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- PDB-8wwd: Crystal structure of (S)-DHPS dehydrogenase HpsP from Dinoroseoba... -

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Basic information

Entry
Database: PDB / ID: 8wwd
TitleCrystal structure of (S)-DHPS dehydrogenase HpsP from Dinoroseobacter shibae DFL 12
ComponentsZinc-containing alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / Zn-dependent
Function / homology: / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / oxidoreductase activity / NAD(P)-binding domain superfamily / Zinc-containing alcohol dehydrogenase
Function and homology information
Biological speciesDinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
Revision 1.2Sep 18, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc-containing alcohol dehydrogenase
B: Zinc-containing alcohol dehydrogenase
C: Zinc-containing alcohol dehydrogenase
D: Zinc-containing alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,71114
Polymers141,0564
Non-polymers65410
Water10,791599
1
A: Zinc-containing alcohol dehydrogenase
hetero molecules

D: Zinc-containing alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8557
Polymers70,5282
Non-polymers3275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
Buried area3420 Å2
ΔGint-113 kcal/mol
Surface area25930 Å2
MethodPISA
2
B: Zinc-containing alcohol dehydrogenase
hetero molecules

C: Zinc-containing alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8557
Polymers70,5282
Non-polymers3275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area3400 Å2
ΔGint-113 kcal/mol
Surface area25070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.183, 290.538, 54.277
Angle α, β, γ (deg.)90.00, 98.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Zinc-containing alcohol dehydrogenase


Mass: 35264.109 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
Gene: Dshi_2036 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A8LPS1
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 599 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 18% PEG 3350, 0.2 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.3→48.47 Å / Num. obs: 56544 / % possible obs: 99.18 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.1744 / Rpim(I) all: 0.07174 / Net I/σ(I): 8.79
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.3612 / Mean I/σ(I) obs: 4.42 / Num. unique obs: 5608 / Rpim(I) all: 0.1443 / % possible all: 98.54

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48.47 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.879 / SU B: 8.302 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.488 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25766 2777 4.9 %RANDOM
Rwork0.20924 ---
obs0.21161 53779 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.204 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å2-0 Å2-0.17 Å2
2---0.1 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.3→48.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9800 0 10 599 10409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01310393
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179931
X-RAY DIFFRACTIONr_angle_refined_deg1.6771.64714196
X-RAY DIFFRACTIONr_angle_other_deg1.3141.57722764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.10951404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.14519.294538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.015151549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.91915118
X-RAY DIFFRACTIONr_chiral_restr0.0650.21387
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213669
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022383
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_it2.2483.0425529
X-RAY DIFFRACTIONr_mcbond_other2.2473.0425527
X-RAY DIFFRACTIONr_mcangle_it3.6154.566962
X-RAY DIFFRACTIONr_mcangle_other3.6154.566963
X-RAY DIFFRACTIONr_scbond_it2.4633.2894864
X-RAY DIFFRACTIONr_scbond_other2.4633.2894865
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.714.8467235
X-RAY DIFFRACTIONr_long_range_B_refined6.07336.27911431
X-RAY DIFFRACTIONr_long_range_B_other6.01136.26811304
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 201 -
Rwork0.249 4008 -
obs--98.11 %

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