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- PDB-6nor: Crystal structure of GenD2 from gentamicin A biosynthesis in comp... -

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Basic information

Entry
Database: PDB / ID: 6nor
TitleCrystal structure of GenD2 from gentamicin A biosynthesis in complex with NAD
ComponentsPutative NAD dependent dehydrogenase
KeywordsOXIDOREDUCTASE / NAD depedent enzyme / 3D swapping domain
Function / homologyGfo/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 / oxidoreductase activity / NAD(P)-binding domain superfamily / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Putative NAD dependent dehydrogenase
Function and homology information
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 Å
AuthorsAraujo, N.C. / Bury, P.S. / Huang, F. / Leadlay, P.F. / Dias, M.V.B.
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: Crystal Structure of GenD2, an NAD-Dependent Oxidoreductase Involved in the Biosynthesis of Gentamicin.
Authors: de Araujo, N.C. / Bury, P.D.S. / Tavares, M.T. / Huang, F. / Parise-Filho, R. / Leadlay, P. / Dias, M.V.B.
History
DepositionJan 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative NAD dependent dehydrogenase
B: Putative NAD dependent dehydrogenase
C: Putative NAD dependent dehydrogenase
D: Putative NAD dependent dehydrogenase
E: Putative NAD dependent dehydrogenase
F: Putative NAD dependent dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,29712
Polymers232,3176
Non-polymers3,9816
Water7,855436
1
A: Putative NAD dependent dehydrogenase
C: Putative NAD dependent dehydrogenase
hetero molecules

A: Putative NAD dependent dehydrogenase
C: Putative NAD dependent dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,5328
Polymers154,8784
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area19070 Å2
ΔGint-96 kcal/mol
Surface area47050 Å2
MethodPISA
2
B: Putative NAD dependent dehydrogenase
E: Putative NAD dependent dehydrogenase
hetero molecules

F: Putative NAD dependent dehydrogenase
hetero molecules

D: Putative NAD dependent dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,5328
Polymers154,8784
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655y+1,x,-z1
crystal symmetry operation5_544x-y,-y-1,-z-1/31
Buried area17660 Å2
ΔGint-85 kcal/mol
Surface area47380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.997, 123.997, 272.569
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2-

VAL

21A-588-

HOH

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Components

#1: Protein
Putative NAD dependent dehydrogenase / Putative gentamicin oxidoreductase


Mass: 38719.457 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: gtmC, genD2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q70KD1
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.71 Å3/Da / Density % sol: 54.69 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1 M sodium acetate, 4.6 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.4→49.96 Å / Num. obs: 95469 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 33.92 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.052 / Rrim(I) all: 0.187 / Net I/σ(I): 13.5 / Num. measured all: 1215767 / Scaling rejects: 36
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.4-2.4411.41.0546650.780.3241.199.7
13.15-49.969.50.0786780.9970.0260.08298

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Processing

Software
NameVersionClassification
REFMACrefinement
XDSdata reduction
Aimless0.5.27data scaling
PDB_EXTRACT3.24data extraction
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.402→49.955 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.28
RfactorNum. reflection% reflection
Rfree0.2233 2007 2.1 %
Rwork0.175 --
obs0.176 95361 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 127.26 Å2 / Biso mean: 34.2915 Å2 / Biso min: 17.23 Å2
Refinement stepCycle: final / Resolution: 2.402→49.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15397 0 264 436 16097
Biso mean--35.59 33.52 -
Num. residues----2049
Refinement TLS params.Method: refined / Origin x: 16.936 Å / Origin y: -39.331 Å / Origin z: -28.959 Å
111213212223313233
T0.2126 Å20.0135 Å2-0.0163 Å2-0.2842 Å2-0.0022 Å2--0.213 Å2
L0.0945 °20.0416 °2-0.0093 °2-0.1518 °2-0.006 °2---0.0724 °2
S0.0066 Å °0.0176 Å °-0.0556 Å °-0.0087 Å °0.02 Å °0.0029 Å °-0.0141 Å °0.0542 Å °-0.0279 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-7 - 341
2X-RAY DIFFRACTION1B0 - 340
3X-RAY DIFFRACTION1C2 - 341
4X-RAY DIFFRACTION1D0 - 340
5X-RAY DIFFRACTION1E3 - 340
6X-RAY DIFFRACTION1F2 - 341
7X-RAY DIFFRACTION1A501 - 587
8X-RAY DIFFRACTION1B501 - 566
9X-RAY DIFFRACTION1C501 - 567
10X-RAY DIFFRACTION1D501 - 550
11X-RAY DIFFRACTION1E501 - 561
12X-RAY DIFFRACTION1F501 - 600
13X-RAY DIFFRACTION1A401
14X-RAY DIFFRACTION1C401
15X-RAY DIFFRACTION1D401
16X-RAY DIFFRACTION1E401
17X-RAY DIFFRACTION1F401
18X-RAY DIFFRACTION1B401

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