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- PDB-6jkh: The NAD+-bound form of human NSDHL -

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Basic information

Entry
Database: PDB / ID: 6jkh
TitleThe NAD+-bound form of human NSDHL
ComponentsSterol-4-alpha-carboxylate 3-dehydrogenase, decarboxylating
KeywordsOXIDOREDUCTASE / Cholesterol / dehydrogenase
Function / homology
Function and homology information


3beta-hydroxysteroid-4alpha-carboxylate 3-dehydrogenase (decarboxylating) / 3-beta-hydroxysteroid dehydrogenase [NAD(P)+]/C4-decarboxylase activity / 3-beta-hydroxysteroid dehydrogenase (NAD+)/C4-decarboxylase activity / 3-beta-hydroxy-Delta5-steroid dehydrogenase (NAD+) activity / Cholesterol biosynthesis / labyrinthine layer blood vessel development / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / smoothened signaling pathway / cholesterol biosynthetic process / hair follicle development ...3beta-hydroxysteroid-4alpha-carboxylate 3-dehydrogenase (decarboxylating) / 3-beta-hydroxysteroid dehydrogenase [NAD(P)+]/C4-decarboxylase activity / 3-beta-hydroxysteroid dehydrogenase (NAD+)/C4-decarboxylase activity / 3-beta-hydroxy-Delta5-steroid dehydrogenase (NAD+) activity / Cholesterol biosynthesis / labyrinthine layer blood vessel development / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / smoothened signaling pathway / cholesterol biosynthetic process / hair follicle development / lipid droplet / cholesterol metabolic process / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
3-beta hydroxysteroid dehydrogenase/isomerase / 3-beta hydroxysteroid dehydrogenase/isomerase family / : / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Sterol-4-alpha-carboxylate 3-dehydrogenase, decarboxylating
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKim, D. / Lee, S.J. / Lee, B.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2016R1C1B2014609 Korea, Republic Of
National Research Foundation (Korea)NRF-2018R1A2A1A19018526 Korea, Republic Of
National Research Foundation (Korea)NRF-2018R1A5A2024425 Korea, Republic Of
CitationJournal: Cell.Mol.Life Sci. / Year: 2021
Title: Crystal structures of human NSDHL and development of its novel inhibitor with the potential to suppress EGFR activity.
Authors: Kim, D.G. / Cho, S. / Lee, K.Y. / Cheon, S.H. / Yoon, H.J. / Lee, J.Y. / Kim, D. / Shin, K.S. / Koh, C.H. / Koo, J.S. / Choi, Y. / Lee, H.H. / Oh, Y.K. / Jeong, Y.S. / Chung, S.J. / Baek, M. ...Authors: Kim, D.G. / Cho, S. / Lee, K.Y. / Cheon, S.H. / Yoon, H.J. / Lee, J.Y. / Kim, D. / Shin, K.S. / Koh, C.H. / Koo, J.S. / Choi, Y. / Lee, H.H. / Oh, Y.K. / Jeong, Y.S. / Chung, S.J. / Baek, M. / Jung, K.Y. / Lim, H.J. / Kim, H.S. / Park, S.J. / Lee, J.Y. / Lee, S.J. / Lee, B.J.
History
DepositionFeb 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 24, 2021Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _struct.title
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sterol-4-alpha-carboxylate 3-dehydrogenase, decarboxylating
B: Sterol-4-alpha-carboxylate 3-dehydrogenase, decarboxylating
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8394
Polymers54,5122
Non-polymers1,3272
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-40 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.027, 77.366, 53.993
Angle α, β, γ (deg.)90.00, 96.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sterol-4-alpha-carboxylate 3-dehydrogenase, decarboxylating / Protein H105e3


Mass: 27256.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NSDHL, H105E3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q15738, 3beta-hydroxysteroid-4alpha-carboxylate 3-dehydrogenase (decarboxylating)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.22 Å3/Da / Density % sol: 44.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M calcium chloride, 44% PEG400, 0.1 M Tris, and pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 8240 / % possible obs: 99.8 % / Redundancy: 3.98 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 22.2
Reflection shellResolution: 3→3.05 Å / Rmerge(I) obs: 0.865 / Num. unique obs: 410

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WJ7

3wj7


Resolution: 3→27.41 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.87 / SU B: 16.514 / SU ML: 0.304 / Cross valid method: THROUGHOUT / ESU R Free: 0.482 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23841 426 5.2 %RANDOM
Rwork0.17323 ---
obs0.17632 7796 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.249 Å2
Baniso -1Baniso -2Baniso -3
1-2.61 Å2-0 Å2-1.39 Å2
2---1.6 Å2-0 Å2
3----0.66 Å2
Refinement stepCycle: 1 / Resolution: 3→27.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3293 0 88 18 3399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133450
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173191
X-RAY DIFFRACTIONr_angle_refined_deg1.491.6434677
X-RAY DIFFRACTIONr_angle_other_deg1.2831.5747409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5795417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0122.989174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.34515573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.421518
X-RAY DIFFRACTIONr_chiral_restr0.0610.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023828
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02704
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_it3.4474.3311686
X-RAY DIFFRACTIONr_mcbond_other3.4224.3311685
X-RAY DIFFRACTIONr_mcangle_it5.7186.4742097
X-RAY DIFFRACTIONr_mcangle_other5.726.4752098
X-RAY DIFFRACTIONr_scbond_it4.3495.0211764
X-RAY DIFFRACTIONr_scbond_other4.3485.0241765
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.2147.32581
X-RAY DIFFRACTIONr_long_range_B_refined10.05252.7443689
X-RAY DIFFRACTIONr_long_range_B_other10.05352.7573690
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.171 13 -
Rwork0.202 548 -
obs--95.25 %

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