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- PDB-9cp7: Crystal structure of DHPS-3-dehydrogenase, HpsN from Cupriavidus ... -

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Basic information

Entry
Database: PDB / ID: 9cp7
TitleCrystal structure of DHPS-3-dehydrogenase, HpsN from Cupriavidus pinatubonensis in complex with product analogue (L-cysteate) 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 / CYSTEINESULFONIC ACID / Sulfopropanediol 3-dehydrogenase
Similarity search - Component
Biological speciesCupriavidus pinatubonensis JMP134 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.751 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)95,7828
Polymers93,9822
Non-polymers1,8006
Water11,295627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13260 Å2
ΔGint-136 kcal/mol
Surface area29240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.931, 76.339, 85.076
Angle α, β, γ (deg.)90.000, 117.038, 90.000
Int Tables number4
Space group name H-MP1211

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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: Chemical ChemComp-OCS / CYSTEINESULFONIC ACID


Type: L-peptide linking / Mass: 169.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO5S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / 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: 2.56 Å3/Da / Density % sol: 51.93 %
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: Jun 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.75→43.898 Å / Num. obs: 94390 / % possible obs: 99.2 % / Redundancy: 2.9 % / CC1/2: 1 / Net I/σ(I): 10.6
Reflection shellResolution: 1.75→1.78 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4448 / CC1/2: 0.74

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.751→43.898 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.117 / SU ML: 0.065 / Cross valid method: FREE R-VALUE / ESU R: 0.093 / ESU R Free: 0.091
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1774 4773 5.058 %
Rwork0.1477 89595 -
all0.149 --
obs-94368 99.088 %
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: 22.437 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0 Å2-0.115 Å2
2--0.57 Å20 Å2
3----0.159 Å2
Refinement stepCycle: LAST / Resolution: 1.751→43.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6590 0 110 627 7327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0126918
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166502
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.829443
X-RAY DIFFRACTIONr_angle_other_deg0.5411.75214962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0645893
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.38560
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.01252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.876101088
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.23210290
X-RAY DIFFRACTIONr_chiral_restr0.0770.21076
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028273
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021561
X-RAY DIFFRACTIONr_nbd_refined0.2150.21324
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.25781
X-RAY DIFFRACTIONr_nbtor_refined0.1760.23407
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.23502
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2500
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0030.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0650.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2370.23
X-RAY DIFFRACTIONr_nbd_other0.1910.223
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1520.214
X-RAY DIFFRACTIONr_mcbond_it1.5692.1953506
X-RAY DIFFRACTIONr_mcbond_other1.5682.1953506
X-RAY DIFFRACTIONr_mcangle_it2.193.9414385
X-RAY DIFFRACTIONr_mcangle_other2.193.9424386
X-RAY DIFFRACTIONr_scbond_it2.6952.5553412
X-RAY DIFFRACTIONr_scbond_other2.6962.5563410
X-RAY DIFFRACTIONr_scangle_it4.3064.5275046
X-RAY DIFFRACTIONr_scangle_other4.3064.5275047
X-RAY DIFFRACTIONr_lrange_it5.24222.1027777
X-RAY DIFFRACTIONr_lrange_other5.1221.1047613
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
1.751-1.7960.2573220.21964220.2269950.9560.96896.41170.207
1.796-1.8450.2413340.20165540.20369030.9620.97499.78270.186
1.845-1.8990.1973560.17962080.1865750.9760.97999.83270.161
1.899-1.9570.23850.17160770.17364730.9740.98199.83010.153
1.957-2.0210.1953430.16258470.16462180.9760.98399.54970.143
2.021-2.0920.1952960.15457200.15660600.9760.98599.27390.136
2.092-2.1710.1853320.14455180.14758630.980.98899.77830.129
2.171-2.2590.1833070.13752790.1455960.9810.98999.82130.122
2.259-2.3590.1753010.13351100.13554250.9820.98999.74190.119
2.359-2.4740.1822900.13648350.13951390.980.98999.72760.122
2.474-2.6080.1792520.13346320.13649240.9810.9999.18770.122
2.608-2.7650.1791930.1444140.14246580.980.98998.90510.131
2.765-2.9550.1841770.14341660.14543820.980.98799.110.136
2.955-3.1910.2111360.16238920.16340630.9740.98499.13860.157
3.191-3.4930.191680.15435800.15537750.9790.98799.28480.155
3.493-3.9030.1451610.1432140.1434110.9870.9998.94460.146
3.903-4.50.1471550.1228210.12230270.9880.99298.31520.132
4.5-5.4980.144980.13324000.13325730.9920.99297.08510.148
5.498-7.7140.171080.15318440.15420030.9870.98997.45380.166
7.714-43.8980.122590.15810620.15611680.9920.98895.9760.19

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