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- PDB-1m8j: Crystal Structure Of Methanobacterium Thermoautotrophicum Nicotin... -

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Basic information

Entry
Database: PDB / ID: 1m8j
TitleCrystal Structure Of Methanobacterium Thermoautotrophicum Nicotinamide Mononucleotide Adenylyltransferase Mutant R136A complexed with NAD
ComponentsNicotinamide-nucleotide Adenylyltransferase
KeywordsTRANSFERASE / nucleotidyltransferase HXGH active site motif
Function / homology
Function and homology information


nicotinamide-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / NAD+ biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Nicotinamide-nucleotide adenylyltransferase, archaeal type / Cytidylyltransferase-like / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide-nucleotide adenylyltransferase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSaridakis, V. / Pai, E.F.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Mutational, Structural, and Kinetic Studies of the ATP-binding Site of Methanobacterium thermoautotrophicum Nicotinamide Mononucleotide Adenylyltransferase
Authors: Saridakis, V. / Pai, E.F.
History
DepositionJul 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nicotinamide-nucleotide Adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2383
Polymers20,4791
Non-polymers7592
Water88349
1
A: Nicotinamide-nucleotide Adenylyltransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)127,42918
Polymers122,8726
Non-polymers4,55712
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area20550 Å2
ΔGint-243 kcal/mol
Surface area36680 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.418, 91.418, 107.755
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
DetailsThe protein is hexameric.

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Components

#1: Protein Nicotinamide-nucleotide Adenylyltransferase / NAD(+) pyrophosphorylase / NAD(+) diphosphorylase / NMN adenylyltransferase


Mass: 20478.613 Da / Num. of mol.: 1 / Mutation: R136A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: mth0150 / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O26253, nicotinamide-nucleotide adenylyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 3.17 Å3/Da / Density % sol: 61.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.5 M Ammonium Sulfate, 100 mM Tris, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.6 Mammonium sulfate1reservoir
25 %glycerol1reservoir
3100 mMTris-HCl1reservoirpH8.0
41.5-1.6 Mammonium sulfate1drop
55 %glycerol1drop
6100 mMTris-HCl1droppH8.0
710 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 10961 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 29.5 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.094 / Net I/σ(I): 49.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 15 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 13.4 / Num. unique all: 1052 / Rsym value: 0.345
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 10085 / % possible obs: 99.8 % / Num. measured all: 185814 / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 12

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1ej2

1ej2


Resolution: 2.4→14.96 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 521275.62 / Data cutoff high rms absF: 521275.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1062 10.3 %RANDOM
Rwork0.225 ---
obs0.225 10271 94.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.833 Å2 / ksol: 0.376268 e/Å3
Displacement parametersBiso mean: 36.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å24.02 Å20 Å2
2---1.44 Å20 Å2
3---2.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.4→14.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1334 0 49 49 1432
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.951.5
X-RAY DIFFRACTIONc_mcangle_it6.192
X-RAY DIFFRACTIONc_scbond_it7.932
X-RAY DIFFRACTIONc_scangle_it11.742.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.363 150 9.6 %
Rwork0.279 1412 -
obs--88.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4NAD.PARAMNAD.TOP
X-RAY DIFFRACTION5CIS_PEPTIDE.PARAMCIS_PEPTIDE.TOP
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.01

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