[English] 日本語
Yorodumi
- PDB-2pfd: Anisotropically refined structure of FTCD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pfd
TitleAnisotropically refined structure of FTCD
ComponentsFormimidoyltransferase-cyclodeaminase
KeywordsTransferase / Lyase / Protein assembly
Function / homology
Function and homology information


Histidine catabolism / glutamate formimidoyltransferase / formimidoyltetrahydrofolate cyclodeaminase / glutamate formimidoyltransferase activity / formimidoyltetrahydrofolate cyclodeaminase activity / intermediate filament binding / smooth endoplasmic reticulum membrane / histidine catabolic process to glutamate and formamide / histidine catabolic process to glutamate and formate / folic acid binding ...Histidine catabolism / glutamate formimidoyltransferase / formimidoyltetrahydrofolate cyclodeaminase / glutamate formimidoyltransferase activity / formimidoyltetrahydrofolate cyclodeaminase activity / intermediate filament binding / smooth endoplasmic reticulum membrane / histidine catabolic process to glutamate and formamide / histidine catabolic process to glutamate and formate / folic acid binding / endoplasmic reticulum-Golgi intermediate compartment / cytoskeleton organization / centriole / microtubule binding / Golgi membrane / Golgi apparatus / endoplasmic reticulum / plasma membrane / cytosol
Similarity search - Function
Formiminotetrahydrofolate cyclodeaminase monomer, up-and-down helical bundle / Formiminotransferase, C-terminal subdomain / Formiminotransferase-cyclodeaminase; Chain B, domain 1 / Formiminotransferase, N-terminal subdomain / Formiminotransferase catalytic domain / Formiminotransferase, N-terminal subdomain / Formiminotransferase, C-terminal subdomain / Formiminotransferase catalytic domain superfamily / Formiminotransferase, N-terminal subdomain superfamily / Formiminotransferase, C-terminal subdomain superfamily ...Formiminotetrahydrofolate cyclodeaminase monomer, up-and-down helical bundle / Formiminotransferase, C-terminal subdomain / Formiminotransferase-cyclodeaminase; Chain B, domain 1 / Formiminotransferase, N-terminal subdomain / Formiminotransferase catalytic domain / Formiminotransferase, N-terminal subdomain / Formiminotransferase, C-terminal subdomain / Formiminotransferase catalytic domain superfamily / Formiminotransferase, N-terminal subdomain superfamily / Formiminotransferase, C-terminal subdomain superfamily / Formiminotransferase domain / Formiminotransferase domain, N-terminal subdomain / Formiminotransferase domain / Formiminotransferase domain, N-terminal subdomain / Cyclodeaminase/cyclohydrolase / Formimidoyltransferase-cyclodeaminase-like superfamily / Formiminotransferase-cyclodeaminase / Four Helix Bundle (Hemerythrin (Met), subunit A) / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Formimidoyltransferase-cyclodeaminase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 3.42 Å
AuthorsPoon, B.K. / Chen, X. / Lu, M. / Quiocho, F.A. / Wang, Q. / Ma, J.
Citation
Journal: To be Published
Title: Anisotropically refined structure of FTCD
Authors: Poon, B.K. / Chen, X. / Lu, M. / Vyas, N.K. / Quiocho, F.A. / Wang, Q. / Ma, J.
#1: Journal: Embo J. / Year: 2004
Title: Structure of the bifunctional and Golgi-associated formiminotransferase cyclodeaminase octamer.
Authors: Mao, Y. / Vyas, N.K. / Vyas, M.N. / Chen, D.H. / Ludtke, S.J. / Chiu, W. / Quiocho, F.A.
History
DepositionApr 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 10, 2011Group: Other

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Formimidoyltransferase-cyclodeaminase
B: Formimidoyltransferase-cyclodeaminase
C: Formimidoyltransferase-cyclodeaminase
D: Formimidoyltransferase-cyclodeaminase


Theoretical massNumber of molelcules
Total (without water)237,6064
Polymers237,6064
Non-polymers00
Water0
1
A: Formimidoyltransferase-cyclodeaminase
B: Formimidoyltransferase-cyclodeaminase

A: Formimidoyltransferase-cyclodeaminase
B: Formimidoyltransferase-cyclodeaminase

A: Formimidoyltransferase-cyclodeaminase
B: Formimidoyltransferase-cyclodeaminase

A: Formimidoyltransferase-cyclodeaminase
B: Formimidoyltransferase-cyclodeaminase


Theoretical massNumber of molelcules
Total (without water)475,2128
Polymers475,2128
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
MethodPQS
2
C: Formimidoyltransferase-cyclodeaminase
D: Formimidoyltransferase-cyclodeaminase

C: Formimidoyltransferase-cyclodeaminase
D: Formimidoyltransferase-cyclodeaminase

C: Formimidoyltransferase-cyclodeaminase
D: Formimidoyltransferase-cyclodeaminase

C: Formimidoyltransferase-cyclodeaminase
D: Formimidoyltransferase-cyclodeaminase


Theoretical massNumber of molelcules
Total (without water)475,2128
Polymers475,2128
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)134.848, 134.848, 156.365
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: SER / End label comp-ID: GLU / Refine code: 1 / Auth seq-ID: 2 - 541 / Label seq-ID: 2 - 541

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
DetailsThe biological assembly is an octamer.

-
Components

#1: Protein
Formimidoyltransferase-cyclodeaminase / Formiminotransferase- cyclodeaminase / FTCD / 58 kDa microtubule-binding protein


Mass: 59401.473 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: Rat / Gene: Ftcd / Plasmid: PET-21(B) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O88618, glutamate formimidoyltransferase, formimidoyltetrahydrofolate cyclodeaminase

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.89 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1TT9.

-
Data collection

DetectorType: SBC-2
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
RefinementResolution: 3.42→10 Å / Cor.coef. Fo:Fc: 0.867 / Cor.coef. Fo:Fc free: 0.855 / SU B: 65.518 / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.615 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1712 4.9 %RANDOM
Rwork0.24 ---
all0.3 36957 --
obs0.241 34749 94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 74.751 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---0.37 Å20 Å2
3---0.74 Å2
Refinement stepCycle: LAST / Resolution: 3.42→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16524 0 0 0 16524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02216812
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.97922800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41152156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.68224.108740
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.879152876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.89515136
X-RAY DIFFRACTIONr_chiral_restr0.0980.22616
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212732
X-RAY DIFFRACTIONr_nbd_refined0.3020.29467
X-RAY DIFFRACTIONr_nbtor_refined0.3260.211485
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2750
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2720.2158
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.26
Refine LS restraints NCS

Ens-ID: 1 / Number: 4121 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT POSITIONAL / Weight position: 0.05

Dom-IDAuth asym-IDRms dev position (Å)
1A0.04
2B0.05
3C0.04
4D0.04
LS refinement shellResolution: 3.422→3.5 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 95 -
Rwork0.334 1856 -
obs-1951 99.9 %

+
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