[English] 日本語
Yorodumi
- PDB-7ccz: Crystal structure of the ES2 intermediate form of human hydroxyme... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ccz
TitleCrystal structure of the ES2 intermediate form of human hydroxymethylbilane synthase
ComponentsPorphobilinogen deaminase
KeywordsTRANSFERASE / Porphyrin synthesis
Function / homology
Function and homology information


hydroxymethylbilane synthase / hydroxymethylbilane synthase activity / heme O biosynthetic process / heme B biosynthetic process / heme A biosynthetic process / protoporphyrinogen IX biosynthetic process / Heme biosynthesis / heme biosynthetic process / cytosol / cytoplasm
Similarity search - Function
Porphobilinogen deaminase / Porphobilinogen deaminase, N-terminal / Porphobilinogen deaminase, C-terminal / Porphobilinogen deaminase, dipyrromethane cofactor binding site / Porphobilinogen deaminase, C-terminal domain superfamily / Porphobilinogen deaminase, dipyromethane cofactor binding domain / Porphobilinogen deaminase, C-terminal domain / Porphobilinogen deaminase cofactor-binding site.
Similarity search - Domain/homology
Chem-7J8 / Porphobilinogen deaminase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsSato, H. / Sugishima, M. / Wada, K. / Hirabayashi, K. / Tsukaguchi, M.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24550201 Japan
Japan Society for the Promotion of Science (JSPS)15K07018 Japan
Japan Society for the Promotion of Science (JSPS)18K05326 Japan
CitationJournal: Biochem.J. / Year: 2021
Title: Crystal structures of hydroxymethylbilane synthase complexed with a substrate analog: a single substrate-binding site for four consecutive condensation steps.
Authors: Sato, H. / Sugishima, M. / Tsukaguchi, M. / Masuko, T. / Iijima, M. / Takano, M. / Omata, Y. / Hirabayashi, K. / Wada, K. / Hisaeda, Y. / Yamamoto, K.
History
DepositionJun 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Porphobilinogen deaminase
B: Porphobilinogen deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4444
Polymers78,7662
Non-polymers1,6782
Water6,593366
1
A: Porphobilinogen deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2222
Polymers39,3831
Non-polymers8391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Porphobilinogen deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2222
Polymers39,3831
Non-polymers8391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.454, 79.542, 108.678
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Porphobilinogen deaminase / PBG-D / Hydroxymethylbilane synthase / HMBS / Pre-uroporphyrinogen synthase


Mass: 39383.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HMBS, PBGD, UPS / Production host: Escherichia coli (E. coli) / References: UniProt: P08397, hydroxymethylbilane synthase
#2: Chemical ChemComp-7J8 / 3-[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-3-(3-hydroxy-3-oxopropyl)-5-methyl-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-1~{H}-pyrrol-3-yl]propanoic acid


Mass: 838.810 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H46N4O16 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: PEG 3350, diammonium hydrogen citrate, dithiothreitol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.79→45.2 Å / Num. obs: 66546 / % possible obs: 99.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 27.88 Å2 / CC1/2: 0.998 / Rsym value: 0.072 / Net I/σ(I): 9.33
Reflection shellResolution: 1.79→1.9 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 20529 / CC1/2: 0.688 / Rsym value: 1.081 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.18.2_3874refinement
XDSdata scaling
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ECR

3ecr


Resolution: 1.79→44.87 Å / SU ML: 0.2453 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.4229
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2428 3260 4.9 %
Rwork0.1982 63275 -
obs0.2004 66535 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.85 Å2
Refinement stepCycle: LAST / Resolution: 1.79→44.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4854 0 120 366 5340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00995116
X-RAY DIFFRACTIONf_angle_d1.21736962
X-RAY DIFFRACTIONf_chiral_restr0.0753802
X-RAY DIFFRACTIONf_plane_restr0.0067912
X-RAY DIFFRACTIONf_dihedral_angle_d22.37221898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.820.44061290.40322646X-RAY DIFFRACTION97.4
1.82-1.850.40231580.36752750X-RAY DIFFRACTION99.86
1.85-1.880.35621320.32722675X-RAY DIFFRACTION99.96
1.88-1.910.34111250.31122757X-RAY DIFFRACTION99.93
1.91-1.950.33951370.30612720X-RAY DIFFRACTION99.97
1.95-1.980.32451400.27062722X-RAY DIFFRACTION99.93
1.98-2.030.29971390.25372716X-RAY DIFFRACTION99.96
2.03-2.070.28291540.2342745X-RAY DIFFRACTION100
2.07-2.120.25251390.22132695X-RAY DIFFRACTION100
2.12-2.170.2571460.212727X-RAY DIFFRACTION99.97
2.17-2.230.24011370.21642761X-RAY DIFFRACTION100
2.23-2.290.30831410.22862721X-RAY DIFFRACTION99.51
2.29-2.370.26411220.21092755X-RAY DIFFRACTION100
2.37-2.450.25261630.2042733X-RAY DIFFRACTION100
2.45-2.550.25931370.21292746X-RAY DIFFRACTION99.97
2.55-2.670.24291460.20052754X-RAY DIFFRACTION100
2.67-2.810.27641420.19922748X-RAY DIFFRACTION99.9
2.81-2.980.23291510.19372763X-RAY DIFFRACTION100
2.98-3.210.20931290.19072789X-RAY DIFFRACTION100
3.22-3.540.23711420.18312787X-RAY DIFFRACTION99.97
3.54-4.050.22831630.15962778X-RAY DIFFRACTION99.93
4.05-5.10.16071370.15022846X-RAY DIFFRACTION99.93
5.1-44.870.23671510.17682941X-RAY DIFFRACTION99.07

+
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