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- PDB-1fyd: CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS ... -

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Basic information

Entry
Database: PDB / ID: 1fyd
TitleCRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS COMPLEXED WITH ONE MOLECULE AMP, ONE PYROPHOSPHATE ION AND ONE MG2+ ION
ComponentsNH(3)-DEPENDENT NAD(+) SYNTHETASE
KeywordsLIGASE / LYASE / AMIDOTRANSFERASE / NH3 DEPENDENT / PYROPHOSPHATASE
Function / homology
Function and homology information


NAD+ synthase / NAD+ synthase activity / NAD+ synthase (glutamine-hydrolyzing) activity / glutaminase activity / NAD biosynthetic process / sporulation resulting in formation of a cellular spore / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
NH(3)-dependent NAD(+) synthetase / NAD(+) synthetase / NAD/GMP synthase / NAD synthase / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / PYROPHOSPHATE 2- / NH(3)-dependent NAD(+) synthetase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsDevedjiev, Y. / Symersky, J. / Singh, R. / Brouillette, W. / Muccio, D. / Jedrzejas, M. / Brouillette, C. / DeLucas, L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Stabilization of active-site loops in NH3-dependent NAD+ synthetase from Bacillus subtilis.
Authors: Devedjiev, Y. / Symersky, J. / Singh, R. / Jedrzejas, M. / Brouillette, C. / Brouillette, W. / Muccio, D. / Chattopadhyay, D. / DeLucas, L.
History
DepositionSep 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 30, 2015Group: Other
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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: NH(3)-DEPENDENT NAD(+) SYNTHETASE
B: NH(3)-DEPENDENT NAD(+) SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1555
Polymers60,6082
Non-polymers5473
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-54 kcal/mol
Surface area21380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.450, 87.200, 61.180
Angle α, β, γ (deg.)90.00, 111.15, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer constructed from chain A a symmetry partner generated by two fold

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Components

#1: Protein NH(3)-DEPENDENT NAD(+) SYNTHETASE / NAD+SYNTHETASE


Mass: 30303.994 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P08164, NAD+ synthase (glutamine-hydrolysing)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 301 K / Method: vapor diffusion / pH: 5.2
Details: PEG 400, sodium acetate, magnesium chloride, ATP, pH 5.2, VAPOR DIFFUSION, temperature 301.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMsodium acetate1drop
250 mM1dropMgCl2
32.5 mMbeta-mercaptoethanol1drop
415 mg/mlprotein1drop
521-23 %(v/v)PEG4001reservoir
60.1 Msodium acetate1reservoir
750 mM1reservoirMgCl2
81 mMATP1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.25→20 Å / Num. obs: 24198 / % possible obs: 91.1 % / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 4.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2 % / Rmerge(I) obs: 0.41 / % possible all: 72.6
Reflection
*PLUS
Num. measured all: 84039
Reflection shell
*PLUS
% possible obs: 72.6 % / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.25→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: ALL PORTIONS OF THE BACKBONE IN SUBUNIT A ARE WELL ORDERED. HOWEVER, BACKBONE ATOMS AND THE SIDE CHAINS OF RESIDUES 83-86 AND 205-225 IN SUBUNIT B ARE NOT VISIBLE ON THE ELECTRON DENSITY MAP. ...Details: ALL PORTIONS OF THE BACKBONE IN SUBUNIT A ARE WELL ORDERED. HOWEVER, BACKBONE ATOMS AND THE SIDE CHAINS OF RESIDUES 83-86 AND 205-225 IN SUBUNIT B ARE NOT VISIBLE ON THE ELECTRON DENSITY MAP. ATP BINDING SITE IN SUBUNIT A IS FULL OCCUPIED WITH AMP AND PP, HOWEVER, NO BINDING OF AMP, PP AND MG2+ WAS FOUND IN SUBUNIT B.
RfactorNum. reflectionSelection details
Rfree0.278 -RANDOM
Rwork0.191 --
obs-24116 -
Refinement stepCycle: LAST / Resolution: 2.25→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4068 0 33 187 4288
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg1.8
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.8

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