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- PDB-3dpi: Crystal Structure of NAD+ synthetase from Burkholderia Pseudomallei -

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Basic information

Entry
Database: PDB / ID: 3dpi
TitleCrystal Structure of NAD+ synthetase from Burkholderia Pseudomallei
ComponentsNAD+ synthetase
KeywordsLIGASE / SSGCID / deCODE / Structural Genomics / PSI / Protein Structure Initiative / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


NAD+ synthase / NAD+ synthase activity / NAD+ synthase (glutamine-hydrolyzing) activity / glutaminase activity / NAD+ biosynthetic process / 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
ACETATE ION / NH(3)-dependent NAD(+) synthetase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal Structure of NAD+ synthetase from Burkholderia Pseudomallei
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionJul 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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 / pdbx_initial_refinement_model / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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

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Assembly

Deposited unit
A: NAD+ synthetase
B: NAD+ synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0833
Polymers62,0242
Non-polymers591
Water4,125229
1
A: NAD+ synthetase
B: NAD+ synthetase
hetero molecules

A: NAD+ synthetase
B: NAD+ synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,1676
Polymers124,0494
Non-polymers1182
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area7870 Å2
ΔGint-68 kcal/mol
Surface area44280 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-29 kcal/mol
Surface area22970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.315, 76.315, 183.772
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein NAD+ synthetase


Mass: 31012.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: 76819159 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3JL79*PLUS
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.16 Å3/Da / Density % sol: 42.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 0.2 M NaCl, 0.1 M BisTris pH 5.5, Hampton Index screen well F10, Crystal ID 109415F10, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97607 Å
DetectorDate: May 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97607 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 28418 / % possible obs: 99.9 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.086 / Χ2: 1.286 / Net I/σ(I): 15.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 13 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 6.1 / Num. unique all: 2778 / Χ2: 1.236 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.4.0067refinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PZ8

2pz8


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.188 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.303 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1419 5 %RANDOM
Rwork0.226 ---
obs0.228 28418 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.44 Å2 / Biso mean: 42.93 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2--0.65 Å20 Å2
3----1.3 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3753 0 4 229 3986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223824
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.9675164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.3345493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92921.742178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.88115612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7141552
X-RAY DIFFRACTIONr_chiral_restr0.0820.2583
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212941
X-RAY DIFFRACTIONr_mcbond_it0.6551.52466
X-RAY DIFFRACTIONr_mcangle_it1.21523878
X-RAY DIFFRACTIONr_scbond_it1.67531358
X-RAY DIFFRACTIONr_scangle_it2.814.51286
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 98 -
Rwork0.259 1955 -
all-2053 -
obs--100 %

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