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- PDB-3q4g: Structure of NAD synthetase from Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 3q4g
TitleStructure of NAD synthetase from Vibrio cholerae
ComponentsNH(3)-dependent NAD(+) synthetase
KeywordsLIGASE / Structural Genomics / CSGID / Center for Structural Genomics of Infectious Diseases / alpha beta / 3-layer(aba) sandwich / Rossmann fold / NAD synthetase
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
: / NH(3)-dependent NAD(+) synthetase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsAnderson, S.M. / Wawrzak, Z. / Onopriyenko, O. / Peterson, S.N. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Structure of NAD synthetase from Vibrio cholerae
Authors: Anderson, S.M. / Wawrzak, Z. / Onopriyenko, O. / Peterson, S.N. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 8, 2014Group: Database references
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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: NH(3)-dependent NAD(+) synthetase
B: NH(3)-dependent NAD(+) synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9916
Polymers61,8312
Non-polymers1604
Water7,404411
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-85 kcal/mol
Surface area22800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.426, 93.426, 165.297
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein NH(3)-dependent NAD(+) synthetase


Mass: 30915.564 Da / Num. of mol.: 2 / Fragment: unp residues 11-285 / Mutation: C37Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: O1 biovar eltor str. N16961 / Gene: nadE, VCD_000045 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL
References: UniProt: C3NY23, UniProt: Q9KMW1*PLUS, NAD+ synthase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.37 Å3/Da / Density % sol: 63.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2M sodium formate, 100mM sodium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 2, 2010 / Details: beryllium lens
RadiationMonochromator: C(111) diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 33479 / Num. obs: 33278 / % possible obs: 99.4 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 2.5 / Redundancy: 13.4 % / Biso Wilson estimate: 33.15 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 22.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3117 / % possible all: 95.3

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
BLU-MAXdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→46.7 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.28 / σ(F): 1.44 / σ(I): 2.5 / Phase error: 21.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2151 1668 5.02 %random
Rwork0.1707 ---
all0.1734 33473 --
obs0.1729 33202 99.2 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.751 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 373.96 Å2 / Biso mean: 46.09 Å2 / Biso min: 13.88 Å2
Baniso -1Baniso -2Baniso -3
1-6.51 Å2-0 Å2-0 Å2
2--6.51 Å20 Å2
3----13.02 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4070 0 4 411 4485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074185
X-RAY DIFFRACTIONf_angle_d0.8475670
X-RAY DIFFRACTIONf_chiral_restr0.061640
X-RAY DIFFRACTIONf_plane_restr0.005746
X-RAY DIFFRACTIONf_dihedral_angle_d12.3611566
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.4-2.480.3141510.2729073058305893.6
2.48-2.580.2581630.22830783241324198.6
2.58-2.70.261650.20231523317331799.9
2.7-2.840.2411650.18431413306330699.9
2.84-3.020.2331670.18131533320332099.9
3.02-3.250.2151680.17314333113311100
3.25-3.580.2141690.159318433533353100
3.58-4.10.1771700.137318233523352100
4.1-5.160.1921730.133323134043404100
5.16-46.720.2041770.19133633540354099.9
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)
10.74910.58040.53841.52191.01271.6496-0.00040.006-0.0088-0.16740.0126-0.1731-0.13990.2373-0.03270.2065-0.0260.02760.18480.02150.163742.599546.204561.1264
21.9993-1.08752.11032.20110.08593.17260.18060.47570.1118-0.3739-0.25660.5725-0.2265-0.32570.03830.67280.1332-0.03310.3370.00810.257926.312257.789647.9113
30.5832-0.2391-0.36140.76150.50721.93030.11810.16750.1378-0.3251-0.24980.2796-0.5901-0.25040.16620.36560.184-0.0570.18770.03430.15726.068646.704439.9171
40.45210.08680.55050.4940.72441.45650.0230.0024-0.0528-0.2282-0.16550.0822-0.3006-0.15530.10480.21720.04780.01140.20090.00590.194731.848244.801354.3249
50.65080.08790.44592.17351.87931.8960.0403-0.0858-0.2495-0.017-0.53630.4550.1733-0.53940.35150.1637-0.070.01610.3422-0.05860.219324.331131.473860.8079
60.92970.2134-0.26110.89150.29681.25990.0231-0.05240.10550.0787-0.0644-0.00670.1109-0.14140.04350.17790.0387-0.01030.1643-0.00320.19334.019617.303637.7625
70.61880.4484-1.62343.57292.21447.8010.2301-0.0938-0.179-0.7439-0.3922-0.5277-1.3080.2730.23750.48650.1519-0.05690.26790.00150.247935.992334.168220.7945
80.42830.41680.16262.08180.7862.0433-0.05440.21130.1601-0.7936-0.0420.187-0.95210.17160.01520.46850.02560.01370.24510.06070.111936.142142.415730.7213
90.18910.4623-0.0411.55660.44340.70160.09690.05790.0106-0.246-0.028-0.0798-0.34830.0391-0.0580.22860.00740.03040.24110.01320.124940.044928.127234.6715
100.74440.2157-1.22541.73941.70444.5434-0.016-0.2262-0.2991-0.18080.2386-0.3019-0.46580.6787-0.18550.146-0.01650.0080.2864-0.04270.316954.759527.321244.6037
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:78)A1 - 78
2X-RAY DIFFRACTION2(chain A and resid 79:92)A79 - 92
3X-RAY DIFFRACTION3(chain A and resid 93:135)A93 - 135
4X-RAY DIFFRACTION4(chain A and resid 136:214)A136 - 214
5X-RAY DIFFRACTION5(chain A and resid 215:276)A215 - 276
6X-RAY DIFFRACTION6(chain B and resid 1:78)B1 - 78
7X-RAY DIFFRACTION7(chain B and resid 79:92)B79 - 92
8X-RAY DIFFRACTION8(chain B and resid 93:135)B93 - 135
9X-RAY DIFFRACTION9(chain B and resid 136:214)B136 - 214
10X-RAY DIFFRACTION10(chain B and resid 215:276)B215 - 276

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