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- PDB-4yp7: Crystal structure of Methanobacterium thermoautotrophicum NMNAT i... -

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Basic information

Entry
Database: PDB / ID: 4yp7
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: 2.3 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

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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)63,8406
Polymers61,6103
Non-polymers2,2303
Water2,792155
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)127,68012
Polymers123,2206
Non-polymers4,4606
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_673x-y+1,-y+2,-z-4/31
Buried area19840 Å2
ΔGint-92 kcal/mol
Surface area35820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.448, 124.448, 111.943
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 / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA3 - 1703 - 170
21ALAALABB3 - 1703 - 170
12LEULEUAA3 - 1693 - 169
22LEULEUCC3 - 1693 - 169
13HISHISBB3 - 1683 - 168
23HISHISCC3 - 1683 - 168

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 20536.648 Da / Num. of mol.: 3 / Mutation: R47E
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.: 155 / 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: 4.06 Å3/Da / Density % sol: 69.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: ammonium sulfate, glycerol, TRIS

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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: 2.3→14.99 Å / Num. obs: 41867 / % possible obs: 93.1 % / Redundancy: 1.56 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.8
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 1.58 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 6.09 / % possible all: 93.3

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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: 2.3→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2112 / WRfactor Rwork: 0.1982 / FOM work R set: 0.872 / SU B: 4.29 / SU ML: 0.105 / SU R Cruickshank DPI: 0.1997 / SU Rfree: 0.1646 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2083 2202 5.3 %RANDOM
Rwork0.19 ---
obs0.1909 39652 93.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 81.12 Å2 / Biso mean: 26.88 Å2 / Biso min: 12.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å2-0.31 Å20 Å2
2---0.62 Å20 Å2
3---2.01 Å2
Refinement stepCycle: final / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4000 0 144 155 4299
Biso mean--29.36 24.36 -
Num. residues----501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194255
X-RAY DIFFRACTIONr_bond_other_d0.0060.024015
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.9925796
X-RAY DIFFRACTIONr_angle_other_deg1.35939231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4585499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.9322.932191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17515713
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9721540
X-RAY DIFFRACTIONr_chiral_restr0.0850.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214642
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02964
X-RAY DIFFRACTIONr_mcbond_it1.6322.5182005
X-RAY DIFFRACTIONr_mcbond_other1.6322.5182004
X-RAY DIFFRACTIONr_mcangle_it2.4153.7672501
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A205800.1
12B205800.1
21A203720.1
22C203720.1
31B205820.09
32C205820.09
LS refinement shellResolution: 2.299→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 128 -
Rwork0.217 2869 -
all-2997 -
obs--92.13 %

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