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- PDB-8w9s: NAD-dependent dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 8w9s
TitleNAD-dependent dehydrogenase
Components
  • NADH-dependent dihydrogenase
  • RifT
KeywordsOXIDOREDUCTASE / heterodimer / NAD-dependent / dehydrogenase / rifamycin biosynthesis
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
: / : / : / GFO/IDH/MocA C-terminal 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 / : / NADH-dependent dihydrogenase / RifT
Similarity search - Component
Biological speciesAmycolatopsis mediterranei S699 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsNiu, M. / Shen, Y.M.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81530091 China
National Basic Research Program of China (973 Program)2019YFA0905402 China
CitationJournal: To Be Published
Title: Deciphering the Naphthalenic Ring Formation mechanism in the Biosynthesis of rifamycins
Authors: Niu, M. / Shen, Y.M.
History
DepositionSep 5, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 12, 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: NADH-dependent dihydrogenase
B: RifT
C: NADH-dependent dihydrogenase
D: RifT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,1097
Polymers123,1664
Non-polymers1,9433
Water12,340685
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11430 Å2
ΔGint-46 kcal/mol
Surface area43630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.539, 82.110, 88.555
Angle α, β, γ (deg.)90.00, 99.64, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-741-

HOH

21D-815-

HOH

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Components

#1: Protein NADH-dependent dihydrogenase


Mass: 35368.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis mediterranei S699 (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: O52541
#2: Protein RifT


Mass: 26214.416 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis mediterranei S699 (bacteria)
Gene: rifT / Production host: Escherichia coli (E. coli) / References: UniProt: O52542
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical ChemComp-US6 / (7E,9S,10S,11R,12R,13R,14R,15R,16S,17S,18E,20Z)-2,4,10,12,14,16-hexahydroxy-3,7,9,11,13,15,17,21-octamethyl-23-azatricyclo[22.3.1.05,27]octacosa-1,3,5(27),7,18,20,24-heptaene-6,22,26,28-tetrone / 34a-Deoxy-rifamycin W


Mass: 639.732 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H45NO10 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 685 / 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: 2.89 Å3/Da / Density % sol: 57.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: PEG3350, 0.2M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.09→87.32 Å / Num. obs: 77192 / % possible obs: 96.3 % / Redundancy: 4 % / Biso Wilson estimate: 31.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03349 / Net I/σ(I): 8.6
Reflection shellResolution: 2.09→2.2 Å / Num. unique obs: 77192 / CC1/2: 0.85

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→44.78 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2161 1910 2.59 %
Rwork0.1759 --
obs0.1769 73845 91.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→44.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8343 0 136 690 9169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088661
X-RAY DIFFRACTIONf_angle_d0.9611828
X-RAY DIFFRACTIONf_dihedral_angle_d17.2861265
X-RAY DIFFRACTIONf_chiral_restr0.0561339
X-RAY DIFFRACTIONf_plane_restr0.0061566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.140.30121390.22634823X-RAY DIFFRACTION87
2.14-2.20.27411310.2164963X-RAY DIFFRACTION89
2.2-2.260.28221320.21115050X-RAY DIFFRACTION90
2.26-2.340.23561320.20355147X-RAY DIFFRACTION92
2.34-2.420.26241370.19545207X-RAY DIFFRACTION94
2.42-2.520.22361400.18615292X-RAY DIFFRACTION94
2.52-2.630.24871420.19245351X-RAY DIFFRACTION96
2.63-2.770.2241010.19413856X-RAY DIFFRACTION69
2.77-2.940.23291470.1845518X-RAY DIFFRACTION98
2.94-3.170.20551460.18235490X-RAY DIFFRACTION98
3.17-3.490.21311360.17825127X-RAY DIFFRACTION91
3.49-3.990.21661290.15864832X-RAY DIFFRACTION86
3.99-5.030.18811480.14625621X-RAY DIFFRACTION99
5.03-44.780.1841500.16865658X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 30.7066 Å / Origin y: -22.6782 Å / Origin z: 20.45 Å
111213212223313233
T0.226 Å20.0043 Å20.0085 Å2-0.2286 Å20.0003 Å2--0.2034 Å2
L0.2469 °2-0.0626 °20.059 °2-0.3155 °2-0.0093 °2--0.1714 °2
S0.0449 Å °-0.018 Å °-0.0039 Å °-0.081 Å °-0.0234 Å °0.0156 Å °-0.0027 Å °-0.0272 Å °-0 Å °
Refinement TLS groupSelection details: all

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