[English] 日本語
Yorodumi
- PDB-4hkp: Crystal structure of human orotidine 5'-monophosphate decarboxyla... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hkp
TitleCrystal structure of human orotidine 5'-monophosphate decarboxylase complexed with CMP-N3-oxide
ComponentsUridine 5'-monophosphate synthase
KeywordsLYASE/LYASE INHIBITOR / Alpha-Beta Barrel / decarboxylase / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


UMP biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / Pyrimidine biosynthesis / UDP biosynthetic process / orotidine-5'-phosphate decarboxylase / 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 / UDP biosynthetic process / orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / lactation / female pregnancy / cellular response to xenobiotic stimulus / identical protein binding / nucleus / cytosol / cytoplasm
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
N-hydroxycytidine 5'-(dihydrogen phosphate) / 5-hydroxycytidine 5'-(dihydrogen phosphate) / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsTo, T.K. / Kotra, L.P. / Pai, E.F.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Novel cytidine-based orotidine-5'-monophosphate decarboxylase inhibitors with an unusual twist.
Authors: Purohit, M.K. / Poduch, E. / Wei, L.W. / Crandall, I.E. / To, T. / Kain, K.C. / Pai, E.F. / Kotra, L.P.
History
DepositionOct 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 2.0Aug 4, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.type / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uridine 5'-monophosphate synthase
B: Uridine 5'-monophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,67811
Polymers68,1082
Non-polymers1,5709
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-25 kcal/mol
Surface area18190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.290, 61.775, 70.523
Angle α, β, γ (deg.)90.00, 112.90, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Uridine 5'-monophosphate synthase / UMP synthase / Orotate phosphoribosyltransferase / OPRT / OPRTase / Orotidine 5'-phosphate ...UMP synthase / Orotate phosphoribosyltransferase / OPRT / OPRTase / Orotidine 5'-phosphate decarboxylase / ODC / OMPdecase


Mass: 34054.156 Da / Num. of mol.: 2 / Fragment: UNP residues 190-480
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UMPS, OK/SW-cl.21 / Production host: Escherichia coli (E. coli)
References: UniProt: P11172, orotidine-5'-phosphate decarboxylase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-TKW / 5-hydroxycytidine 5'-(dihydrogen phosphate)


Mass: 339.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O9P
#4: Chemical ChemComp-16B / N-hydroxycytidine 5'-(dihydrogen phosphate)


Type: RNA linking / Mass: 339.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O9P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.04 Å3/Da / Density % sol: 39.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6M-1.7M Ammonium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 53546 / % possible obs: 96.4 % / Redundancy: 4 % / Rmerge(I) obs: 0.041 / Χ2: 1.008 / Net I/σ(I): 16.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.75-1.813.40.24850951.094192.7
1.81-1.893.80.20752071.151194.3
1.89-1.974.10.15252311.125194.7
1.97-2.074.10.11552751.107195.4
2.07-2.24.20.08653201.047195.7
2.2-2.384.20.07153681.057197.1
2.38-2.614.20.05254210.987198.1
2.61-2.994.20.03854860.869198.6
2.99-3.774.20.02455470.795199.3
3.77-504.10.02255960.923198.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å15.48 Å
Translation3 Å15.48 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→64.97 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.1763 / WRfactor Rwork: 0.155 / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.8915 / SU B: 1.828 / SU ML: 0.059 / SU R Cruickshank DPI: 0.1059 / SU Rfree: 0.0988 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.186 2715 5.1 %RANDOM
Rwork0.161 ---
all0.161 ---
obs0.162 50805 96.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 56.98 Å2 / Biso mean: 17.8707 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20.75 Å2
2---0.45 Å20 Å2
3---0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.75→64.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3916 0 102 300 4318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224173
X-RAY DIFFRACTIONr_angle_refined_deg1.5922.0035653
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1485539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61923.772167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64515746
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7481529
X-RAY DIFFRACTIONr_chiral_restr0.1160.2654
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213044
X-RAY DIFFRACTIONr_mcbond_it0.7961.52579
X-RAY DIFFRACTIONr_mcangle_it1.52924142
X-RAY DIFFRACTIONr_scbond_it2.88231594
X-RAY DIFFRACTIONr_scangle_it4.8564.51498
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 201 -
Rwork0.282 3570 -
all-3771 -
obs--92.68 %

+
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