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- PDB-9cp9: Crystal structure of DHPS-3-dehydrogenase, HpsN H319A variant fro... -

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Basic information

Entry
Database: PDB / ID: 9cp9
TitleCrystal structure of DHPS-3-dehydrogenase, HpsN H319A variant from Cupriavidus pinatubonensis in complex with substrate (R-DHPS) and NADH
ComponentsSulfopropanediol 3-dehydrogenase
KeywordsOXIDOREDUCTASE / DHPS-3-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: 2.013 Å
AuthorsLee, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) 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
DepositionJul 18, 2024Deposition 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)95,91011
Polymers93,8482
Non-polymers2,0629
Water8,269459
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Mass photometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13780 Å2
ΔGint-175 kcal/mol
Surface area29050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.324, 75.809, 84.674
Angle α, β, γ (deg.)90.000, 117.099, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Sulfopropanediol 3-dehydrogenase / 2 / 3-dihydroxypropane-1-sulfonate 3-dehydrogenase (sulfolactate forming) / DHPS 3-dehydrogenase ...2 / 3-dihydroxypropane-1-sulfonate 3-dehydrogenase (sulfolactate forming) / DHPS 3-dehydrogenase (sulfolactate forming)


Mass: 46924.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: HpsN H319A mutant
Source: (gene. exp.) Cupriavidus pinatubonensis JMP134 (bacteria)
Gene: hpsN, Reut_C6092 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q46N53, sulfopropanediol 3-dehydrogenase

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Non-polymers , 5 types, 468 molecules

#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: Chemical ChemComp-A1AZH / (2R)-2,3-dihydroxypropane-1-sulfonic acid


Mass: 156.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.55 Å3/Da / Density % sol: 51.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, BIS-TRIS, lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.01→43.82 Å / Num. obs: 62003 / % possible obs: 99.4 % / Redundancy: 3.9 % / CC1/2: 1 / Net I/σ(I): 7.6
Reflection shellResolution: 2.01→2.06 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4296 / CC1/2: 0.61

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.013→42.299 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.541 / SU ML: 0.117 / Cross valid method: FREE R-VALUE / ESU R: 0.165 / ESU R Free: 0.138
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1936 2921 4.713 %
Rwork0.1665 59063 -
all0.168 --
obs-61984 99.397 %
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: 29.161 Å2
Baniso -1Baniso -2Baniso -3
1-0.088 Å2-0 Å2-0.403 Å2
2--0.143 Å20 Å2
3---0.119 Å2
Refinement stepCycle: LAST / Resolution: 2.013→42.299 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6572 0 123 459 7154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0126832
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166406
X-RAY DIFFRACTIONr_angle_refined_deg1.2451.8179310
X-RAY DIFFRACTIONr_angle_other_deg0.4431.74914730
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2155868
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.596556
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.01452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.696101062
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.70110282
X-RAY DIFFRACTIONr_chiral_restr0.0620.21063
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028110
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021524
X-RAY DIFFRACTIONr_nbd_refined0.2060.21358
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.25757
X-RAY DIFFRACTIONr_nbtor_refined0.1730.23379
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.23383
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2429
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0040.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1250.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1020.26
X-RAY DIFFRACTIONr_nbd_other0.1610.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.28
X-RAY DIFFRACTIONr_mcbond_it1.5322.9223478
X-RAY DIFFRACTIONr_mcbond_other1.5312.9223478
X-RAY DIFFRACTIONr_mcangle_it2.3255.2514344
X-RAY DIFFRACTIONr_mcangle_other2.3255.2514345
X-RAY DIFFRACTIONr_scbond_it2.2983.2543354
X-RAY DIFFRACTIONr_scbond_other2.2793.243340
X-RAY DIFFRACTIONr_scangle_it3.7325.8424966
X-RAY DIFFRACTIONr_scangle_other3.7245.8184949
X-RAY DIFFRACTIONr_lrange_it4.91128.6517667
X-RAY DIFFRACTIONr_lrange_other4.84128.4577562
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
2.013-2.0650.2542090.26141190.26146120.9550.95193.84210.256
2.065-2.1220.242180.23942100.23944310.9630.96199.93230.23
2.122-2.1830.2472130.21841430.2243600.960.96899.90830.205
2.183-2.250.2392380.21539780.21642170.9620.9799.97630.199
2.25-2.3240.241760.20238940.20340750.9650.97499.87730.183
2.324-2.4050.2021480.19337770.19339250.9740.9771000.173
2.405-2.4950.2321880.17736480.1838380.9690.9899.94790.156
2.495-2.5970.2251830.15934990.16236830.970.98599.97280.139
2.597-2.7120.1771250.16334010.16335300.9790.98599.88670.142
2.712-2.8440.2031400.1532330.15233740.980.98799.97040.131
2.844-2.9970.191410.15230790.15332220.9770.98699.93790.135
2.997-3.1780.1931440.1628920.16230370.9780.98499.96710.144
3.178-3.3960.1811330.1627370.16128750.9780.98599.82610.147
3.396-3.6660.1991450.15925420.16126930.9760.98699.77720.152
3.666-4.0130.1791050.14823500.14924590.9820.98899.83730.143
4.013-4.4810.141040.12721220.12822290.9890.99199.86540.126
4.481-5.1650.1561000.13618820.13719870.9890.99199.74840.137
5.165-6.3020.222860.17315890.17616840.9810.98899.46560.168
6.302-8.8150.152810.14412420.14513250.9880.9999.84910.147
8.815-42.2990.179440.1847260.1847830.9830.98598.33970.211

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