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- PDB-4f4h: Crystal structure of a Glutamine dependent NAD+ synthetase from B... -

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Basic information

Entry
Database: PDB / ID: 4f4h
TitleCrystal structure of a Glutamine dependent NAD+ synthetase from Burkholderia thailandensis
ComponentsGlutamine dependent NAD+ synthetase
KeywordsLIGASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


NAD+ synthase (glutamine-hydrolysing) / NAD+ synthase activity / NAD+ synthase (glutamine-hydrolyzing) activity / glutaminase activity / NAD biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Glutamine-dependent NAD(+) synthetase / NAD(+) synthetase / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / NAD/GMP synthase / NAD synthase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase ...Glutamine-dependent NAD(+) synthetase / NAD(+) synthetase / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / NAD/GMP synthase / NAD synthase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / PHOSPHATE ION / Glutamine-dependent NAD(+) synthetase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionMay 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Sep 13, 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_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Glutamine dependent NAD+ synthetase
B: Glutamine dependent NAD+ synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,6188
Polymers121,1802
Non-polymers4386
Water13,493749
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10800 Å2
ΔGint-55 kcal/mol
Surface area36320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.090, 73.080, 116.890
Angle α, β, γ (deg.)90.000, 102.760, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glutamine dependent NAD+ synthetase


Mass: 60589.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / Gene: BTH_I0882 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2T061
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 749 / 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: 2.48 Å3/Da / Density % sol: 50.37 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Internal tracking number 232316c5. Morpheus well C5, 10% w/v PEG20K, 20% PEG MME 550, 0.03M NPS (Sodium nitrate, disodium hydrogen phosphate, ammonium sulfate ), 0.1M MOPS / HEPES-Na pH 7.5 ...Details: Internal tracking number 232316c5. Morpheus well C5, 10% w/v PEG20K, 20% PEG MME 550, 0.03M NPS (Sodium nitrate, disodium hydrogen phosphate, ammonium sulfate ), 0.1M MOPS / HEPES-Na pH 7.5 ButhA.18002.a.A1.PS01197 20.0mg/ml., vapor diffusion, sitting drop, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2012 / Details: mirrors Rh/Pt coated Si
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.75→49.3 Å / Num. all: 119513 / Num. obs: 119307 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.74 % / Biso Wilson estimate: 28.063 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 18.48
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.75-1.80.5183.450731878199.9
1.8-1.840.4174.2493878525100
1.84-1.90.3395.248749841099.9
1.9-1.960.2626.7469078072100
1.96-2.020.2068.345569783899.9
2.02-2.090.16610.244300762499.9
2.09-2.170.13112.7426617317100
2.17-2.260.11114.940933704599.9
2.26-2.360.09317.3394546787100
2.36-2.470.0819.737723647399.8
2.47-2.610.07221.635700617499.9
2.61-2.770.06125.333643583499.9
2.77-2.960.05328.2313915483100
2.96-3.20.04531.928941513699.9
3.2-3.50.03937.326309472699.9
3.5-3.910.03441.723060425699.6
3.91-4.520.02945.521056379199.7
4.52-5.530.02746.8182483203100
5.53-7.830.02745.4141652515100
7.830.02149.87264131792.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.73 Å
Translation2.5 Å19.73 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.004data extraction
BOSdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N05

3n05


Resolution: 1.75→49.3 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.367 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.092 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18 5975 5 %RANDOM
Rwork0.153 ---
all0.154 119513 --
obs0.154 119282 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.246 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20.21 Å2
2--1.34 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.75→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8013 0 26 749 8788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0198218
X-RAY DIFFRACTIONr_bond_other_d0.0010.025421
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.97311183
X-RAY DIFFRACTIONr_angle_other_deg0.926313167
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85651085
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.52423.129342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.238151241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6931570
X-RAY DIFFRACTIONr_chiral_restr0.0870.21291
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219388
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021706
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 404 -
Rwork0.198 8155 -
all-8559 -
obs-8155 99.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8741-0.18660.00140.70690.09380.45390.00790.0101-0.11280.0416-0.03560.04380.0774-0.0110.02770.03010.00360.01230.00580.00280.024424.3746-5.826985.5732
20.65220.00790.010.687-0.35110.67710.0061-0.0362-0.00530.0696-0.1016-0.0966-0.04310.13180.09560.0199-0.0052-0.00640.03550.02550.020137.25262.288491.3259
30.7542-0.17220.22490.1792-0.22340.36960.00470.13680.0979-0.0176-0.0272-0.0409-0.01320.03330.02250.0279-0.00250.00840.05440.03320.033625.105921.950263.208
40.8384-0.0361-0.0290.23440.02070.15150.04310.1691-0.0185-0.0248-0.0390.02510.0046-0.005-0.00420.01530.0121-0.00860.0394-0.00850.007114.891312.701873.1548
50.4915-0.1269-0.27340.34370.10840.8232-0.0274-0.0359-0.01230.06580.01410.00280.0386-0.00620.01330.0368-0.00240.00490.0055-0.00140.00290.790220.1718105.8899
60.6403-0.0039-0.22250.0984-0.10610.44820.00550.14480.0576-0.0048-0.02180.006-0.0452-0.09440.01630.01540.01-0.01230.06550.01320.0289-4.220126.629167.0425
71.2603-0.03280.23220.2006-0.25390.37580.02850.1052-0.0251-0.0143-0.01220.0250.0192-0.0033-0.01630.00430.0038-0.00920.0584-0.02210.0273-9.7417.581373.7638
80.9304-0.1294-0.36430.377-0.03180.57510.0759-0.03270.1319-0.0062-0.0504-0.0369-0.09070.0424-0.02550.0421-0.01790.00630.0156-0.00010.044321.067230.37685.6173
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 148
2X-RAY DIFFRACTION2A149 - 254
3X-RAY DIFFRACTION3A255 - 411
4X-RAY DIFFRACTION4A412 - 560
5X-RAY DIFFRACTION5B1 - 272
6X-RAY DIFFRACTION6B273 - 407
7X-RAY DIFFRACTION7B408 - 465
8X-RAY DIFFRACTION8B466 - 561

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