[English] 日本語
Yorodumi
- PDB-4imo: Crystal structure of wild type human Lipocalin PGDS in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4imo
TitleCrystal structure of wild type human Lipocalin PGDS in complex with substrate analog U44069
ComponentsLipocalin-type prostaglandin-D synthase
KeywordsISOMERASE / Beta barrel / Endoplasmic reticulum
Function / homology
Function and homology information


prostaglandin-D synthase / prostaglandin-D synthase activity / negative regulation of male germ cell proliferation / Transcriptional regulation of testis differentiation / regulation of circadian sleep/wake cycle, sleep / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / cyclooxygenase pathway / retinoid binding / prostaglandin biosynthetic process / mast cell degranulation ...prostaglandin-D synthase / prostaglandin-D synthase activity / negative regulation of male germ cell proliferation / Transcriptional regulation of testis differentiation / regulation of circadian sleep/wake cycle, sleep / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / cyclooxygenase pathway / retinoid binding / prostaglandin biosynthetic process / mast cell degranulation / response to glucocorticoid / rough endoplasmic reticulum / fatty acid binding / gene expression / nuclear membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Lipocalin / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-PWZ / THIOCYANATE ION / Prostaglandin-H2 D-isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsLim, S.M. / Chen, D. / Teo, H. / Roos, A. / Nyman, T. / Tresaugues, L. / Pervushin, K. / Nordlund, P.
CitationJournal: J.Lipid Res. / Year: 2013
Title: Structural and dynamic insights into substrate binding and catalysis of human lipocalin prostaglandin D synthase.
Authors: Lim, S.M. / Chen, D. / Teo, H. / Roos, A. / Jansson, A.E. / Nyman, T. / Tresaugues, L. / Pervushin, K. / Nordlund, P.
History
DepositionJan 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lipocalin-type prostaglandin-D synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5655
Polymers19,7481
Non-polymers8174
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.240, 56.380, 72.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Lipocalin-type prostaglandin-D synthase / Beta-trace protein / Cerebrin-28 / Glutathione-independent PGD synthase / Prostaglandin-H2 D- ...Beta-trace protein / Cerebrin-28 / Glutathione-independent PGD synthase / Prostaglandin-H2 D-isomerase / Prostaglandin-D2 synthase / PGD2 synthase / PGDS / PGDS2


Mass: 19748.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDS, PTGDS / Plasmid: pNIC-CH4 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta BL21 / References: UniProt: P41222, prostaglandin-D synthase
#2: Chemical ChemComp-PWZ / (5E)-7-{(1R,4S,5S,6R)-5-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-2-oxabicyclo[2.2.1]hept-6-yl}hept-5-enoic acid


Mass: 350.492 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H34O4
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 1.89 Å3/Da / Density % sol: 34.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M potassium thiocyanate, 30% PEG MME 2000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 198 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 30, 2011
RadiationMonochromator: LN2-cooled, fixed-exit double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.88→36.49 Å / Num. all: 12735 / Num. obs: 12735 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 7.4
Reflection shellResolution: 1.88→1.98 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1826 / Rsym value: 0.274 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERMRphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CZT

2czt


Resolution: 1.88→36.49 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.34 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.165 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24154 620 4.9 %RANDOM
Rwork0.18911 ---
obs0.19174 12074 99.98 %-
all-12074 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.509 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2---0.71 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.88→36.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1215 0 56 82 1353
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021324
X-RAY DIFFRACTIONr_bond_other_d0.0070.021240
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.9871792
X-RAY DIFFRACTIONr_angle_other_deg1.4783.0162877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3165164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.65323.45555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99415214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.963158
X-RAY DIFFRACTIONr_chiral_restr0.0820.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211475
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02315
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 45 -
Rwork0.192 869 -
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