[English] 日本語
Yorodumi
- PDB-5hms: X-ray structure of human recombinant 5-aminolaevulinic acid dehyd... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hms
TitleX-ray structure of human recombinant 5-aminolaevulinic acid dehydratase (hrALAD).
ComponentsDelta-aminolevulinic acid dehydratase
KeywordsLYASE / TIM barrel / tetrapyrrole biosynthesis / dehydratase
Function / homology
Function and homology information


proteasome core complex binding / response to vitamin B1 / cellular response to lead ion / response to platinum ion / porphobilinogen synthase / porphobilinogen synthase activity / heme O biosynthetic process / heme A biosynthetic process / response to aluminum ion / negative regulation of proteasomal protein catabolic process ...proteasome core complex binding / response to vitamin B1 / cellular response to lead ion / response to platinum ion / porphobilinogen synthase / porphobilinogen synthase activity / heme O biosynthetic process / heme A biosynthetic process / response to aluminum ion / negative regulation of proteasomal protein catabolic process / heme B biosynthetic process / response to mercury ion / protoporphyrinogen IX biosynthetic process / response to fatty acid / response to selenium ion / response to cobalt ion / response to arsenic-containing substance / response to methylmercury / Heme biosynthesis / response to iron ion / heme biosynthetic process / response to herbicide / response to zinc ion / response to vitamin E / response to ionizing radiation / catalytic activity / response to amino acid / response to cadmium ion / cellular response to interleukin-4 / response to glucocorticoid / response to activity / protein homooligomerization / response to oxidative stress / response to ethanol / secretory granule lumen / response to lipopolysaccharide / ficolin-1-rich granule lumen / response to hypoxia / response to xenobiotic stimulus / Neutrophil degranulation / extracellular exosome / extracellular region / zinc ion binding / 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
Delta-aminolevulinic acid dehydratase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsButler, D. / Erskine, P.T. / Cooper, J.B. / Shoolingin-Jordan, P.M.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Structural studies of substrate and product complexes of 5-aminolaevulinic acid dehydratase from humans, Escherichia coli and the hyperthermophile Pyrobaculum calidifontis.
Authors: Mills-Davies, N. / Butler, D. / Norton, E. / Thompson, D. / Sarwar, M. / Guo, J. / Gill, R. / Azim, N. / Coker, A. / Wood, S.P. / Erskine, P.T. / Coates, L. / Cooper, J.B. / Rashid, N. / ...Authors: Mills-Davies, N. / Butler, D. / Norton, E. / Thompson, D. / Sarwar, M. / Guo, J. / Gill, R. / Azim, N. / Coker, A. / Wood, S.P. / Erskine, P.T. / Coates, L. / Cooper, J.B. / Rashid, N. / Akhtar, M. / Shoolingin-Jordan, P.M.
History
DepositionJan 17, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Mar 1, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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)72,8094
Polymers72,6782
Non-polymers1312
Water7,116395
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

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


Theoretical massNumber of molelcules
Total (without water)291,23416
Polymers290,7118
Non-polymers5238
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 area42480 Å2
ΔGint-543 kcal/mol
Surface area79540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.079, 127.079, 91.231
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

-
Components

#1: Protein Delta-aminolevulinic acid dehydratase / ALADH / Porphobilinogen synthase / 5-aminolaevulinic acid dehydratase


Mass: 36338.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALAD / Plasmid: pT7-7 / Production host: Escherichia coli BL21(DE3) (bacteria) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 0.1 M MES pH 6.2 - 6.5, 1 - 1.6 M ammonium sulphate, 10 mM dithiothreitol, 100 microM zinc chloride, 0 - 10 % dioxane.
PH range: 6.2 - 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 14, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.8→29.2 Å / Num. all: 18874 / Num. obs: 18874 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 69.1 Å2 / Rmerge(I) obs: 0.134 / Net I/σ(I): 11.1
Reflection shellResolution: 2.8→3 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 5.3 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 1.0E+51 / Resolution: 2.8→29.2 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.887 / SU B: 16.305 / SU ML: 0.323 / Cross valid method: THROUGHOUT / ESU R Free: 0.418 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26517 973 5.1 %RANDOM
Rwork0.17229 ---
obs0.17708 17923 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.649 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2---0.71 Å2-0 Å2
3---1.42 Å2
Refinement stepCycle: 1 / Resolution: 2.8→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5076 0 2 395 5473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195196
X-RAY DIFFRACTIONr_bond_other_d0.0020.024994
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.9747052
X-RAY DIFFRACTIONr_angle_other_deg1.05311482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.595656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.48522.613222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.00815848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4731546
X-RAY DIFFRACTIONr_chiral_restr0.0860.2778
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215870
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021180
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2074.9612630
X-RAY DIFFRACTIONr_mcbond_other3.2074.962629
X-RAY DIFFRACTIONr_mcangle_it5.3277.4343284
X-RAY DIFFRACTIONr_mcangle_other5.3277.4353285
X-RAY DIFFRACTIONr_scbond_it3.0745.2732566
X-RAY DIFFRACTIONr_scbond_other3.0735.2742567
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1637.7613769
X-RAY DIFFRACTIONr_long_range_B_refined9.12638.9215679
X-RAY DIFFRACTIONr_long_range_B_other9.08538.8015627
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 77 -
Rwork0.23 1244 -
obs--97.2 %

+
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