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- PDB-1zsv: Crystal structure of human NADP-dependent leukotriene B4 12-hydro... -

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Basic information

Entry
Database: PDB / ID: 1zsv
TitleCrystal structure of human NADP-dependent leukotriene B4 12-hydroxydehydrogenase
ComponentsNADP-dependent leukotriene B4 12-hydroxydehydrogenase
KeywordsOXIDOREDUCTASE / medium-chain dehydrogenase/reductase family / leukotriene B4 / human / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


2-alkenal reductase (NADPH) activity / leukotriene B4 metabolic process / 13-lipoxin reductase activity / leukotriene B4 12-hydroxy dehydrogenase activity / lipoxin A4 metabolic process / 2-alkenal reductase [NAD(P)+] / 13,14-dehydro-15-oxoprostaglandin 13-reductase / 15-oxoprostaglandin 13-oxidase [NAD(P)+] activity / : / Synthesis of Lipoxins (LX) ...2-alkenal reductase (NADPH) activity / leukotriene B4 metabolic process / 13-lipoxin reductase activity / leukotriene B4 12-hydroxy dehydrogenase activity / lipoxin A4 metabolic process / 2-alkenal reductase [NAD(P)+] / 13,14-dehydro-15-oxoprostaglandin 13-reductase / 15-oxoprostaglandin 13-oxidase [NAD(P)+] activity / : / Synthesis 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 / Medium-chain dehydrogenase/reductase / Oxidoreductase, N-terminal domain / 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 / Medium-chain dehydrogenase/reductase / Oxidoreductase, N-terminal domain / 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
Prostaglandin reductase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTurnbull, A.P. / Johansson, C. / Savitsky, P. / Guo, K. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / von Delft, F. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human NADP-dependent leukotriene B4 12-hydroxydehydrogenase
Authors: Turnbull, A.P. / Johansson, C. / Savitsky, P. / Guo, K. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / von Delft, F. / Oppermann, U.
History
DepositionMay 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: NADP-dependent leukotriene B4 12-hydroxydehydrogenase
B: NADP-dependent leukotriene B4 12-hydroxydehydrogenase
C: NADP-dependent leukotriene B4 12-hydroxydehydrogenase
D: NADP-dependent leukotriene B4 12-hydroxydehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,69726
Polymers152,9174
Non-polymers78022
Water5,675315
1
A: NADP-dependent leukotriene B4 12-hydroxydehydrogenase
B: NADP-dependent leukotriene B4 12-hydroxydehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,81312
Polymers76,4582
Non-polymers35510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-131 kcal/mol
Surface area26890 Å2
MethodPISA
2
C: NADP-dependent leukotriene B4 12-hydroxydehydrogenase
D: NADP-dependent leukotriene B4 12-hydroxydehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,88414
Polymers76,4582
Non-polymers42512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-131 kcal/mol
Surface area26690 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10010 Å2
ΔGint-278 kcal/mol
Surface area51220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.543, 92.543, 202.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
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: 5 / Auth seq-ID: 2 - 329 / Label seq-ID: 22 - 349

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

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Components

#1: Protein
NADP-dependent leukotriene B4 12-hydroxydehydrogenase


Mass: 38229.164 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LTB4DH / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q14914
#2: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.8 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG3350, NaI, ethylene glycol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98402 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 9, 2005
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98402 Å / Relative weight: 1
ReflectionResolution: 2.3→67.57 Å / Num. all: 74944 / Num. obs: 74944 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.139
Reflection shellResolution: 2.3→2.42 Å / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V3V.pdb

1v3v


Resolution: 2.3→62.3 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.935 / SU B: 14.847 / SU ML: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.258 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24933 1920 2.6 %RANDOM
Rwork0.19511 ---
all0.1969 72302 --
obs0.1969 72302 98.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.497 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2---0.55 Å20 Å2
3---1.11 Å2
Refinement stepCycle: LAST / Resolution: 2.3→62.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9834 0 22 315 10171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02210040
X-RAY DIFFRACTIONr_bond_other_d0.0010.029388
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.98113619
X-RAY DIFFRACTIONr_angle_other_deg0.843321844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.38451308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.28925.101347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.573151708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9731524
X-RAY DIFFRACTIONr_chiral_restr0.0880.21564
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211100
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021876
X-RAY DIFFRACTIONr_nbd_refined0.190.21821
X-RAY DIFFRACTIONr_nbd_other0.1690.28928
X-RAY DIFFRACTIONr_nbtor_refined0.1750.24749
X-RAY DIFFRACTIONr_nbtor_other0.0880.25940
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2300
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1590.215
X-RAY DIFFRACTIONr_mcbond_it1.99137037
X-RAY DIFFRACTIONr_mcbond_other0.52332704
X-RAY DIFFRACTIONr_mcangle_it2.905510404
X-RAY DIFFRACTIONr_scbond_it5.18174008
X-RAY DIFFRACTIONr_scangle_it7.035113215
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1913medium positional0.130.5
2B1913medium positional0.130.5
3C1913medium positional0.130.5
4D1913medium positional0.130.5
1A2838loose positional0.375
2B2838loose positional0.395
3C2838loose positional0.385
4D2838loose positional0.395
1A1913medium thermal0.732
2B1913medium thermal0.752
3C1913medium thermal0.752
4D1913medium thermal0.732
1A2838loose thermal1.9110
2B2838loose thermal1.8910
3C2838loose thermal1.810
4D2838loose thermal1.8710
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 105 -
Rwork0.317 4456 -
obs-4456 82.3 %

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