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- PDB-8v36: Crystal structure of DHPS-3-dehydrogenase, HpsN from Cupriavidus ... -

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Basic information

Entry
Database: PDB / ID: 8v36
TitleCrystal structure of DHPS-3-dehydrogenase, HpsN from Cupriavidus pinatubonensis in complex with NADH
ComponentsSulfopropanediol 3-dehydrogenase
KeywordsOXIDOREDUCTASE / DHPS / sulfolactate / dehydrogenase
Function / homology
Function and homology information


sulfopropanediol 3-dehydrogenase / histidinol dehydrogenase activity / L-histidine biosynthetic process / NAD binding / zinc ion binding / cytosol
Similarity search - Function
Sulfopropanediol 3-dehydrogenase / Histidinol dehydrogenase, conserved site / Histidinol dehydrogenase / Histidinol dehydrogenase, monofunctional / Histidinol dehydrogenase / Histidinol dehydrogenase signature. / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Sulfopropanediol 3-dehydrogenase
Similarity search - Component
Biological speciesCupriavidus pinatubonensis JMP134 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.235 Å
AuthorsLee, M.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP210100233 Australia
Australian Research Council (ARC)DP210100235 Australia
CitationJournal: Chem Sci / Year: 2024
Title: Structural and kinetic insights into the stereospecific oxidation of R -2,3-dihydroxypropanesulfonate by DHPS-3-dehydrogenase from Cupriavidus pinatubonensis.
Authors: Burchill, L. / Kaur, A. / Nastasovici, A. / Lee, M. / Williams, S.J.
History
DepositionNov 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sulfopropanediol 3-dehydrogenase
B: Sulfopropanediol 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4446
Polymers93,9822
Non-polymers1,4624
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11280 Å2
ΔGint-133 kcal/mol
Surface area33070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.307, 87.556, 134.197
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sulfopropanediol 3-dehydrogenase


Mass: 46991.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus pinatubonensis JMP134 (bacteria)
Gene: hpsN / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q46N53
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES, magnesium chloride, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.235→44.73 Å / Num. obs: 44738 / % possible obs: 99.7 % / Redundancy: 6.7 % / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.022 / Net I/σ(I): 12.7
Reflection shellResolution: 2.24→2.31 Å / Rmerge(I) obs: 1.139 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3950 / CC1/2: 0.752 / Rpim(I) all: 0.512

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.235→43.896 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.264 / WRfactor Rwork: 0.211 / SU B: 12.074 / SU ML: 0.27 / Average fsc free: 0.9214 / Average fsc work: 0.9427 / Cross valid method: FREE R-VALUE / ESU R: 0.315 / ESU R Free: 0.249
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2805 2261 5.061 %
Rwork0.2226 42413 -
all0.226 --
obs-44674 99.639 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 71.98 Å2
Baniso -1Baniso -2Baniso -3
1-5.424 Å2-0 Å20 Å2
2---1.048 Å20 Å2
3----4.377 Å2
Refinement stepCycle: LAST / Resolution: 2.235→43.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6268 0 90 82 6440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0126483
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166096
X-RAY DIFFRACTIONr_angle_refined_deg0.921.6568826
X-RAY DIFFRACTIONr_angle_other_deg0.3151.57614004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1325825
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.439544
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.0551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.322101011
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.70710270
X-RAY DIFFRACTIONr_chiral_restr0.0420.21013
X-RAY DIFFRACTIONr_chiral_restr_other0.0070.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027679
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021447
X-RAY DIFFRACTIONr_nbd_refined0.2050.21369
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.25617
X-RAY DIFFRACTIONr_nbtor_refined0.1740.23183
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.23322
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2193
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1690.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0640.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0910.28
X-RAY DIFFRACTIONr_nbd_other0.2220.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0970.23
X-RAY DIFFRACTIONr_mcbond_it3.8027.2713315
X-RAY DIFFRACTIONr_mcbond_other3.8027.2713315
X-RAY DIFFRACTIONr_mcangle_it6.1513.0524132
X-RAY DIFFRACTIONr_mcangle_other6.14913.0534133
X-RAY DIFFRACTIONr_scbond_it3.5447.6123168
X-RAY DIFFRACTIONr_scbond_other3.5437.6123169
X-RAY DIFFRACTIONr_scangle_it5.89113.8734693
X-RAY DIFFRACTIONr_scangle_other5.8913.8734694
X-RAY DIFFRACTIONr_lrange_it8.96768.4227091
X-RAY DIFFRACTIONr_lrange_other8.96768.4637083
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.235-2.2930.3741560.36329790.36432720.8430.86495.8130.352
2.293-2.3560.3461570.35430070.35331640.8830.8761000.337
2.356-2.4240.3831490.33529600.33731090.8750.8991000.313
2.424-2.4980.3871790.31228450.31630240.9010.9221000.285
2.498-2.580.3261310.27427750.27629070.9260.94499.96560.242
2.58-2.670.3481390.28126840.28428240.9030.94399.96460.246
2.67-2.7710.3231250.25725960.2627230.9320.95799.92660.223
2.771-2.8830.3461450.25324850.25826300.9290.9581000.217
2.883-3.0110.2971220.24424060.24625280.9340.9611000.213
3.011-3.1570.2741130.25223040.25324170.9460.961000.22
3.157-3.3270.3251220.24721910.25123130.9240.9631000.225
3.327-3.5280.3071100.23320990.23622090.9410.9671000.215
3.528-3.7690.321990.22519570.22920570.9360.96999.95140.213
3.769-4.0690.2511080.20518190.20819290.9570.97499.89630.197
4.069-4.4530.233980.17716930.1817910.9630.981000.181
4.453-4.9730.216970.17615150.17916120.9690.9811000.186
4.973-5.730.255630.19114000.19414630.9650.9811000.197
5.73-6.9880.28680.20111680.20512360.9580.9771000.213
6.988-9.7590.196450.169610.16210070.9750.98599.90070.187
9.759-43.8960.314350.2495690.2536070.9220.95299.50580.294

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