C.M. / Zielinski, M. / Berghuis, A.M. / Tsantrizos, Y.S.
History
DepositionJul 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
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 / 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
F: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8785
Polymers43,1451
Non-polymers7334
Water2,594144
1
F: Farnesyl pyrophosphate synthase
hetero molecules

F: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,75710
Polymers86,2902
Non-polymers1,4678
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area5590 Å2
ΔGint-62 kcal/mol
Surface area27580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.650, 110.650, 77.920
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
11F-515-

HOH

21F-557-

HOH

-
Components

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


Mass: 43144.980 Da / Num. of mol.: 1 / Fragment: UNP residues 67-419
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FDPS, FPS, KIAA1293 / Production host: Escherichia coli (E. coli)
References: UniProt: P14324, (2E,6E)-farnesyl diphosphate synthase, dimethylallyltranstransferase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-WC1 / (2-{2-[(2S)-3-methylbutan-2-yl]-5-phenyl-1H-indol-3-yl}ethane-1,1-diyl)bis(phosphonic acid)


Mass: 451.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27NO6P2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.76 Å3/Da / Density % sol: 55.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.6 M ammonium phosphate, 20% glycerol, 0.08 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 8, 2014
RadiationMonochromator: ACCEL/Bruker double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.9→55.21 Å / Num. all: 38434 / Num. obs: 38434 / % possible obs: 99.4 % / Redundancy: 9.7 % / Biso Wilson estimate: 36.5 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 28.2
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 9.6 % / Rmerge(I) obs: 1.177 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2768 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
MxDCdata collection
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0073phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2F7M

2f7m


Resolution: 1.9→55.21 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.955 / SU B: 7.827 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20649 2023 5.3 %RANDOM
Rwork0.16952 ---
all0.17145 36355 --
obs0.17145 36355 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.447 Å2
Baniso -1Baniso -2Baniso -3
1--3.38 Å20 Å20 Å2
2---3.38 Å20 Å2
3---6.75 Å2
Refinement stepCycle: LAST / Resolution: 1.9→55.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2674 0 46 144 2864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022777
X-RAY DIFFRACTIONr_bond_other_d0.0020.022597
X-RAY DIFFRACTIONr_angle_refined_deg1.8661.9823780
X-RAY DIFFRACTIONr_angle_other_deg0.9073.0035942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8915340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53124.724127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8415445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0221512
X-RAY DIFFRACTIONr_chiral_restr0.1040.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023147
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02641
X-RAY DIFFRACTIONr_mcbond_it2.7693.3511363
X-RAY DIFFRACTIONr_mcbond_other2.7533.3491362
X-RAY DIFFRACTIONr_mcangle_it4.0025.0011702
X-RAY DIFFRACTIONr_mcangle_other4.0045.0021703
X-RAY DIFFRACTIONr_scbond_it3.8953.6351413
X-RAY DIFFRACTIONr_scbond_other3.8923.6351413
X-RAY DIFFRACTIONr_scangle_other5.5995.3432079
X-RAY DIFFRACTIONr_long_range_B_refined8.14528.1763394
X-RAY DIFFRACTIONr_long_range_B_other8.14428.1873395
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 149 -
Rwork0.305 2615 -
obs-2764 98.57 %
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)
112.95848.8388-8.5279.4133-4.354710.6279-0.3220.7171-0.2567-0.56780.15970.54920.5452-0.90580.16230.2145-0.1289-0.14050.3786-0.02020.2422.700180.62999.5944
29.3974-0.2436-0.69290.00830.01730.05390.0771-0.19940.3742-0.0163-0.01750.0001-0.00440.0085-0.05950.49180.0205-0.01160.38570.02370.365714.480490.7021-3.267
36.4570.1679-4.59673.0632-0.05915.5918-0.04510.6236-0.1299-0.50350.19010.61610.1112-0.6489-0.1450.1282-0.1024-0.09910.17880.02860.15795.746182.587314.6637
44.1573-0.1597-1.42892.7741-0.5432.0455-0.05490.1492-0.0862-0.17190.11690.3420.1285-0.2252-0.0620.0419-0.0389-0.01710.04390.01050.044112.78585.680619.2192
54.0845-0.9081-0.00574.4985-2.31483.9067-0.0347-0.42110.00040.4396-0.00790.0810.03080.34430.04260.0983-0.01080.05040.21350.00960.06149.900581.90735.9589
66.1562-2.22611.05664.547-2.29352.57720-0.3633-0.51410.2608-0.2425-0.14940.40350.45630.24240.25750.05380.09090.38420.14280.2311.446771.120241.921
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1F13 - 29
2X-RAY DIFFRACTION2F30 - 36
3X-RAY DIFFRACTION3F37 - 76
4X-RAY DIFFRACTION4F77 - 178
5X-RAY DIFFRACTION5F179 - 253
6X-RAY DIFFRACTION6F254 - 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