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- PDB-3kvo: Crystal structure of the catalytic domain of human Hydroxysteroid... -

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Basic information

Entry
Database: PDB / ID: 3kvo
TitleCrystal structure of the catalytic domain of human Hydroxysteroid dehydrogenase like 2 (HSDL2)
ComponentsHydroxysteroid dehydrogenase-like protein 2
KeywordsOXIDOREDUCTASE / HSDL2 / human Hydroxysteroid dehydrogenase like 2 / SDHL2 / Structural Genomics / Structural Genomics Consortium / SGC / NAD / NADP / Peroxisome
Function / homology
Function and homology information


Oxidoreductases / peroxisome / oxidoreductase activity / mitochondrion / membrane
Similarity search - Function
SCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain superfamily / 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 ...SCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain superfamily / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Hydroxysteroid dehydrogenase-like protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsUgochukwu, E. / Bhatia, C. / Huang, J. / Pilka, E. / Muniz, J.R.C. / Pike, A.C.W. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. ...Ugochukwu, E. / Bhatia, C. / Huang, J. / Pilka, E. / Muniz, J.R.C. / Pike, A.C.W. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / Verdin, E.M. / Oppermann, U. / Kavanagh, K.L. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the catalytic domain of human Hydroxysteroid dehydrogenase like 2 (HSDL2)
Authors: Ugochukwu, E. / Bhatia, C. / Huang, J. / Pilka, E. / Muniz, J.R.C. / Pike, A.C.W. / Krojer, T. / von Delft, F. / Verdin, E.M. / Oppermann, U. / Kavanagh, K.L.
History
DepositionNov 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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.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_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: Hydroxysteroid dehydrogenase-like protein 2
B: Hydroxysteroid dehydrogenase-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0696
Polymers74,0962
Non-polymers2,9744
Water1,856103
1
A: Hydroxysteroid dehydrogenase-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5353
Polymers37,0481
Non-polymers1,4872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hydroxysteroid dehydrogenase-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5353
Polymers37,0481
Non-polymers1,4872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-33 kcal/mol
Surface area21290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.149, 78.332, 121.765
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

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: NAP / End label comp-ID: NAP / Refine code: 5 / Auth seq-ID: 1 - 502 / Label seq-ID: 36

Dom-IDAuth asym-IDLabel asym-ID
1AA - D
2BB - F

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Components

#1: Protein Hydroxysteroid dehydrogenase-like protein 2


Mass: 37047.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSDL2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q6YN16, Oxidoreductases
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 1.97 Å3/Da / Density % sol: 37.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 0.1M BIS-TRIS pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97959 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97959 Å / Relative weight: 1
ReflectionResolution: 2.25→48.07 Å / Num. obs: 28262 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 9.4
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.895 / Mean I/σ(I) obs: 2 / Num. unique all: 17872 / Rsym value: 0.895 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.5.0089refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E03.pdb

3e03


Resolution: 2.25→48.07 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / SU B: 17.095 / SU ML: 0.182 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.313 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24679 1441 5.1 %RANDOM
Rwork0.19948 ---
all0.20187 26820 --
obs0.20187 26820 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.678 Å2
Baniso -1Baniso -2Baniso -3
1-3.44 Å20 Å20 Å2
2---1.99 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 2.25→48.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4078 0 142 103 4323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224360
X-RAY DIFFRACTIONr_bond_other_d0.0010.022816
X-RAY DIFFRACTIONr_angle_refined_deg1.4422.0095958
X-RAY DIFFRACTIONr_angle_other_deg0.90536968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8665558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.58325.17147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93915701
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8531511
X-RAY DIFFRACTIONr_chiral_restr0.0770.2698
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214759
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02774
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_it0.4811.52763
X-RAY DIFFRACTIONr_mcbond_other0.1081.51119
X-RAY DIFFRACTIONr_mcangle_it0.87624451
X-RAY DIFFRACTIONr_scbond_it1.57931597
X-RAY DIFFRACTIONr_scangle_it2.5014.51506
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1581MEDIUM POSITIONAL0.160.5
1811LOOSE POSITIONAL0.395
1581MEDIUM THERMAL1.392
1811LOOSE THERMAL1.7710
LS refinement shellResolution: 2.253→2.312 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 79 -
Rwork0.299 1903 -
obs--95.33 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.46050.086-1.45942.24270.58034.7146-0.02730.20040.1010.3579-0.09980.4289-0.1001-0.58690.1270.08380.0040.05470.0767-0.02980.143116.85894.638594.234
22.1026-0.3561-1.22333.01210.60813.55580.00870.20660.1926-0.3682-0.0478-0.3831-0.05970.27110.03910.0853-0.02110.01360.09190.07240.110238.86951.456567.0058
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 275
2X-RAY DIFFRACTION2B1 - 276

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