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- PDB-1kqp: NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS AT 1 A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1kqp
TitleNH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS AT 1 A RESOLUTION
ComponentsNH(3)-dependent NAD(+) synthetase
KeywordsLIGASE / AMIDOTRANSFERASE / ATP PYROPHOSPHATASE / NAD-ADENYLATE
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
Chem-ADJ / PYROPHOSPHATE 2- / NH(3)-dependent NAD(+) synthetase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.03 Å
AuthorsSymersky, J. / Devedjiev, Y. / Moore, K. / Brouillette, C. / DeLucas, L.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: NH3-dependent NAD+ synthetase from Bacillus subtilis at 1 A resolution.
Authors: Symersky, J. / Devedjiev, Y. / Moore, K. / Brouillette, C. / DeLucas, L.
#1: Journal: 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.
#2: Journal: Structure / Year: 1998
Title: A novel deamido-NAD+ binding site revealed by the trapped NAD-adenylate intermediate in the NAD+ synthetase structure
Authors: Rizzi, M. / Bolognesi, M. / Coda, A.
#3: Journal: Embo J. / Year: 1996
Title: Crystal structure of NH3-dependent NAD+ synthetase from Bacillus subtilis
Authors: Rizzi, M. / Nessi, C. / Mattevi, A. / Coda, A. / Bolognesi, M. / Galizzi, A.
History
DepositionJan 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 3, 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 / diffrn_source / pdbx_initial_refinement_model / 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 / _diffrn_source.pdbx_synchrotron_site / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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)63,70121
Polymers60,6082
Non-polymers3,09319
Water12,863714
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11530 Å2
ΔGint-95 kcal/mol
Surface area21110 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.280, 84.790, 59.640
Angle α, β, γ (deg.)90.00, 110.50, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
DetailsThe biological assembly is a dimer from the asymmetric unit (chains A,B).

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NH(3)-dependent NAD(+) synthetase / E.C.6.3.5.1 / NH3-dependent NAD+ synthetase / NAD+ synthase / Sporulation protein outB / spore outgrowth factor B ...NH3-dependent NAD+ synthetase / NAD+ synthase / Sporulation protein outB / spore outgrowth factor B / General stress protein 38 / GSP38


Mass: 30303.994 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: complexed with a reaction intermediate NAD-A, residue ADJ
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: OutB / Plasmid: pET-21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DH3)plysS
References: UniProt: P08164, NAD+ synthase (glutamine-hydrolysing)

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Non-polymers , 5 types, 733 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ADJ / NICOTINAMIDE-ADENINE-DINUCLEOTIDE-ADENYLATE INTERMEDIATE / NADP-A


Mass: 999.663 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H44N11O21P3
#5: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 714 / 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: 1.97 Å3/Da / Density % sol: 36 %
Crystal growTemperature: 298 K / Method: microgravity/vapor diffusion / pH: 8.5
Details: 25% PEG 400, 0.05M Tris, 0.05M MgCl2, 0.005M NaAD, 0.0025M ATP, pH 8.5, microgravity/vapor diffusion at 298K, microgravity/vapor diffusion
Crystal grow
*PLUS
pH: 5.2 / Method: vapor diffusion, hanging drop
Details: Devedjiev, Y., (2001) Acta Crystallogr., Sect.D, 57, 806.
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
85 mMNaAD1reservoir
90.5 mMATP1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.905 / Wavelength: 0.905 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.905 Å / Relative weight: 1
ReflectionResolution: 1.028→30 Å / Num. all: 239033 / Num. obs: 231200 / % possible obs: 96.7 % / Observed criterion σ(I): -1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 32.8
Reflection shellResolution: 1.028→1.08 Å / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 2.4 / % possible all: 72.3
Reflection
*PLUS
Highest resolution: 1.03 Å / % possible obs: 90 % / Num. measured all: 790765
Reflection shell
*PLUS
Highest resolution: 1.03 Å / Lowest resolution: 1.1 Å / % possible obs: 75 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97refinement
RefinementStarting model: 1EE1

1ee1


Resolution: 1.03→10 Å / Num. parameters: 47101 / Num. restraintsaints: 52229 / Cross valid method: FREE R / σ(F): 4 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1354 10811 5 %RANDOM
Rwork0.1063 ---
all0.1077 216026 --
obs0.1063 179414 83 %-
Refine analyzeLuzzati coordinate error obs: 0.05 Å / Num. disordered residues: 18 / Occupancy sum hydrogen: 4272.09 / Occupancy sum non hydrogen: 5072.19
Refinement stepCycle: LAST / Resolution: 1.03→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4264 0 195 714 5173
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_from_restr_planes0.0282
X-RAY DIFFRACTIONs_zero_chiral_vol0.083
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.089
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.149
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.039
X-RAY DIFFRACTIONs_approx_iso_adps0.068
LS refinement shellResolution: 1.03→1.08 Å /
RfactorNum. reflection
Rwork0.221 -
obs-22308
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection obs: 205215 / Rfactor obs: 0.118 / Rfactor Rfree: 0.1472 / Rfactor Rwork: 0.1163
Solvent computation
*PLUS
Displacement parameters
*PLUS

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