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- PDB-2gdz: Crystal structure of 15-hydroxyprostaglandin dehydrogenase type1,... -

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Basic information

Entry
Database: PDB / ID: 2gdz
TitleCrystal structure of 15-hydroxyprostaglandin dehydrogenase type1, complexed with NAD+
ComponentsNAD+-dependent 15-hydroxyprostaglandin dehydrogenase
KeywordsOXIDOREDUCTASE / hydroxyprostaglandin / dehydrogenase / Structural Genomics / SHORT-CHAIN DEHYDROGENASE/REDUCTASE / INFLAMMATION / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


15-hydroxyprostaglandin dehydrogenase (NAD+) / 15-hydroxyicosatetraenoate dehydrogenase / regulation of prostaglandin catabolic process / ductus arteriosus closure / ovulation / thrombin-activated receptor signaling pathway / prostaglandin E receptor activity / 15-hydroxyprostaglandin dehydrogenase (NAD+) activity / Synthesis of Lipoxins (LX) / parturition ...15-hydroxyprostaglandin dehydrogenase (NAD+) / 15-hydroxyicosatetraenoate dehydrogenase / regulation of prostaglandin catabolic process / ductus arteriosus closure / ovulation / thrombin-activated receptor signaling pathway / prostaglandin E receptor activity / 15-hydroxyprostaglandin dehydrogenase (NAD+) activity / Synthesis of Lipoxins (LX) / parturition / lipoxygenase pathway / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / prostaglandin metabolic process / negative regulation of cell cycle / NAD+ binding / positive regulation of vascular associated smooth muscle cell proliferation / transforming growth factor beta receptor signaling pathway / kidney development / female pregnancy / NAD binding / response to estradiol / basolateral plasma membrane / response to ethanol / response to lipopolysaccharide / positive regulation of apoptotic process / extracellular exosome / nucleoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 15-hydroxyprostaglandin dehydrogenase [NAD(+)]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsPilka, E.S. / Guo, K. / Kavanagh, K. / Von Delft, F. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Sundstrom, M. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2010
Title: High-Affinity Inhibitors of Human NAD-Dependent 15-Hydroxyprostaglandin Dehydrogenase: Mechanisms of Inhibition and Structure-Activity Relationships.
Authors: Niesen, F.H. / Schultz, L. / Jadhav, A. / Bhatia, C. / Guo, K. / Maloney, D.J. / Pilka, E.S. / Wang, M. / Oppermann, U. / Heightman, T.D. / Simeonov, A.
History
DepositionMar 17, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD+-dependent 15-hydroxyprostaglandin dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8432
Polymers29,1801
Non-polymers6631
Water5,386299
1
A: NAD+-dependent 15-hydroxyprostaglandin dehydrogenase
hetero molecules

A: NAD+-dependent 15-hydroxyprostaglandin dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6864
Polymers58,3592
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area7160 Å2
ΔGint-53 kcal/mol
Surface area19960 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)49.540, 49.540, 195.771
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe second part of the biological assembly is generated by the following symmetry operation: Y, X, -Z + (0 0 1)

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Components

#1: Protein NAD+-dependent 15-hydroxyprostaglandin dehydrogenase / 15 hydroxyprostaglandin dehydrogenase type1


Mass: 29179.539 Da / Num. of mol.: 1 / Fragment: residues (-1)-265
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET-SGC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-R3
References: UniProt: P15428, 15-hydroxyprostaglandin dehydrogenase (NAD+)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.06 Å3/Da / Density % sol: 40.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 PCB, 30% PEG 1000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: OSMIC
RadiationMonochromator: OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→196.12 Å / Num. all: 30422 / Num. obs: 30422 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.9 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 23.9
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.688 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WMB, 1IY8, 1ZK3

1wmb

1iy8

1zk3


Resolution: 1.65→21.86 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.826 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21214 1538 5.1 %RANDOM
Rwork0.17568 ---
all0.17746 28883 --
obs0.17746 28883 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.567 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2--0.38 Å20 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.65→21.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 44 299 2369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222136
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.9812899
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2845269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.23325.65292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52215372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.858157
X-RAY DIFFRACTIONr_chiral_restr0.1110.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021581
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.21146
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21484
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2241
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.292
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0541.51365
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48922116
X-RAY DIFFRACTIONr_scbond_it2.4823887
X-RAY DIFFRACTIONr_scangle_it3.7364.5781
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 105 -
Rwork0.381 1952 -
obs--94.71 %

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