[English] 日本語
Yorodumi
- PDB-2qcm: Crystal structure of the orotidine-5'-monophosphate decarboxylase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qcm
TitleCrystal structure of the orotidine-5'-monophosphate decarboxylase domain (Asp312Asn mutant) of human UMP synthase bound to 6-hydroxymethyl-UMP
ComponentsUridine 5'-monophosphate synthase (UMP synthase)
KeywordsLYASE / UMP synthase / decarboxylase / catalytic proficiency
Function / homology
Function and homology information


UMP biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / Pyrimidine biosynthesis / orotidine-5'-phosphate decarboxylase / UDP biosynthetic process / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process ...UMP biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / Pyrimidine biosynthesis / orotidine-5'-phosphate decarboxylase / UDP biosynthetic process / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Orotate phosphoribosyl transferase domain / Orotate phosphoribosyltransferase / Purine/pyrimidine phosphoribosyl transferases signature. / Orotidine 5'-phosphate decarboxylase / Orotidine 5'-phosphate decarboxylase, active site / Orotidine 5'-phosphate decarboxylase active site. / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Phosphoribosyl transferase domain ...Orotate phosphoribosyl transferase domain / Orotate phosphoribosyltransferase / Purine/pyrimidine phosphoribosyl transferases signature. / Orotidine 5'-phosphate decarboxylase / Orotidine 5'-phosphate decarboxylase, active site / Orotidine 5'-phosphate decarboxylase active site. / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-JW5 / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsWittmann, J. / Rudolph, M.
CitationJournal: Structure / Year: 2008
Title: Structures of the human orotidine-5'-monophosphate decarboxylase support a covalent mechanism and provide a framework for drug design.
Authors: Wittmann, J.G. / Heinrich, D. / Gasow, K. / Frey, A. / Diederichsen, U. / Rudolph, M.G.
History
DepositionJun 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 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_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uridine 5'-monophosphate synthase (UMP synthase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6852
Polymers28,3311
Non-polymers3541
Water5,567309
1
A: Uridine 5'-monophosphate synthase (UMP synthase)
hetero molecules

A: Uridine 5'-monophosphate synthase (UMP synthase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3704
Polymers56,6622
Non-polymers7082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area5290 Å2
ΔGint-33 kcal/mol
Surface area18370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.378, 116.607, 61.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-485-

HOH

-
Components

#1: Protein Uridine 5'-monophosphate synthase (UMP synthase)


Mass: 28330.824 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UMPS / Plasmid: pETM-30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta 2(DE3)
References: UniProt: P11172, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-JW5 / 6-(HYDROXYMETHYL)URIDINE 5'-(DIHYDROGEN PHOSPHATE)


Type: RNA linking / Mass: 354.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O10P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5419 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.66→32.24 Å / Num. obs: 32717 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rsym value: 0.05 / Net I/σ(I): 26
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 2466 / Rsym value: 0.243 / % possible all: 73.9

-
Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→32.24 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.426 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The atoms that are in close contact have occupancy less than 1 and are mutually exclusive.
RfactorNum. reflection% reflectionSelection details
Rfree0.15927 1640 5 %RANDOM
Rwork0.14123 ---
obs0.14213 31057 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.58 Å2
Baniso -1Baniso -2Baniso -3
1-1.98 Å20 Å20 Å2
2---0.9 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 1.67→32.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2125 0 24 309 2458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222209
X-RAY DIFFRACTIONr_bond_other_d0.0020.021536
X-RAY DIFFRACTIONr_angle_refined_deg1.4212.0053023
X-RAY DIFFRACTIONr_angle_other_deg0.91933797
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7445309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34524.06296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07315425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2621517
X-RAY DIFFRACTIONr_chiral_restr0.0820.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022479
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02434
X-RAY DIFFRACTIONr_nbd_refined0.2260.2462
X-RAY DIFFRACTIONr_nbd_other0.2060.21674
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21071
X-RAY DIFFRACTIONr_nbtor_other0.0830.21162
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2239
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3210.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1421.51808
X-RAY DIFFRACTIONr_mcbond_other0.2051.5556
X-RAY DIFFRACTIONr_mcangle_it1.11322203
X-RAY DIFFRACTIONr_scbond_it2.1913954
X-RAY DIFFRACTIONr_scangle_it3.2084.5792
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.67→1.71 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 105 -
Rwork0.191 1929 -
obs--83.84 %

+
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