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- PDB-8zn9: A vast marine sulfonate-based carbon cycle fueled by novel sulfoq... -

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Basic information

Entry
Database: PDB / ID: 8zn9
TitleA vast marine sulfonate-based carbon cycle fueled by novel sulfoquinovosidases
ComponentsOxidoreductase, putative
KeywordsPROTEIN BINDING / ROSSMAN-fold
Function / homology
Function and homology information


: / Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Oxidoreductase, putative
Similarity search - Component
Biological speciesRoseobacter denitrificans OCh 114 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTang, K. / Ma, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: A vast marine sulfonate-based carbon cycle fueled by novel sulfoquinovosidases
Authors: Ma, X. / Tang, K.
History
DepositionMay 26, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxidoreductase, putative
B: Oxidoreductase, putative
C: Oxidoreductase, putative
D: Oxidoreductase, putative
E: Oxidoreductase, putative
F: Oxidoreductase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,56883
Polymers261,0536
Non-polymers11,51577
Water38,3002126
1
A: Oxidoreductase, putative
D: Oxidoreductase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,89128
Polymers87,0182
Non-polymers3,87426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10020 Å2
ΔGint-3 kcal/mol
Surface area29210 Å2
MethodPISA
2
B: Oxidoreductase, putative
C: Oxidoreductase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,10430
Polymers87,0182
Non-polymers4,08628
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10940 Å2
ΔGint15 kcal/mol
Surface area29530 Å2
MethodPISA
3
F: Oxidoreductase, putative
hetero molecules

E: Oxidoreductase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,57325
Polymers87,0182
Non-polymers3,55523
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area11850 Å2
ΔGint30 kcal/mol
Surface area27920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.920, 56.690, 217.300
Angle α, β, γ (deg.)90.00, 96.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Oxidoreductase, putative / Glycoside hydrolase


Mass: 43508.848 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Roseobacter denitrificans OCh 114 (bacteria)
Gene: RD1_2308 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q167F5
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 71 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2126 / 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: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 291.2 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 16 % PEG 10000

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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: Nov 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.8→30.48 Å / Num. obs: 232860 / % possible obs: 99.03 % / Redundancy: 6.7 % / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 11.01
Reflection shellResolution: 1.8→1.86 Å / Num. unique obs: 232860 / CC1/2: 0.999 / CC star: 1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→30.48 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 46.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 11721 5.06 %
Rwork0.2189 --
obs0.2198 231803 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→30.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16887 0 761 2126 19774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01818197
X-RAY DIFFRACTIONf_angle_d1.81324590
X-RAY DIFFRACTIONf_dihedral_angle_d24.2596825
X-RAY DIFFRACTIONf_chiral_restr0.0982678
X-RAY DIFFRACTIONf_plane_restr0.0113164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.42293980.38777338X-RAY DIFFRACTION99
1.82-1.840.41694110.38387217X-RAY DIFFRACTION99
1.84-1.860.37554060.36297293X-RAY DIFFRACTION100
1.86-1.893877413X-RAY DIFFRACTION99
1.89-1.910.38653940.33777222X-RAY DIFFRACTION99
1.91-1.940.35513880.33447340X-RAY DIFFRACTION99
1.94-1.973517317X-RAY DIFFRACTION99
1.97-20.32443870.3097341X-RAY DIFFRACTION99
2-2.030.31373800.29427369X-RAY DIFFRACTION99
2.03-2.060.30594020.28557199X-RAY DIFFRACTION99
2.06-2.10.31123830.28697395X-RAY DIFFRACTION99
2.1-2.130.29463960.27347244X-RAY DIFFRACTION99
2.13-2.180.26293770.25557375X-RAY DIFFRACTION99
2.18-2.220.25864020.25117260X-RAY DIFFRACTION99
2.22-2.270.26323880.24287442X-RAY DIFFRACTION99
2.27-2.320.24693770.23617240X-RAY DIFFRACTION99
2.32-2.380.24933900.22697344X-RAY DIFFRACTION99
2.38-2.440.24243950.21837307X-RAY DIFFRACTION99
2.44-2.510.22813830.21157306X-RAY DIFFRACTION99
2.51-2.60.24314160.20857336X-RAY DIFFRACTION99
2.6-2.690.2154120.19237326X-RAY DIFFRACTION99
2.69-2.83477370X-RAY DIFFRACTION99
2.8-2.920.20354160.19247318X-RAY DIFFRACTION99
2.92-3.080.21383660.19487429X-RAY DIFFRACTION99
3.08-3.270.20834090.18437394X-RAY DIFFRACTION100
3.27-3.520.21043800.17397433X-RAY DIFFRACTION99
3.52-3.880.17773960.15657401X-RAY DIFFRACTION100
3.88-4.430.14394100.13677456X-RAY DIFFRACTION99
4.44-5.580.17353860.14447524X-RAY DIFFRACTION100

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