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- PDB-1k4k: Crystal structure of E. coli Nicotinic acid mononucleotide adenyl... -

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Basic information

Entry
Database: PDB / ID: 1k4k
TitleCrystal structure of E. coli Nicotinic acid mononucleotide adenylyltransferase
ComponentsNicotinic acid mononucleotide adenylyltransferase
KeywordsTRANSFERASE / Nucleotidyltransferase
Function / homology
Function and homology information


NAD+ biosynthetic process via the salvage pathway / 'de novo' NAD+ biosynthetic process from L-aspartate / nicotinamide-nucleotide adenylyltransferase activity / nicotinate-nucleotide adenylyltransferase / nicotinate-nucleotide adenylyltransferase activity / NAD+ biosynthetic process / ATP binding
Similarity search - Function
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
XENON / Nicotinate-nucleotide adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsZhang, H. / Zhou, T. / Kurnasov, O. / Cheek, S. / Grishin, N.V. / Osterman, A.L.
CitationJournal: Structure / Year: 2002
Title: Crystal structures of E. coli nicotinate mononucleotide adenylyltransferase and its complex with deamido-NAD.
Authors: Zhang, H. / Zhou, T. / Kurnasov, O. / Cheek, S. / Grishin, N.V. / Osterman, A.
History
DepositionOct 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Nicotinic acid mononucleotide adenylyltransferase
B: Nicotinic acid mononucleotide adenylyltransferase
C: Nicotinic acid mononucleotide adenylyltransferase
D: Nicotinic acid mononucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,7418
Polymers98,2154
Non-polymers5254
Water10,539585
1
A: Nicotinic acid mononucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8163
Polymers24,5541
Non-polymers2632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nicotinic acid mononucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6852
Polymers24,5541
Non-polymers1311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nicotinic acid mononucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6852
Polymers24,5541
Non-polymers1311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nicotinic acid mononucleotide adenylyltransferase


Theoretical massNumber of molelcules
Total (without water)24,5541
Polymers24,5541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.435, 66.528, 72.855
Angle α, β, γ (deg.)72.68, 88.77, 69.55
Int Tables number1
Space group name H-MP1
DetailsThe functional unit of this protein is monomer.

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Components

#1: Protein
Nicotinic acid mononucleotide adenylyltransferase


Mass: 24553.871 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: NADD / Production host: Escherichia coli (E. coli)
References: UniProt: P0A752, nicotinate-nucleotide adenylyltransferase
#2: Chemical
ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Xe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 585 / 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: 2.57 Å3/Da / Density % sol: 52.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Na Citrate, sodium chloride, Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal grow
*PLUS
pH: 7.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
250 mMHEPES1droppH7.2
3150 mM1dropNaCl
41 mMdithiothreitol1drop
50.1 MTris1reservoirpH7.0
60.2 M1reservoirNaCl
70.8 Msodium citrate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU30011.5418
SYNCHROTRONAPS 19-BM20.98
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV1IMAGE PLATEJan 20, 2001Osmic mirrors
CUSTOM-MADE2CCDFeb 21, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2Bending magnetMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.981
ReflectionResolution: 2→40 Å / Num. all: 66058 / Num. obs: 62463 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 20.9
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4 / % possible all: 81.9
Reflection
*PLUS
Highest resolution: 2 Å / Num. measured all: 169804 / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
% possible obs: 81.9 % / Rmerge(I) obs: 0.25

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 3050 5 %RANDOM
Rwork0.21 ---
all0.21 66058 --
obs0.21 60416 91.5 %-
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6837 0 4 585 7426
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.012
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.7
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
LS refinement shellHighest resolution: 2 Å
Refinement
*PLUS
Highest resolution: 2 Å / % reflection Rfree: 5 % / Rfactor obs: 0.21 / Rfactor Rfree: 0.262 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: o_angle_deg / Dev ideal: 1.7

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