[English] 日本語
Yorodumi
- PDB-1i8j: CRYSTAL STRUCTURE OF PORPHOBILINOGEN SYNTHASE COMPLEXED WITH THE ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1i8j
TitleCRYSTAL STRUCTURE OF PORPHOBILINOGEN SYNTHASE COMPLEXED WITH THE INHIBITOR 4,7-DIOXOSEBACIC ACID
ComponentsPORPHOBILINOGEN SYNTHASEDelta-aminolevulinic acid dehydratase
KeywordsLYASE / HEME BIOSYNTHESIS / MAGNESIUM / 4 / 7-DIOXOSEBACIC ACID
Function / homology
Function and homology information


porphobilinogen synthase / porphobilinogen synthase activity / protoporphyrinogen IX biosynthetic process / heme biosynthetic process / magnesium ion binding / zinc ion binding / cytosol
Similarity search - Function
Delta-aminolevulinic acid dehydratase / Delta-aminolevulinic acid dehydratase, active site / Delta-aminolevulinic acid dehydratase / Delta-aminolevulinic acid dehydratase active site. / Delta-aminolevulinic acid dehydratase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
4,7-DIOXOSEBACIC ACID / Delta-aminolevulinic acid dehydratase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKervinen, J. / Jaffe, E.K. / Stauffer, F. / Neier, R. / Wlodawer, A. / Zdanov, A.
CitationJournal: Biochemistry / Year: 2001
Title: Mechanistic basis for suicide inactivation of porphobilinogen synthase by 4,7-dioxosebacic acid, an inhibitor that shows dramatic species selectivity.
Authors: Kervinen, J. / Jaffe, E.K. / Stauffer, F. / Neier, R. / Wlodawer, A. / Zdanov, A.
History
DepositionMar 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 9, 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 / struct_site
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.ptnr1_label_seq_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.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN Atoms C4 and C7 of DSB form a Schiff base to NZ of Lys246 and NZ of Lys194. The oxygens ...HETEROGEN Atoms C4 and C7 of DSB form a Schiff base to NZ of Lys246 and NZ of Lys194. The oxygens on the C4 and C7 are eliminated during this reaction.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PORPHOBILINOGEN SYNTHASE
B: PORPHOBILINOGEN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7158
Polymers71,0752
Non-polymers6406
Water5,693316
1
A: PORPHOBILINOGEN SYNTHASE
B: PORPHOBILINOGEN SYNTHASE
hetero molecules

A: PORPHOBILINOGEN SYNTHASE
B: PORPHOBILINOGEN SYNTHASE
hetero molecules

A: PORPHOBILINOGEN SYNTHASE
B: PORPHOBILINOGEN SYNTHASE
hetero molecules

A: PORPHOBILINOGEN SYNTHASE
B: PORPHOBILINOGEN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,86032
Polymers284,3018
Non-polymers2,55924
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area46270 Å2
ΔGint-379 kcal/mol
Surface area74710 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)128.741, 128.741, 142.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

-
Components

#1: Protein PORPHOBILINOGEN SYNTHASE / Delta-aminolevulinic acid dehydratase / DELTA-AMINOLEVULINIC ACID DEHYDRATASE / 5-AMINOLEVULINIC ACID DEHYDRATASE


Mass: 35537.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACB2, porphobilinogen synthase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-DSB / 4,7-DIOXOSEBACIC ACID


Mass: 230.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14O6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsATOMS C4 AND C7 OF DSB FORM A SCHIFF BASE TO NZ OF LYS246 AND NZ OF LYS194. THE OXYGENS ON THE C4 ...ATOMS C4 AND C7 OF DSB FORM A SCHIFF BASE TO NZ OF LYS246 AND NZ OF LYS194. THE OXYGENS ON THE C4 AND C7 ARE ELIMINATED DURING THIS REACTION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.16 Å3/Da / Density % sol: 70.43 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 3350, GLYCEROL, TRIS-HCL, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
19 mg/mlprotein1drop
250 mMTris-HCl1drop
310 mMbeta-mercaptoethanol1drop
40.020 mM1dropZnCl2
510 mM1dropMgCl2
62.5 %PEG33501reservoir
710 %glycerol1reservoir
80.1 MTris-HCl1reservoir
90.02 %sodium azide1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 10, 2000 / Details: OSMIC
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→35 Å / Num. all: 94638 / Num. obs: 94536 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 12
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.5 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 35 Å

-
Processing

Software
NameClassification
AMoREphasing
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1b4e

1b4e


Resolution: 1.9→35 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.247 9416 RANDOM
Rwork0.1983 --
all-94638 -
obs-94242 -
Refinement stepCycle: LAST / Resolution: 1.9→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4906 0 32 316 5254
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.91
X-RAY DIFFRACTIONc_bond_d0.018
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 35 Å / σ(F): 0 / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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