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- PDB-1nut: CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC NMN/NaMN ADENYLYLTRANSFERASE... -

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Basic information

Entry
Database: PDB / ID: 1nut
TitleCRYSTAL STRUCTURE OF HUMAN CYTOSOLIC NMN/NaMN ADENYLYLTRANSFERASE COMPLEXED WITH ATP ANALOG
ComponentsFKSG76
KeywordsTRANSFERASE / NAD BIOSYNTHESIS / MITOCHONDRIA / PYRIDINE ADENYLYLTRANSFERASE / ENZYME CATALYSIS
Function / homology
Function and homology information


nicotinamide-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / nicotinate-nucleotide adenylyltransferase / nucleotide biosynthetic process / nicotinate-nucleotide adenylyltransferase activity / Nicotinate metabolism / NAD+ biosynthetic process / response to tumor necrosis factor / neuron projection maintenance / response to wounding ...nicotinamide-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / nicotinate-nucleotide adenylyltransferase / nucleotide biosynthetic process / nicotinate-nucleotide adenylyltransferase activity / Nicotinate metabolism / NAD+ biosynthetic process / response to tumor necrosis factor / neuron projection maintenance / response to wounding / mitochondrial matrix / axon / neuronal cell body / mitochondrion / ATP binding
Similarity search - Function
Nicotinamide/nicotinate mononucleotide adenylyltransferase, eukaryotic / : / Nicotinate/nicotinamide nucleotide adenylyltransferase / 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
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhang, X. / Kurnasov, O.V. / Karthikeyan, S. / Grishin, N.V. / Osterman, A.L. / Zhang, H.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: STRUCTURAL CHARACTERIZATION OF A HUMAN CYTOSOLIC NMN/NaMN ADENYLYLTRANSFERASE AND IMPLICATION IN HUMAN NAD BIOSYNTHESIS
Authors: ZHANG, X. / KURNASOV, O.V. / KARTHIKEYAN, S. / GRISHIN, N.V. / OSTERMAN, A.L. / ZHANG, H.
#1: Journal: J.Biol.Chem. / Year: 2002
Title: STRUCTURE OF HUMAN NICOTINAMIDE/NICOTONIC ACID MONONUCLEOTIDE ADENYLYLTRANSFERASE BASIS FOR THE DUAL SUBSTRATE SPECIFICITY AND ACTIVATION OF THE ONCOLYTIC AGENT TIAZOFURIN
Authors: ZHOU, T. / KURNASOV, O. / TOMCHICK, D.R. / BINNS, D.D. / GRISHIN, N.V. / MARQUEZ, V.E. / OSTERMAN, A.L. / ZHANG, H.
History
DepositionFeb 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FKSG76
B: FKSG76
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9966
Polymers56,7942
Non-polymers1,2034
Water4,522251
1
A: FKSG76
B: FKSG76
hetero molecules

A: FKSG76
B: FKSG76
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,99212
Polymers113,5874
Non-polymers2,4058
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area13860 Å2
ΔGint-67 kcal/mol
Surface area34180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)79.281, 79.281, 146.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-698-

HOH

21A-706-

HOH

31B-699-

HOH

DetailsBiological assembly is tetramer and is generated by two fold axis : Y,X,-Z

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Components

#1: Protein FKSG76 / NMN/NaMN ADENYLYLTRANSFERASE


Mass: 28396.768 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKSG76 / Plasmid: pPROEX / Production host: Escherichia coli (E. coli) / Strain (production host): DH10-beta / References: UniProt: Q96T66
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.22 Å3/Da / Density % sol: 44.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: NA CADODALYTE, LITHIUM SULPHATE, PEG 400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 7 / PH range high: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
2100 mMsodium cacodylate1reservoirpH6.0-7.0
3200 mM1reservoirLi2SO4
420-25 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 1, 2002 / Details: OSMIC MIRROR
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 37195 / Num. obs: 36285 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 23 Å2 / Rsym value: 0.05 / Net I/σ(I): 38.5
Reflection shellResolution: 1.9→1.93 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.383 / % possible all: 91.3
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 37195 / % possible obs: 98.5 % / Num. measured all: 214627 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 91.3 % / Rmerge(I) obs: 0.383

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KQN

1kqn


Resolution: 1.9→35.46 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 444067.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1815 5 %RANDOM
Rwork0.198 ---
obs0.198 36285 96.3 %-
all-37195 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.4973 Å2 / ksol: 0.347196 e/Å3
Displacement parametersBiso mean: 32.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.53 Å20 Å20 Å2
2---2.53 Å20 Å2
3---5.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.9→35.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3379 0 72 251 3702
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.541.5
X-RAY DIFFRACTIONc_mcangle_it2.432
X-RAY DIFFRACTIONc_scbond_it2.042
X-RAY DIFFRACTIONc_scangle_it32.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 284 5.2 %
Rwork0.246 5175 -
obs--89 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3SO4.PARSO4.TOP
X-RAY DIFFRACTION4APC.PARAPC.TOP
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92

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