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- PDB-1hyb: CRYSTAL STRUCTURE OF AN ACTIVE SITE MUTANT OF METHANOBACTERIUM TH... -

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Basic information

Entry
Database: PDB / ID: 1hyb
TitleCRYSTAL STRUCTURE OF AN ACTIVE SITE MUTANT OF METHANOBACTERIUM THERMOAUTOTROPHICUM NICOTINAMIDE MONONUCLEOTIDE ADENYLYLTRANSFERASE
ComponentsNICOTINAMIDE MONONUCLEOTIDE ADENYLYLTRANSFERASE
KeywordsTRANSFERASE / dinucleotide binding fold / active site mutant
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
BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / Nicotinamide-nucleotide adenylyltransferase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / isomorphous to native / Resolution: 2 Å
AuthorsSaridakis, V. / Christendat, D. / Kimber, M.S. / Edwards, A.M. / Pai, E.F.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Insights into ligand binding and catalysis of a central step in NAD+ synthesis: structures of Methanobacterium thermoautotrophicum NMN adenylyltransferase complexes.
Authors: Saridakis, V. / Christendat, D. / Kimber, M.S. / Dharamsi, A. / Edwards, A.M. / Pai, E.F.
History
DepositionJan 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 1.4Aug 9, 2023Group: 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 MONONUCLEOTIDE ADENYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9613
Polymers20,5301
Non-polymers4312
Water1,26170
1
A: NICOTINAMIDE MONONUCLEOTIDE ADENYLYLTRANSFERASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)125,76618
Polymers123,1786
Non-polymers2,58812
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 area16900 Å2
ΔGint-195 kcal/mol
Surface area35580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)89.778, 89.778, 108.946
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
DetailsThe biological assembly is a hexamer constructed from chain A and five symmetry partners generated by crystallographic symmetry.

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Components

#1: Protein NICOTINAMIDE MONONUCLEOTIDE ADENYLYLTRANSFERASE


Mass: 20529.725 Da / Num. of mol.: 1 / Mutation: H19A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NMN / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / NICOTINAMIDE MONONUCLEOTIDE / Nicotinamide mononucleotide


Mass: 335.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N2O8P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6 M LiSO4, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
21.6 M1reservoirLiSO4
3100 mMHEPES1reservoir

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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 28, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 253617 / Num. obs: 17892 / % possible obs: 98.1 % / Observed criterion σ(F): 16525 / Observed criterion σ(I): 486 / Redundancy: 12 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 34
Reflection shellResolution: 2→30 Å / Redundancy: 10 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 7 / Num. unique all: 1710 / % possible all: 98.1
Reflection shell
*PLUS
% possible obs: 98.1 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: isomorphous to native
Starting model: pdb 1ej2

1ej2


Resolution: 2→14.96 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 929092.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: CNS 0.9 / Details: simulated annealing
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1699 9.8 %RANDOM
Rwork0.237 ---
obs0.237 17249 95.5 %-
all-253617 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.48 Å2 / ksol: 0.409 e/Å3
Displacement parametersBiso mean: 37.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å23.59 Å20 Å2
2--1.16 Å20 Å2
3----2.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2→14.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1274 0 27 70 1371
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_mcangle_it1.832
X-RAY DIFFRACTIONc_scbond_it1.92
X-RAY DIFFRACTIONc_scangle_it2.752.5
LS refinement shellResolution: 2→2.12 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.314 263 9.7 %
Rwork0.287 2460 -
obs--93.1 %
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 DIFFRACTION4NMN.PARAMNMN.TOP
X-RAY DIFFRACTION5CIS_PEPTIDE.PARAMCIS_PEPTIDE.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.01

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