[English] 日本語
Yorodumi
- PDB-3gvw: Single-chain UROD F217Y (YF) mutation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gvw
TitleSingle-chain UROD F217Y (YF) mutation
ComponentsUroporphyrinogen decarboxylase
KeywordsLYASE / uroporphyrinogen / decarboxylase / heme biosynthesis / Acetylation / Cytoplasm / Disease mutation / Phosphoprotein / Porphyrin biosynthesis
Function / homology
Function and homology information


porphyrin-containing compound catabolic process / uroporphyrinogen decarboxylase / uroporphyrinogen decarboxylase activity / porphyrin-containing compound metabolic process / heme O biosynthetic process / heme A biosynthetic process / heme B biosynthetic process / protoporphyrinogen IX biosynthetic process / Heme biosynthesis / heme biosynthetic process ...porphyrin-containing compound catabolic process / uroporphyrinogen decarboxylase / uroporphyrinogen decarboxylase activity / porphyrin-containing compound metabolic process / heme O biosynthetic process / heme A biosynthetic process / heme B biosynthetic process / protoporphyrinogen IX biosynthetic process / Heme biosynthesis / heme biosynthetic process / nucleoplasm / cytosol
Similarity search - Function
Uroporphyrinogen decarboxylase HemE / Uroporphyrinogen decarboxylase signature 1. / Uroporphyrinogen decarboxylase signature 2. / Uroporphyrinogen decarboxylase (URO-D) / Uroporphyrinogen decarboxylase (URO-D) / TIM Barrel - #210 / UROD/MetE-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Uroporphyrinogen decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsHill, C.P. / Phillips, J.D. / Whitby, F.G. / Warby, C. / Kushner, J.P.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Substrate shuttling between active sites of uroporphyrinogen decarboxylase is not required to generate coproporphyrinogen.
Authors: Phillips, J.D. / Warby, C.A. / Whitby, F.G. / Kushner, J.P. / Hill, C.P.
History
DepositionMar 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Oct 13, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uroporphyrinogen decarboxylase


Theoretical massNumber of molelcules
Total (without water)40,8481
Polymers40,8481
Non-polymers00
Water48627
1
A: Uroporphyrinogen decarboxylase

A: Uroporphyrinogen decarboxylase


Theoretical massNumber of molelcules
Total (without water)81,6962
Polymers81,6962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_676x-y+1,-y+2,-z+5/31
Buried area2300 Å2
ΔGint-6 kcal/mol
Surface area26700 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.291, 103.291, 71.463
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Uroporphyrinogen decarboxylase / URO-D / UPD


Mass: 40847.766 Da / Num. of mol.: 1 / Mutation: F217Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UROD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P06132, uroporphyrinogen decarboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.69 Å3/Da / Density % sol: 54.34 %
Crystal growMethod: hanging drop / Details: hanging drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 18, 2008 / Details: yale mirrors
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 7.5 % / Av σ(I) over netI: 19.75 / Number: 83299 / Rmerge(I) obs: 0.086 / Χ2: 1.03 / D res high: 2.8 Å / D res low: 40 Å / Num. obs: 11174 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.034099.710.0341.0076.9
4.796.0310010.0521.0077.5
4.184.7910010.0591.0167.4
3.84.1810010.0790.9527.5
3.533.810010.111.0277.5
3.323.5310010.1741.0187.5
3.153.3210010.2641.0727.5
3.023.1510010.3691.0577.6
2.93.0210010.5271.1257.5
2.82.910010.7041.0367.5
ReflectionResolution: 2.8→40 Å / Num. obs: 11174 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.086 / Χ2: 1.032 / Net I/σ(I): 19.754
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.8-2.97.50.70410671.036100
2.9-3.027.50.52711121.125100
3.02-3.157.60.36911081.057100
3.15-3.327.50.26410961.072100
3.32-3.537.50.17410971.018100
3.53-3.87.50.1111221.027100
3.8-4.187.50.07911170.952100
4.18-4.797.40.05911191.016100
4.79-6.037.50.05211411.007100
6.03-406.90.03411951.00799.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 2.8→33.81 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.903 / WRfactor Rfree: 0.27 / WRfactor Rwork: 0.188 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.784 / SU B: 16.09 / SU ML: 0.319 / SU Rfree: 0.423 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.423 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY THE PROTEIN IS A SINGLE-CHAIN FUSION DIMER OF HUMAN UROD WITH F217 MUTATED TO A Y IN THE SECOND OF THE TWO ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY THE PROTEIN IS A SINGLE-CHAIN FUSION DIMER OF HUMAN UROD WITH F217 MUTATED TO A Y IN THE SECOND OF THE TWO HALVES. BECAUSE THE CRYSTAL IS ISOMORPHOUS WITH WTUROD IN WHICH THERE IS A MONOMER IN THE ASYMMETRIC UNIT, WE HAVE MODELED Y217 IN TWO CONFORMATIONS AT ONE-HALF OCCUPANCY EACH. THIS ACCOUNTS FOR THE STOCHASTIC ARRANGEMENT OF THE FUSION DIMER IN THE CRYSTAL SUCH THAT RESIDUE 217 IS EFFECTIVELY HALF F AND HALF Y.
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1086 9.8 %RANDOM
Rwork0.194 ---
obs0.202 11111 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 128.62 Å2 / Biso mean: 70.948 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--3.69 Å2-1.85 Å20 Å2
2---3.69 Å20 Å2
3---5.54 Å2
Refinement stepCycle: LAST / Resolution: 2.8→33.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2811 0 0 27 2838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222884
X-RAY DIFFRACTIONr_angle_refined_deg1.7391.973921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0915357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.19723.209134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.40115468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1231524
X-RAY DIFFRACTIONr_chiral_restr0.1140.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212239
X-RAY DIFFRACTIONr_mcbond_it0.9441.51784
X-RAY DIFFRACTIONr_mcangle_it1.80622867
X-RAY DIFFRACTIONr_scbond_it2.08631100
X-RAY DIFFRACTIONr_scangle_it3.614.51054
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 83 -
Rwork0.244 718 -
all-801 -
obs--100 %

+
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