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- PDB-3l0g: Crystal structure of Nicotinate-nucleotide pyrophosphorylase from... -

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Basic information

Entry
Database: PDB / ID: 3l0g
TitleCrystal structure of Nicotinate-nucleotide pyrophosphorylase from Ehrlichia chaffeensis at 2.05A resolution
ComponentsNicotinate-nucleotide pyrophosphorylase
KeywordsTRANSFERASE / SSGCID / NIH / NIAID / SBRI / UW / EMERALD BIOSTRUCTURES / ALS COLLABORATIVE CRYSTALLOGRAPHY / EHRLICHIA CHAFFEENSIS / NICOTINATE-NUCLEOTIDE PYROPHOSPHORYLASE / Glycosyltransferase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


nicotinate-nucleotide diphosphorylase (carboxylating) / nicotinate-nucleotide diphosphorylase (carboxylating) activity / NAD biosynthetic process
Similarity search - Function
Nicotinate-nucleotide pyrophosphorylase / Nicotinate-nucleotide pyrophosphorylase/Putative pyrophosphorylase ModD / Quinolinate phosphoribosyl transferase, N-terminal / Quinolinate phosphoribosyl transferase, N-terminal domain / Quinolinate phosphoribosyl transferase, N-terminal domain / Quinolinate phosphoribosyl transferase, C-terminal / Quinolinate phosphoribosyl transferase, N-terminal domain superfamily / Quinolinate phosphoribosyl transferase, C-terminal domain / Nicotinate phosphoribosyltransferase-like, C-terminal / Aldehyde Oxidoreductase; domain 3 ...Nicotinate-nucleotide pyrophosphorylase / Nicotinate-nucleotide pyrophosphorylase/Putative pyrophosphorylase ModD / Quinolinate phosphoribosyl transferase, N-terminal / Quinolinate phosphoribosyl transferase, N-terminal domain / Quinolinate phosphoribosyl transferase, N-terminal domain / Quinolinate phosphoribosyl transferase, C-terminal / Quinolinate phosphoribosyl transferase, N-terminal domain superfamily / Quinolinate phosphoribosyl transferase, C-terminal domain / Nicotinate phosphoribosyltransferase-like, C-terminal / Aldehyde Oxidoreductase; domain 3 / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Quinolinate phosphoribosyltransferase [decarboxylating]
Similarity search - Component
Biological speciesEhrlichia chaffeensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of Nicotinate-nucleotide pyrophosphorylase from Ehrlichia chaffeensis at 2.05A resolution
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Sankaran, B. / Arakaki, T. / Staker, B.
History
DepositionDec 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 6, 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: Nicotinate-nucleotide pyrophosphorylase
B: Nicotinate-nucleotide pyrophosphorylase
C: Nicotinate-nucleotide pyrophosphorylase
D: Nicotinate-nucleotide pyrophosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,36412
Polymers132,9324
Non-polymers4328
Water15,367853
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nicotinate-nucleotide pyrophosphorylase
C: Nicotinate-nucleotide pyrophosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6826
Polymers66,4662
Non-polymers2164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-16 kcal/mol
Surface area21680 Å2
MethodPISA
3
B: Nicotinate-nucleotide pyrophosphorylase
D: Nicotinate-nucleotide pyrophosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6826
Polymers66,4662
Non-polymers2164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-15 kcal/mol
Surface area21650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.530, 77.320, 78.320
Angle α, β, γ (deg.)113.01, 91.82, 111.68
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 275
2116B1 - 275
3116C1 - 275
4116D1 - 275

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Components

#1: Protein
Nicotinate-nucleotide pyrophosphorylase


Mass: 33232.953 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ehrlichia chaffeensis (bacteria) / Strain: Arkansas / Gene: nadC, ECH_0026 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2GI74, nicotinate-nucleotide diphosphorylase (carboxylating)
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 853 / 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: 2.31 Å3/Da / Density % sol: 46.71 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 0
Details: MD PACT SCREEN E6: 20% PEG 3350, 200MM NA-FORMATE; EHCHA.01074.A AT 29MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 74747 / Num. obs: 72223 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 24.47 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.27
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.4 / Num. unique all: 5510 / % possible all: 95.4

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.5.0104refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb deposition 3GNN modified with CCP4 program CHAINSAW

3gnn


Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.907 / SU B: 9.15 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.226 3640 5 %RANDOM
Rwork0.174 ---
all0.177 74747 --
obs0.177 72216 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å2-0.2 Å2-0.05 Å2
2---0.43 Å2-0.26 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8303 0 28 853 9184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228526
X-RAY DIFFRACTIONr_bond_other_d0.0010.025571
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.96711558
X-RAY DIFFRACTIONr_angle_other_deg0.964313805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.00951135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91725.89365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.669151581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6331541
X-RAY DIFFRACTIONr_chiral_restr0.0930.21425
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029512
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021521
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7321.55477
X-RAY DIFFRACTIONr_mcbond_other0.1861.52274
X-RAY DIFFRACTIONr_mcangle_it1.34228896
X-RAY DIFFRACTIONr_scbond_it2.19333049
X-RAY DIFFRACTIONr_scangle_it3.5034.52638
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3304 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Aloose positional0.45
Bloose positional0.345
Cloose positional0.395
Dloose positional0.385
Aloose thermal1.4810
Bloose thermal1.3810
Cloose thermal1.3610
Dloose thermal1.6810
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 266 -
Rwork0.226 4976 -
obs--95.48 %
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)
10.5658-0.04240.61640.19560.01521.02390.0376-0.01330.00590.032-0.00130.01020.0442-0.0328-0.03630.02910.010.00880.0104-0.00680.037822.17451.9724.064
20.6471-0.0037-0.61810.26620.08890.95980.05120.00060.0012-0.0239-0.01810.037-0.0445-0.0144-0.03310.01640.0049-0.0060.0031-0.00510.030724.19995.649-10.912
30.53610.10690.47410.21590.10610.98-0.00330.08350.0029-0.04680.0194-0.0545-0.03330.0803-0.0160.040.00550.00810.0143-0.00150.030630.67857.523-15.355
40.5453-0.1149-0.15050.39450.04880.854-0.0017-0.0905-0.05760.10780.0345-0.0303-0.00940.0111-0.03280.05250.0133-0.00960.01870.01040.019232.70990.18.337
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 274
2X-RAY DIFFRACTION1A300 - 301
3X-RAY DIFFRACTION1A280 - 868
4X-RAY DIFFRACTION2B3 - 275
5X-RAY DIFFRACTION2B300 - 301
6X-RAY DIFFRACTION2B280 - 852
7X-RAY DIFFRACTION3C1 - 274
8X-RAY DIFFRACTION3C300 - 301
9X-RAY DIFFRACTION3C280 - 866
10X-RAY DIFFRACTION4D2 - 275
11X-RAY DIFFRACTION4D300 - 301
12X-RAY DIFFRACTION4D280 - 862

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