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- PDB-6ofb: Crystal structure of human glutamine-dependent NAD+ synthetase co... -

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Basic information

Entry
Database: PDB / ID: 6ofb
TitleCrystal structure of human glutamine-dependent NAD+ synthetase complexed with NaAD+, AMP, pyrophosphate, and Mg2+
ComponentsGlutamine-dependent NAD(+) synthetase
KeywordsLIGASE / GLUTAMINE-AMIDO TRANSFERASE / GAT / NAD+ SYNTHETASE / GLUTAMINE-DEPENDENT NAD+ SYNTHETASE / NAD SYNTHETASE 1 / GLUTAMINASE / AMMONIA TUNNELING / ENZYME / ATP-BINDING / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


'de novo' NAD biosynthetic process / NAD+ synthase (glutamine-hydrolysing) / NAD+ synthase (glutamine-hydrolyzing) activity / Nicotinate metabolism / NAD metabolic process / glutaminase activity / NAD biosynthetic process / ATP binding / cytosol / cytoplasm
Similarity search - Function
Glutamine-dependent NAD(+) synthetase / NAD(+) synthetase / NAD/GMP synthase / NAD synthase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / NICOTINIC ACID ADENINE DINUCLEOTIDE / PYROPHOSPHATE 2- / Glutamine-dependent NAD(+) synthetase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsChuenchor, W. / Doukov, T.I. / Gerratana, B.
CitationJournal: Nat Commun / Year: 2020
Title: Different ways to transport ammonia in human and Mycobacterium tuberculosis NAD+synthetases.
Authors: Chuenchor, W. / Doukov, T.I. / Chang, K.T. / Resto, M. / Yun, C.S. / Gerratana, B.
History
DepositionMar 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 1, 2023Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_database_PDB_obs_spr / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_label_asym_id
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamine-dependent NAD(+) synthetase
B: Glutamine-dependent NAD(+) synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,70819
Polymers158,9632
Non-polymers2,74517
Water84747
1
A: Glutamine-dependent NAD(+) synthetase
B: Glutamine-dependent NAD(+) synthetase
hetero molecules

A: Glutamine-dependent NAD(+) synthetase
B: Glutamine-dependent NAD(+) synthetase
hetero molecules

A: Glutamine-dependent NAD(+) synthetase
B: Glutamine-dependent NAD(+) synthetase
hetero molecules

A: Glutamine-dependent NAD(+) synthetase
B: Glutamine-dependent NAD(+) synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)646,83376
Polymers635,8548
Non-polymers10,98068
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area85910 Å2
ΔGint-785 kcal/mol
Surface area169110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.250, 198.890, 219.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glutamine-dependent NAD(+) synthetase / NAD(+) synthase [glutamine-hydrolyzing] / NAD(+) synthetase


Mass: 79481.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NADSYN1 / Plasmid: PI-SUMOSTAR / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q6IA69, NAD+ synthase (glutamine-hydrolysing)

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Non-polymers , 6 types, 64 molecules

#2: Chemical ChemComp-DND / NICOTINIC ACID ADENINE DINUCLEOTIDE / DEAMIDO-NAD+


Mass: 665.418 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N6O15P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


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


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.51 Å3/Da / Density % sol: 64.99 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.8 M AMMONIUM SULFATE, 30% MPD, 15% GLYCEROL, 85 MM HEPES
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2010 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.84→40 Å / Num. obs: 52456 / % possible obs: 99.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 71.78 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.063 / Net I/σ(I): 13
Reflection shellResolution: 2.84→2.91 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3857 / Rsym value: 0.586 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ILV

3ilv


Resolution: 2.84→37.4 Å / SU ML: 0.4285 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.8257
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2173 2668 5.09 %
Rwork0.1794 49781 -
obs0.1813 52449 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.82 Å2
Refinement stepCycle: LAST / Resolution: 2.84→37.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10986 0 163 47 11196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011511422
X-RAY DIFFRACTIONf_angle_d1.361115529
X-RAY DIFFRACTIONf_chiral_restr0.0761717
X-RAY DIFFRACTIONf_plane_restr0.00441982
X-RAY DIFFRACTIONf_dihedral_angle_d21.88054187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.84-2.890.41571210.33732166X-RAY DIFFRACTION83.35
2.89-2.950.34741350.30462624X-RAY DIFFRACTION99.86
2.95-3.010.35071580.28782622X-RAY DIFFRACTION99.89
3.01-3.070.37481410.30452614X-RAY DIFFRACTION99.78
3.07-3.140.33691520.27832608X-RAY DIFFRACTION99.96
3.14-3.220.29311160.2542643X-RAY DIFFRACTION99.71
3.22-3.310.29791650.22592606X-RAY DIFFRACTION99.89
3.31-3.410.26251630.20992613X-RAY DIFFRACTION99.82
3.41-3.520.24781580.19542610X-RAY DIFFRACTION99.86
3.52-3.640.21411290.18632656X-RAY DIFFRACTION99.86
3.64-3.790.18631400.16732645X-RAY DIFFRACTION99.89
3.79-3.960.17861420.15262626X-RAY DIFFRACTION99.68
3.96-4.170.17031500.1482627X-RAY DIFFRACTION99.86
4.17-4.430.16771320.13752664X-RAY DIFFRACTION99.79
4.43-4.770.1441430.13132670X-RAY DIFFRACTION99.89
4.77-5.250.19361370.14522661X-RAY DIFFRACTION99.79
5.25-6.010.25461320.18042705X-RAY DIFFRACTION99.79
6.01-7.560.21391320.17212692X-RAY DIFFRACTION98.78
7.56-37.40.17171220.16192729X-RAY DIFFRACTION95.77

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