[English] 日本語
Yorodumi
- PDB-5hxp: Crystal Structure of Z,Z-Farnesyl Diphosphate Synthase (D71M, E75... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hxp
TitleCrystal Structure of Z,Z-Farnesyl Diphosphate Synthase (D71M, E75A and H103Y Mutants) Complexed with IPP
Components(2Z,6Z)-farnesyl diphosphate synthase, chloroplastic
KeywordsTRANSFERASE / prenyltransferase
Function / homology
Function and homology information


(2Z,6Z)-farnesyl diphosphate synthase / (2Z,6Z)-farnesyl diphosphate synthase activity / plastid membrane organization / ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] activity / polyprenol biosynthetic process / chloroplast stroma / response to cold / magnesium ion binding
Similarity search - Function
Di-trans-poly-cis-decaprenylcistransferase-like, conserved site / Undecaprenyl pyrophosphate synthase family signature. / Undecaprenyl pyrophosphate synthetase / Decaprenyl diphosphate synthase-like / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPENTYL PYROPHOSPHATE / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / (2Z,6Z)-farnesyl diphosphate synthase, chloroplastic
Similarity search - Component
Biological speciesSolanum habrochaites (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLee, C.C. / Chan, Y.T. / Wang, A.H.J.
CitationJournal: Acs Omega / Year: 2017
Title: Crystal Structure and Potential Head-to-Middle Condensation Function of aZ,Z-Farnesyl Diphosphate Synthase.
Authors: Chan, Y.T. / Ko, T.P. / Yao, S.H. / Chen, Y.W. / Lee, C.C. / Wang, A.H.
History
DepositionJan 31, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 8, 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
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.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.value / _struct_conn.pdbx_dist_value / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: (2Z,6Z)-farnesyl diphosphate synthase, chloroplastic
C: (2Z,6Z)-farnesyl diphosphate synthase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8658
Polymers53,5682
Non-polymers1,2976
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-11 kcal/mol
Surface area19050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.311, 64.545, 127.156
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein (2Z,6Z)-farnesyl diphosphate synthase, chloroplastic / Z / Z-FPP synthase / Z-farnesyl pyrophosphate synthase


Mass: 26783.754 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 72-303 / Mutation: E75A, H103Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum habrochaites (plant) / Gene: ZFPS / Plasmid: pET-32 Xa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: B8XA40, (2Z,6Z)-farnesyl diphosphate synthase
#2: Chemical ChemComp-IPR / ISOPENTYL PYROPHOSPHATE


Mass: 248.108 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H14O7P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-O4B / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE


Mass: 264.315 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5 / Details: 13% PEG 10K, 20mM 18-crown-6, 0.1M MES, pH 6.5

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. obs: 35453 / % possible obs: 99.7 % / Redundancy: 4 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 33
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data processing
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JP3

1jp3


Resolution: 1.95→25 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.906 / SU B: 4.039 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.165 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1761 5 %RANDOM
Rwork0.19916 ---
obs0.20134 33319 98.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.525 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0 Å2
2--0.05 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.95→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3587 0 79 204 3870
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023730
X-RAY DIFFRACTIONr_bond_other_d0.0040.023607
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.9845015
X-RAY DIFFRACTIONr_angle_other_deg1.2193.0128318
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4515444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.83824.971175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.16715681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2931517
X-RAY DIFFRACTIONr_chiral_restr0.070.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024112
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02839
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2492.1691785
X-RAY DIFFRACTIONr_mcbond_other1.2432.1681784
X-RAY DIFFRACTIONr_mcangle_it2.0583.2422226
X-RAY DIFFRACTIONr_mcangle_other2.0583.2432227
X-RAY DIFFRACTIONr_scbond_it1.5912.4411945
X-RAY DIFFRACTIONr_scbond_other1.592.4421946
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.63.5582790
X-RAY DIFFRACTIONr_long_range_B_refined4.85817.8754324
X-RAY DIFFRACTIONr_long_range_B_other4.85817.8834325
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.952→2.003 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 105 -
Rwork0.246 2079 -
obs--84.49 %

+
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