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- PDB-2y05: Crystal structure of human leukotriene B4 12-hydroxydehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 2y05
TitleCrystal structure of human leukotriene B4 12-hydroxydehydrogenase in complex with NADP and raloxifene
ComponentsPROSTAGLANDIN REDUCTASE 1
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


leukotriene B4 metabolic process / 13-lipoxin reductase activity / leukotriene B4 12-hydroxy dehydrogenase activity / lipoxin A4 metabolic process / 2-alkenal reductase [NAD(P)+] / 2-alkenal reductase (NADPH) activity / 13,14-dehydro-15-oxoprostaglandin 13-reductase / 15-oxoprostaglandin 13-reductase [NAD(P)+] activity / Biosynthesis of Lipoxins (LX) / leukotriene metabolic process ...leukotriene B4 metabolic process / 13-lipoxin reductase activity / leukotriene B4 12-hydroxy dehydrogenase activity / lipoxin A4 metabolic process / 2-alkenal reductase [NAD(P)+] / 2-alkenal reductase (NADPH) activity / 13,14-dehydro-15-oxoprostaglandin 13-reductase / 15-oxoprostaglandin 13-reductase [NAD(P)+] activity / Biosynthesis of Lipoxins (LX) / leukotriene metabolic process / Synthesis of Leukotrienes (LT) and Eoxins (EX) / prostaglandin metabolic process / extracellular exosome / cytoplasm
Similarity search - Function
Leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase / Oxidoreductase, N-terminal domain / Medium-chain dehydrogenase/reductase / N-terminal domain of oxidoreductase / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase ...Leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase / Oxidoreductase, N-terminal domain / Medium-chain dehydrogenase/reductase / N-terminal domain of oxidoreductase / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / RALOXIFENE / Prostaglandin reductase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYue, W.W. / Shafqat, N. / Krojer, T. / Pike, A.C.W. / von Delft, F. / Sethi, R. / Savitsky, P. / Johansson, C. / Arrowsmith, C. / Weigelt, J. ...Yue, W.W. / Shafqat, N. / Krojer, T. / Pike, A.C.W. / von Delft, F. / Sethi, R. / Savitsky, P. / Johansson, C. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Bountra, C. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of Human Leukotriene B4 12-Hydroxydehydrogenase in Complex with Nadp and Raloxifene
Authors: Yue, W.W. / Shafqat, N. / Krojer, T. / Pike, A.C.W. / von Delft, F. / Sethi, R. / Savitsky, P. / Johansson, C. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Bountra, C. / Oppermann, U.
History
DepositionNov 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references / Structure summary / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: PROSTAGLANDIN REDUCTASE 1
B: PROSTAGLANDIN REDUCTASE 1
C: PROSTAGLANDIN REDUCTASE 1
D: PROSTAGLANDIN REDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,68724
Polymers143,0304
Non-polymers4,65720
Water7,891438
1
A: PROSTAGLANDIN REDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6438
Polymers35,7581
Non-polymers1,8867
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROSTAGLANDIN REDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6966
Polymers35,7581
Non-polymers9385
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PROSTAGLANDIN REDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7236
Polymers35,7581
Non-polymers9655
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PROSTAGLANDIN REDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6254
Polymers35,7581
Non-polymers8683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.274, 116.599, 154.607
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 4 / Auth seq-ID: 2 - 329 / Label seq-ID: 1 - 328

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
PROSTAGLANDIN REDUCTASE 1 / 15-OXOPROSTAGLANDIN 13-REDUCTASE / NADP-DEPENDENT LEUKOTRIENE B4 12-HYDROXYDEHYDROGENASE / PRG-1 / ...15-OXOPROSTAGLANDIN 13-REDUCTASE / NADP-DEPENDENT LEUKOTRIENE B4 12-HYDROXYDEHYDROGENASE / PRG-1 / LEUKOTRIENE B4 12-HYDROXYDEHYDROGENASE


Mass: 35757.516 Da / Num. of mol.: 4 / Fragment: MDR DOMAIN, RESIDUES 4-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2
References: UniProt: Q14914, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor, 13,14-dehydro-15-oxoprostaglandin 13-reductase, 2-alkenal reductase [NAD(P)+]

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Non-polymers , 5 types, 458 molecules

#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-RAL / RALOXIFENE


Mass: 473.583 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H27NO4S / Comment: medication*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / 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: 2.75 Å3/Da / Density % sol: 55.34 % / Description: NONE
Crystal growDetails: 10% PEG 10K, 8% ETGLY, 0.1M HEPES, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9788
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 24, 2008
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.2→59.5 Å / Num. obs: 82606 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.6 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZSV

1zsv


Resolution: 2.2→59.55 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.943 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23085 4025 5 %RANDOM
Rwork0.19383 ---
obs0.1957 77068 94.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.235 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.2→59.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9909 0 301 438 10648
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02210461
X-RAY DIFFRACTIONr_bond_other_d0.0020.027016
X-RAY DIFFRACTIONr_angle_refined_deg1.432.01714207
X-RAY DIFFRACTIONr_angle_other_deg0.873.00317107
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.11451318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.04825.125361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.835151763
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3861527
X-RAY DIFFRACTIONr_chiral_restr0.0780.21618
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111350
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021901
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.46336499
X-RAY DIFFRACTIONr_mcbond_other0.64432697
X-RAY DIFFRACTIONr_mcangle_it2.507510454
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.03373962
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.989113748
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 4059 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.260.5
2Bmedium positional0.30.5
3Cmedium positional0.30.5
4Dmedium positional0.250.5
1Amedium thermal1.072
2Bmedium thermal1.262
3Cmedium thermal1.022
4Dmedium thermal0.982
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 271 -
Rwork0.249 5754 -
obs--96.26 %

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