[English] 日本語
Yorodumi
- PDB-1vcf: Crystal Structure of IPP isomerase at I422 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vcf
TitleCrystal Structure of IPP isomerase at I422
Componentsisopentenyl-diphosphate delta-isomerase
KeywordsISOMERASE / TIM barrel / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


isopentenyl-diphosphate Delta-isomerase / isopentenyl-diphosphate delta-isomerase activity / isoprenoid biosynthetic process / NADPH binding / FMN binding / oxidoreductase activity / magnesium ion binding / cytoplasm
Similarity search - Function
Isopentenyl-diphosphate delta-isomerase, FMN-dependent / FMN-dependent dehydrogenase / FMN-dependent dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / FLAVIN MONONUCLEOTIDE / Isopentenyl-diphosphate delta-isomerase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsWada, T. / Park, S.-Y. / Tame, R.H. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of IPP isomerase at I422
Authors: Wada, T. / Park, S.-Y. / Tame, R.H. / Kuramitsu, S. / Yokoyama, S.
History
DepositionMar 8, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_label_seq_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: isopentenyl-diphosphate delta-isomerase
B: isopentenyl-diphosphate delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7225
Polymers72,6962
Non-polymers1,0253
Water00
1
A: isopentenyl-diphosphate delta-isomerase
B: isopentenyl-diphosphate delta-isomerase
hetero molecules

A: isopentenyl-diphosphate delta-isomerase
B: isopentenyl-diphosphate delta-isomerase
hetero molecules

A: isopentenyl-diphosphate delta-isomerase
B: isopentenyl-diphosphate delta-isomerase
hetero molecules

A: isopentenyl-diphosphate delta-isomerase
B: isopentenyl-diphosphate delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,88620
Polymers290,7868
Non-polymers4,10012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_645-y+1,x-1,z1
crystal symmetry operation4_665y+1,-x+1,z1
2
A: isopentenyl-diphosphate delta-isomerase
hetero molecules

A: isopentenyl-diphosphate delta-isomerase
hetero molecules

A: isopentenyl-diphosphate delta-isomerase
hetero molecules

A: isopentenyl-diphosphate delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,66812
Polymers145,3934
Non-polymers2,2758
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_645-y+1,x-1,z1
crystal symmetry operation4_665y+1,-x+1,z1
Buried area11860 Å2
ΔGint-75 kcal/mol
Surface area44530 Å2
MethodPISA, PQS
3
B: isopentenyl-diphosphate delta-isomerase
hetero molecules

B: isopentenyl-diphosphate delta-isomerase
hetero molecules

B: isopentenyl-diphosphate delta-isomerase
hetero molecules

B: isopentenyl-diphosphate delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,2188
Polymers145,3934
Non-polymers1,8254
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_645-y+1,x-1,z1
crystal symmetry operation4_665y+1,-x+1,z1
Buried area11970 Å2
ΔGint-76 kcal/mol
Surface area43300 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)144.427, 144.427, 169.821
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

-
Components

#1: Protein isopentenyl-diphosphate delta-isomerase


Mass: 36348.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: Q746I8, isopentenyl-diphosphate Delta-isomerase
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Tris-HCl, sodium acetate, cadmium sulfate, glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9794, 0.9799, 0.9709, 0.9822
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 11, 2002
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97991
30.97091
40.98221
ReflectionResolution: 2.6→20 Å / Num. obs: 25755 / % possible obs: 92.3 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 26.5 Å2 / Rsym value: 0.05 / Net I/σ(I): 35.8
Reflection shellResolution: 2.6→2.69 Å / Mean I/σ(I) obs: 5.1 / Num. unique all: 1912 / Rsym value: 0.131 / % possible all: 69.6

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→19.94 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 637504.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1237 4.8 %RANDOM
Rwork0.242 ---
obs0.242 25702 92.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.7378 Å2 / ksol: 0.336304 e/Å3
Displacement parametersBiso mean: 55.4 Å2
Baniso -1Baniso -2Baniso -3
1--19.23 Å20 Å20 Å2
2---19.23 Å20 Å2
3---38.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4506 0 63 0 4569
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.12
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.452
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it3.32.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.375 155 4.6 %
Rwork0.349 3180 -
obs--73 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3FMN.PARAMFMN.TOP

+
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://pdbjlvh1.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