[English] 日本語
Yorodumi
- PDB-1pv8: Crystal structure of a low activity F12L mutant of human porphobi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pv8
TitleCrystal structure of a low activity F12L mutant of human porphobilinogen synthase
ComponentsDelta-aminolevulinic acid dehydratase
KeywordsLYASE / PORPHOBILINOGEN SYNTHASE / TETRAPYRROLE BIOSYNTHESIS / REACTION INTERMEDIATE
Function / homology
Function and homology information


proteasome core complex binding / response to vitamin B1 / response to platinum ion / porphobilinogen synthase / porphobilinogen synthase activity / heme B biosynthetic process / heme O biosynthetic process / heme A biosynthetic process / negative regulation of proteasomal protein catabolic process / cellular response to lead ion ...proteasome core complex binding / response to vitamin B1 / response to platinum ion / porphobilinogen synthase / porphobilinogen synthase activity / heme B biosynthetic process / heme O biosynthetic process / heme A biosynthetic process / negative regulation of proteasomal protein catabolic process / cellular response to lead ion / response to mercury ion / response to aluminum ion / response to selenium ion / protoporphyrinogen IX biosynthetic process / response to fatty acid / response to cobalt ion / response to methylmercury / response to arsenic-containing substance / response to iron ion / response to herbicide / Heme biosynthesis / heme biosynthetic process / response to ionizing radiation / response to zinc ion / response to vitamin E / response to amino acid / response to cadmium ion / catalytic activity / response to glucocorticoid / cellular response to interleukin-4 / response to activity / protein homooligomerization / response to ethanol / secretory granule lumen / response to oxidative stress / ficolin-1-rich granule lumen / response to lipopolysaccharide / response to hypoxia / response to xenobiotic stimulus / Neutrophil degranulation / extracellular exosome / zinc ion binding / extracellular region / identical protein binding / nucleus / 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
3-(2-AMINOETHYL)-4-(AMINOMETHYL)HEPTANEDIOIC ACID / Delta-aminolevulinic acid dehydratase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBreinig, S. / Kervinen, J. / Stith, L. / Wasson, A.S. / Fairman, R. / Wlodawer, A. / Zdanov, A. / Jaffe, E.K.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Control of tetrapyrrole biosynthesis by alternate quaternary forms of porphobilinogen synthase.
Authors: Breinig, S. / Kervinen, J. / Stith, L. / Wasson, A.S. / Fairman, R. / Wlodawer, A. / Zdanov, A. / Jaffe, E.K.
History
DepositionJun 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 600heterogen The porphobilinogen intermediate PB1 is bound to the enzyme active site at Lys252 and ...heterogen The porphobilinogen intermediate PB1 is bound to the enzyme active site at Lys252 and Lys199. The link between the C5 atom of PB1 and the NZ atom of Lys199 is a double bond.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Delta-aminolevulinic acid dehydratase
B: Delta-aminolevulinic acid dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9735
Polymers72,6102
Non-polymers3633
Water4,342241
1
A: Delta-aminolevulinic acid dehydratase
B: Delta-aminolevulinic acid dehydratase
hetero molecules

A: Delta-aminolevulinic acid dehydratase
B: Delta-aminolevulinic acid dehydratase
hetero molecules

A: Delta-aminolevulinic acid dehydratase
B: Delta-aminolevulinic acid dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,91815
Polymers217,8296
Non-polymers1,0899
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area20390 Å2
ΔGint-275 kcal/mol
Surface area61080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)89.571, 89.571, 153.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsThere is a dimer in the asymmetric unit. Biologically meaningful aggregate is hexamer made by crystallographic 6(3) axis.

-
Components

#1: Protein Delta-aminolevulinic acid dehydratase / / Porphobilinogen synthase / ALADH


Mass: 36304.836 Da / Num. of mol.: 2 / Mutation: F12L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALAD / Production host: Escherichia coli (E. coli) / References: UniProt: P13716, 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-PB1 / 3-(2-AMINOETHYL)-4-(AMINOMETHYL)HEPTANEDIOIC ACID


Mass: 232.277 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20N2O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50mM BTP, 10mM beta-mercaptoethanol, 10uM ZnCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14.0 mg/mlprotein1drop
20.4 Mmonoammonium hydrogen phosphate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 8, 2002
RadiationMonochromator: OSMIC optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→45 Å / Num. all: 35282 / Num. obs: 34615 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.05
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.2 / % possible all: 72.5
Reflection
*PLUS
Lowest resolution: 45 Å / Num. obs: 33615

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 1.0E+51 / Resolution: 2.2→45 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 198949.12 / Data cutoff high rms absF: 198949.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 3327 10 %RANDOM
Rwork0.199 ---
all0.21 34615 --
obs0.199 33434 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 86.5926 Å2 / ksol: 0.411764 e/Å3
Displacement parametersBiso mean: 39.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.87 Å24.32 Å20 Å2
2---3.87 Å20 Å2
3---7.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4238 0 18 241 4497
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d1.2
X-RAY DIFFRACTIONc_mcbond_it22.884.5
X-RAY DIFFRACTIONc_mcangle_it20.745
X-RAY DIFFRACTIONc_scbond_it25.554.5
X-RAY DIFFRACTIONc_scangle_it24.185
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.383 459 10.3 %
Rwork0.293 4003 -
obs--76.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMIONS.TOP
X-RAY DIFFRACTION4LIGANDS.PARLIGANDS.TOP
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.286
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.2

+
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