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- PDB-8wwf: Crystal structure of (R)-DHPS dehydrogenase HpsO from Ruegeria po... -

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Basic information

Entry
Database: PDB / ID: 8wwf
TitleCrystal structure of (R)-DHPS dehydrogenase HpsO from Ruegeria pomeroyi DSS-3
Components(R)-DHPS dehydrogenase HpsO
KeywordsOXIDOREDUCTASE / NAD-dependent
Function / homologygluconate 5-dehydrogenase / gluconate 5-dehydrogenase activity / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / R or S-dihydroxypropanesulfonate-2-dehydrogenase
Function and homology information
Biological speciesRuegeria pomeroyi DSS-3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLiu, L. / Tang, K.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92251306 China
Other government2020YFA0608300
National Natural Science Foundation of China (NSFC)42188102 China
National Natural Science Foundation of China (NSFC)42276120 China
Other government121311KYSB20190029
CitationJournal: Isme J / Year: 2024
Title: Enantioselective transformation of phytoplankton-derived dihydroxypropanesulfonate by marine bacteria.
Authors: Liu, L. / Gao, X. / Dong, C. / Wang, H. / Chen, X. / Ma, X. / Liu, S. / Chen, Q. / Lin, D. / Jiao, N. / Tang, K.
History
DepositionOct 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: (R)-DHPS dehydrogenase HpsO
B: (R)-DHPS dehydrogenase HpsO
C: (R)-DHPS dehydrogenase HpsO
D: (R)-DHPS dehydrogenase HpsO


Theoretical massNumber of molelcules
Total (without water)105,8514
Polymers105,8514
Non-polymers00
Water20,1771120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12170 Å2
ΔGint-84 kcal/mol
Surface area32010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.140, 56.156, 76.185
Angle α, β, γ (deg.)96.27, 105.96, 90.70
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
(R)-DHPS dehydrogenase HpsO


Mass: 26462.756 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruegeria pomeroyi DSS-3 (bacteria) / Gene: hpsO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5LVV0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1120 / 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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4 / Details: 0.8 M Sodium formate, 0.1 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.7→41.95 Å / Num. obs: 93413 / % possible obs: 95.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 17.6
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 4549 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→41.95 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.809 / SU ML: 0.062 / Cross valid method: FREE R-VALUE / ESU R: 0.109 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19412 4672 5 %RANDOM
Rwork0.1572 ---
obs0.15906 88739 95.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.017 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.09 Å20.06 Å2
2--0.01 Å20.02 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.7→41.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7363 0 0 1120 8483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0197523
X-RAY DIFFRACTIONr_bond_other_d0.0020.027086
X-RAY DIFFRACTIONr_angle_refined_deg2.1241.95110244
X-RAY DIFFRACTIONr_angle_other_deg1.059316192
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5625996
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17522.897321
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.314151073
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0871568
X-RAY DIFFRACTIONr_chiral_restr0.1760.21132
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0218852
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021788
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_it1.81.6223996
X-RAY DIFFRACTIONr_mcbond_other1.81.6223995
X-RAY DIFFRACTIONr_mcangle_it2.4992.434988
X-RAY DIFFRACTIONr_mcangle_other2.4982.434989
X-RAY DIFFRACTIONr_scbond_it3.0291.9733527
X-RAY DIFFRACTIONr_scbond_other3.0291.9733528
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4472.8365257
X-RAY DIFFRACTIONr_long_range_B_refined6.49215.7359681
X-RAY DIFFRACTIONr_long_range_B_other6.13314.568913
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 340 -
Rwork0.193 6336 -
obs--93.14 %

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