[English] 日本語
Yorodumi
- PDB-1p0k: IPP:DMAPP isomerase type II apo structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1p0k
TitleIPP:DMAPP isomerase type II apo structure
ComponentsIsopentenyl-diphosphate delta-isomeraseIsopentenyl-diphosphate delta isomerase
KeywordsISOMERASE / terpene biosynthesis / isopentenyl diphosphate / dimethylallyl diphosphate / flavoprotein
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 / IMP dehydrogenase / GMP reductase domain / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Isopentenyl-diphosphate delta-isomerase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.9 Å
AuthorsSteinbacher, S. / Kaiser, J. / Gerhardt, S. / Eisenreich, W. / Huber, R. / Bacher, A. / Rohdich, F.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal Structure of the Type II Isopentenyl Diphosphate:Dimethylallyl Diphosphate Isomerase from Bacillus subtilis
Authors: Steinbacher, S. / Kaiser, J. / Gerhardt, S. / Eisenreich, W. / Huber, R. / Bacher, A. / Rohdich, F.
History
DepositionApr 10, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)74,7154
Polymers74,5252
Non-polymers1902
Water9,692538
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)298,86016
Polymers298,1008
Non-polymers7608
Water1448
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
Buried area26330 Å2
ΔGint-244 kcal/mol
Surface area88240 Å2
MethodPISA
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)149,4308
Polymers149,0504
Non-polymers3804
Water724
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
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)149,4308
Polymers149,0504
Non-polymers3804
Water724
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
Unit cell
Length a, b, c (Å)115.833, 115.833, 141.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

-
Components

#1: Protein Isopentenyl-diphosphate delta-isomerase / Isopentenyl-diphosphate delta isomerase / IPP:DMAPP isomerase type II


Mass: 37262.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pQE30 / Production host: Escherichia coli (E. coli)
References: UniProt: P50740, isopentenyl-diphosphate Delta-isomerase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 538 / 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: 3.33 Å3/Da / Density % sol: 62.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.7
Details: PEG 400, pH 8.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
250 mMTris-HCl1drop
30.02 %(w/v)1droppH8.0NaN3
470 mMtricine1reservoir
530 mMTris-HCl1reservoir
6170 mM1reservoirNaCl
714 %(v/v)PEG4001reservoir
82.5 %(w/v)PEG80001reservoirpH8.7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 12, 2002 / Details: Osmic
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 72016 / Num. obs: 72016 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.043
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.47 / % possible all: 100
Reflection shell
*PLUS
Highest resolution: 1.9 Å / % possible obs: 100 % / Rmerge(I) obs: 0.47

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
CCP4model building
CNS1.1refinement
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→15 Å / Isotropic thermal model: isoptropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The bond dinstance of SD-CE in MET A 95 is slightly long
RfactorNum. reflection% reflectionSelection details
Rfree0.2209 3646 -random
Rwork0.1991 ---
all0.2002 71797 --
obs0.2002 71797 98.3 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.822 Å20 Å20 Å2
2--2.822 Å20 Å2
3----5.643 Å2
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4545 0 10 538 5093
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011313
X-RAY DIFFRACTIONc_angle_deg1.38744
Refinement
*PLUS
Rfactor Rfree: 0.221 / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.39

+
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