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- PDB-4yp5: Crystal structure of Methanobacterium thermoautotrophicum NMNAT i... -

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Basic information

Entry
Database: PDB / ID: 4yp5
TitleCrystal structure of Methanobacterium thermoautotrophicum NMNAT in complex with NADP
ComponentsNicotinamide-nucleotide adenylyltransferase
KeywordsTRANSFERASE / inhibitor
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide-nucleotide adenylyltransferase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsPfoh, R. / Christendat, D. / Pai, E.F. / Saridakis, V.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2015
Title: Nicotinamide mononucleotide adenylyltransferase displays alternate binding modes for nicotinamide nucleotides.
Authors: Pfoh, R. / Pai, E.F. / Saridakis, V.
History
DepositionMar 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Derived calculations
Category: citation / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)63,9246
Polymers61,6943
Non-polymers2,2303
Water2,738152
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)127,84912
Polymers123,3886
Non-polymers4,4606
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_673x-y+1,-y+2,-z-4/31
Buried area20090 Å2
ΔGint-94 kcal/mol
Surface area36390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.586, 124.586, 111.959
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 3 - 171 / Label seq-ID: 3 - 171

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 20564.729 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) (archaea)
Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H
Gene: MTH_150 / Plasmid: pET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3)
References: UniProt: O26253, nicotinamide-nucleotide adenylyltransferase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 4.07 Å3/Da / Density % sol: 69.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: ammonium sulfate, glycerol, TRIS, NADP

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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 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.21→20 Å / Num. obs: 45535 / % possible obs: 89.3 % / Redundancy: 1.27 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 15.68
Reflection shellResolution: 2.21→2.31 Å / Redundancy: 1.15 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 4.84 / % possible all: 87

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Processing

Software
NameVersionClassification
REFMACrefinement
PDB_EXTRACT3.15data extraction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EJ2

1ej2


Resolution: 2.21→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.2064 / WRfactor Rwork: 0.1923 / FOM work R set: 0.8659 / SU B: 3.895 / SU ML: 0.097 / SU R Cruickshank DPI: 0.1729 / SU Rfree: 0.1446 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1955 2356 5.2 %RANDOM
Rwork0.1806 ---
obs0.1814 43177 89.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.02 Å2 / Biso mean: 37.612 Å2 / Biso min: 20.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0.23 Å20 Å2
2---0.45 Å20 Å2
3---1.47 Å2
Refinement stepCycle: final / Resolution: 2.21→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4033 0 144 152 4329
Biso mean--43.22 35.7 -
Num. residues----505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194300
X-RAY DIFFRACTIONr_bond_other_d0.0060.024086
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.995851
X-RAY DIFFRACTIONr_angle_other_deg1.34139390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5335505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.58322.656192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91315730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3721543
X-RAY DIFFRACTIONr_chiral_restr0.0840.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214679
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02982
X-RAY DIFFRACTIONr_mcbond_it2.4093.4982026
X-RAY DIFFRACTIONr_mcbond_other2.4093.4982025
X-RAY DIFFRACTIONr_mcangle_it3.3785.2312529
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A20822
12B20822
21A20762
22C20762
31B21252
32C21252
LS refinement shellResolution: 2.205→2.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 151 -
Rwork0.233 3060 -
all-3211 -
obs--87.14 %

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