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- PDB-1m8k: Crystal Structure Of Methanobacterium Thermoautotrophicum Nicotin... -

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Basic information

Entry
Database: PDB / ID: 1m8k
TitleCrystal Structure Of Methanobacterium Thermoautotrophicum Nicotinamide Mononucleotide Adenylyltransferase Mutant H19A 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 / MOLECULAR REPLACEMENT / Resolution: 3 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
B: Nicotinamide-nucleotide Adenylyltransferase
C: Nicotinamide-nucleotide Adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7719
Polymers61,4933
Non-polymers2,2786
Water00
1
A: Nicotinamide-nucleotide Adenylyltransferase
B: Nicotinamide-nucleotide Adenylyltransferase
C: Nicotinamide-nucleotide Adenylyltransferase
hetero molecules

A: Nicotinamide-nucleotide Adenylyltransferase
B: Nicotinamide-nucleotide Adenylyltransferase
C: Nicotinamide-nucleotide Adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,54318
Polymers122,9866
Non-polymers4,55712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554y,x,-z-11
MethodPQS
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20710 Å2
ΔGint-231 kcal/mol
Surface area36450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.480, 124.480, 111.826
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe protein is made up of a dimer of trimers.

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Components

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


Mass: 20497.660 Da / Num. of mol.: 3 / Mutation: H19A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: mth150 / 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.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM

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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: 4.07 Å3/Da / Density % sol: 69.74 %
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: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 18, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3→15 Å / Num. obs: 20207 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11 % / Rmerge(I) obs: 0.14 / Rsym value: 0.192 / Net I/σ(I): 20.6
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 6.5 / Num. unique all: 2012 / Rsym value: 0.418
Reflection
*PLUS
Highest resolution: 3 Å / Num. measured all: 223204 / Rmerge(I) obs: 0.14
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1ej2

1ej2


Resolution: 3→14.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 317851.62 / Data cutoff high rms absF: 317851.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1822 9.9 %RANDOM
Rwork0.194 ---
obs0.194 18423 91.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 14.3492 Å2 / ksol: 0.342116 e/Å3
Displacement parametersBiso mean: 28.4 Å2
Baniso -1Baniso -2Baniso -3
1--4.61 Å210.61 Å20 Å2
2---4.61 Å20 Å2
3---9.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.8 Å
Refinement stepCycle: LAST / Resolution: 3→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4053 0 147 0 4200
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.341.5
X-RAY DIFFRACTIONc_mcangle_it8.262
X-RAY DIFFRACTIONc_scbond_it7.022
X-RAY DIFFRACTIONc_scangle_it10.332.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 279 10.2 %
Rwork0.259 2448 -
obs--82 %
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: 15 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_deg22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.99

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