[English] 日本語
Yorodumi
- PDB-4n9u: The role of lysine 200 in the human farnesyl pyrophosphate syntha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4n9u
TitleThe role of lysine 200 in the human farnesyl pyrophosphate synthase catalytic mechanism and the mode of inhibition by the nitrogen-containing bisphosphonates
ComponentsFarnesyl pyrophosphate synthaseDimethylallyltranstransferase
KeywordsTRANSFERASE / alpha-helical prenyltransferase fold / Isoprene Biosynthesis / Lipid Synthesis / Steroid Biosynthesis / Dimethylallyl Pyrophosphate / Isopentenyl Pyrophosphate
Function / homology
Function and homology information


geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / dimethylallyltranstransferase activity / Cholesterol biosynthesis / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / RNA binding ...geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / dimethylallyltranstransferase activity / Cholesterol biosynthesis / 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
Chem-RIS / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsTsoumpra, M.K. / Muniz, J.R.C. / Barnett, B.L. / Pilka, E. / Kwaasi, A.A. / Kavanagh, K.L. / Evdokimov, A. / Walter, R.L. / Ebetino, F.H. / Oppermann, U. ...Tsoumpra, M.K. / Muniz, J.R.C. / Barnett, B.L. / Pilka, E. / Kwaasi, A.A. / Kavanagh, K.L. / Evdokimov, A. / Walter, R.L. / Ebetino, F.H. / Oppermann, U. / Russell, R.G.G. / Dunford, J.E.
CitationJournal: TO BE PUBLISHED
Title: The role of lysine 200 in the human farnesyl pyrophosphate synthase catalytic mechanism and the mode of inhibition by the nitrogen-containing bisphosphonates
Authors: Tsoumpra, M.K. / Muniz, J.R.C. / Barnett, B.L. / Pilka, E. / Kwaasi, A.A. / Kavanagh, K.L. / Evdokimov, A. / Walter, R.L. / Ebetino, F.H. / Oppermann, U. / Russell, R.G.G. / Dunford, J.E.
History
DepositionOct 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / 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: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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)43,5837
Polymers43,1031
Non-polymers4806
Water2,180121
1
A: Farnesyl pyrophosphate synthase
hetero molecules

A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,16614
Polymers86,2062
Non-polymers96012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area7090 Å2
ΔGint-63 kcal/mol
Surface area26030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.110, 111.110, 69.580
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-600-

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: 43102.879 Da / Num. of mol.: 1 / Fragment: UNP residues 67-419 / Mutation: K200G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FDPS, FPS, KIAA1293 / Plasmid: PET 11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
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-RIS / 1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID / Risedronate / Risedronic acid


Mass: 283.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11NO7P2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.49 Å3/Da / Density % sol: 50.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M NH4CL, PEG6000, 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: Sep 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: 2.11→52.09 Å / Num. all: 25635 / Num. obs: 25619 / % possible obs: 99.8 % / Observed criterion σ(F): 2.9 / Observed criterion σ(I): 2.9 / Biso Wilson estimate: 41.51 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 14.7
Reflection shellResolution: 2.11→2.2 Å / % possible all: 80.9

-
Processing

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

3cp6


Resolution: 2.11→49.69 Å / Cor.coef. Fo:Fc: 0.9515 / Cor.coef. Fo:Fc free: 0.9351 / SU R Cruickshank DPI: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2402 1303 5.1 %RANDOM
Rwork0.191 ---
obs0.1935 25568 99.75 %-
all-2835 --
Displacement parametersBiso mean: 61.93 Å2
Baniso -1Baniso -2Baniso -3
1-4.5317 Å20 Å20 Å2
2--4.5317 Å20 Å2
3----9.0635 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.11→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2662 0 28 121 2811
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012773HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.933769HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1288SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes71HARMONIC2
X-RAY DIFFRACTIONt_gen_planes401HARMONIC5
X-RAY DIFFRACTIONt_it2773HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.7
X-RAY DIFFRACTIONt_other_torsion2.97
X-RAY DIFFRACTIONt_chiral_improper_torsion355SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3439SEMIHARMONIC4
LS refinement shellResolution: 2.11→2.2 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2711 133 4.69 %
Rwork0.2287 2702 -
all0.2305 2835 -
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)
13.56681.055-0.58251.5194-1.56540.05-0.02950.08790.06020.17450.0722-0.0456-0.20610.1763-0.04270.0493-0.152-0.087-0.304-0.14770.275229.90530.876524.9107
20.6157-2.874-2.55360.12191.32495.12870.0009-0.28120.1460.40560.0332-0.1333-0.1563-0.1183-0.0342-0.2154-0.0648-0.0661-0.2818-0.040.30426.0072-15.876433.2467
33.25672.91040.57078.116-0.55463.79540.0433-0.09270.14630.2802-0.07020.0378-0.5387-0.00880.0269-0.0238-0.0823-0.003-0.3040.00870.30425.92595.577917.3363
41.8243-0.25540.01084.5538-0.37111.84640.1222-0.10330.11710.3912-0.04280.0487-0.31770.1093-0.0794-0.2505-0.0655-0.0077-0.304-0.0320.30425.4723-11.688421.3491
52.0453-0.1798-0.45722.6551-0.26391.6182-0.07090.18810.3543-0.05440.07740.2517-0.1822-0.1262-0.0065-0.304-0.0516-0.03-0.3040.03280.30419.0775-13.45698.9971
61.7585-0.46810.06193.63440.04741.2170.04610.35360.1039-0.3756-0.0478-0.22510.01610.09190.0017-0.2432-0.0382-0.0083-0.3040.05150.30433.5699-13.89910.6439
72.3698-0.61420.95995.0923-0.71721.1839-0.21890.39220.0819-0.52520.0765-0.46730.020.32010.1424-0.2103-0.06430.0838-0.3040.07890.30441.4552-8.0932-4.4737
81.29852.70871.25127.18861.83590.38890.03930.01280.12760.1556-0.0120.0654-0.0985-0.0608-0.0272-0.14340.0008-0.0574-0.3040.12550.30429.57656.53564.3729
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 - 177}A153 - 177
6X-RAY DIFFRACTION6{A|178 - 294}A178 - 294
7X-RAY DIFFRACTION7{A|295 - 332}A295 - 332
8X-RAY DIFFRACTION8{A|333 - 349}A333 - 349

+
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