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- PDB-2czt: lipocalin-type prostaglandin D synthase -

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Basic information

Entry
Database: PDB / ID: 2czt
Titlelipocalin-type prostaglandin D synthase
ComponentsProstaglandin-H2 D-isomerase
KeywordsISOMERASE / LIPOCALIN / C2221 native / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


prostaglandin-D synthase / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / prostaglandin-D synthase activity / negative regulation of male germ cell proliferation / regulation of circadian sleep/wake cycle, sleep / retinoid binding / prostaglandin biosynthetic process / mast cell degranulation / rough endoplasmic reticulum / response to glucocorticoid ...prostaglandin-D synthase / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / prostaglandin-D synthase activity / negative regulation of male germ cell proliferation / regulation of circadian sleep/wake cycle, sleep / retinoid binding / prostaglandin biosynthetic process / mast cell degranulation / rough endoplasmic reticulum / response to glucocorticoid / fatty acid binding / gene expression / nuclear membrane / perinuclear region of cytoplasm / Golgi apparatus / extracellular space / extracellular region / nucleoplasm
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
Prostaglandin-H2 D-isomerase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKumasaka, T. / Irikura, D. / Ago, H. / Aritake, K. / Yamamoto, M. / Inoue, T. / Miyano, M. / Urade, Y. / Hayaishi, O. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Citation
Journal: J.Biol.Chem. / Year: 2009
Title: Structural basis of the catalytic mechanism operating in open-closed conformers of lipocalin type prostaglandin D synthase.
Authors: Kumasaka, T. / Aritake, K. / Ago, H. / Irikura, D. / Tsurumura, T. / Yamamoto, M. / Miyano, M. / Urade, Y. / Hayaishi, O.
#1: Journal: J.Biochem.(Tokyo) / Year: 2003
Title: Cloning, expression, crystallization, and preliminary X-ray analysis of recombinant mouse lipocalin-type prostaglandin D synthase, a somnogen-producing enzyme
Authors: Irikura, D. / Kumasaka, T. / Yamamoto, M. / Ago, H. / Miyano, M. / Kubata, K.B. / Sakai, H. / Hayaishi, O. / Urade, Y.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Lack of tactile pain (allodynia) in lipocalin-type prostaglandin D synthase-deficient mice
Authors: Eguchi, N. / Minami, T. / Shirafuji, N. / Kanaoka, Y. / Tanaka, T. / Nagata, A. / Yoshida, N. / Urade, Y. / Ito, S. / Hayaishi, O.
History
DepositionJul 17, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prostaglandin-H2 D-isomerase


Theoretical massNumber of molelcules
Total (without water)18,6181
Polymers18,6181
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.3, 67.1, 104.6
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Prostaglandin-H2 D-isomerase / Lipocalin-type prostaglandin-D synthase / Glutathione-independent PGD synthetase / Prostaglandin-H2 ...Lipocalin-type prostaglandin-D synthase / Glutathione-independent PGD synthetase / Prostaglandin-H2 D-isomerase / PGD2 synthase / PTGDS / PGDS


Mass: 18617.859 Da / Num. of mol.: 1 / Mutation: C65A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: O09114, prostaglandin-D synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, hanging drop / pH: 8
Details: sodium citrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.5K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.01 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 10, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionNum. obs: 11368
Reflection shellResolution: 2→10 Å / % possible all: 77.2

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→10 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.917 / SU B: 6.452 / SU ML: 0.181 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.365 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.278 850 9.8 %RANDOM
Rwork0.242 ---
all0.245 8773 --
obs0.245 7821 77.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.411 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å20 Å20 Å2
2--0.84 Å20 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1223 0 0 32 1255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211252
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.9531690
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8383153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.39115228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0920.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02943
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2950.3523
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.5117
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4410.337
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.6430.55
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8451.5770
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.76821237
X-RAY DIFFRACTIONr_scbond_it4.4283482
X-RAY DIFFRACTIONr_scangle_it6.4614.5453
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.314 48
Rwork0.266 490
Refinement TLS params.Method: refined / Origin x: 18.369 Å / Origin y: 14.63 Å / Origin z: 10.187 Å
111213212223313233
T0.094 Å2-0.0279 Å20.0052 Å2-0.2099 Å20.0963 Å2--0.0478 Å2
L5.6119 °20.1364 °2-0.4168 °2-1.7883 °20.1244 °2--5.3268 °2
S0.0455 Å °-0.6594 Å °-0.4957 Å °0.314 Å °-0.0103 Å °0.0883 Å °0.346 Å °-0.1142 Å °-0.0352 Å °

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