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- PDB-5hul: Crystal Structure of NadC Deletion Mutant in Cubic Space Group -

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Basic information

Entry
Database: PDB / ID: 5hul
TitleCrystal Structure of NadC Deletion Mutant in Cubic Space Group
ComponentsQuinolinate phosphoribosyltransferase
KeywordsTRANSFERASE / Quinolinate phosphoribosyltransferase
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
PHOSPHATE ION / nicotinate-nucleotide diphosphorylase (carboxylating)
Similarity search - Component
Biological speciesStreptococcus pyogenes serotype M49 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.855 Å
AuthorsBooth, W.T. / Chruszcz, M.
CitationJournal: FEBS J. / Year: 2017
Title: Streptococcus pyogenes quinolinate-salvage pathway-structural and functional studies of quinolinate phosphoribosyl transferase and NH3 -dependent NAD(+) synthetase.
Authors: Booth, W.T. / Morris, T.L. / Mysona, D.P. / Shah, M.J. / Taylor, L.K. / Karlin, T.W. / Clary, K. / Majorek, K.A. / Offermann, L.R. / Chruszcz, M.
History
DepositionJan 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 23, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Quinolinate phosphoribosyltransferase
B: Quinolinate phosphoribosyltransferase
C: Quinolinate phosphoribosyltransferase
D: Quinolinate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,50823
Polymers137,7044
Non-polymers1,80419
Water543
1
A: Quinolinate phosphoribosyltransferase
B: Quinolinate phosphoribosyltransferase
hetero molecules

A: Quinolinate phosphoribosyltransferase
B: Quinolinate phosphoribosyltransferase
hetero molecules

A: Quinolinate phosphoribosyltransferase
B: Quinolinate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,40536
Polymers206,5556
Non-polymers2,84930
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area33760 Å2
ΔGint-295 kcal/mol
Surface area55820 Å2
MethodPISA
2
C: Quinolinate phosphoribosyltransferase
D: Quinolinate phosphoribosyltransferase
hetero molecules

C: Quinolinate phosphoribosyltransferase
D: Quinolinate phosphoribosyltransferase
hetero molecules

C: Quinolinate phosphoribosyltransferase
D: Quinolinate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,12033
Polymers206,5556
Non-polymers2,56427
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation10_656-y+1,z,-x+11
Buried area32100 Å2
ΔGint-276 kcal/mol
Surface area57530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.630, 179.630, 179.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERASPASPAA5 - 28830 - 313
21SERSERASPASPBB5 - 28830 - 313
12THRTHRLEULEUAA6 - 28731 - 312
22THRTHRLEULEUCC6 - 28731 - 312
13SERSERASPASPAA5 - 28830 - 313
23SERSERASPASPDD5 - 28830 - 313
14THRTHRASPASPBB6 - 28831 - 313
24THRTHRASPASPCC6 - 28831 - 313
15SERSERASPASPBB5 - 28830 - 313
25SERSERASPASPDD5 - 28830 - 313
16THRTHRLEULEUCC6 - 28731 - 312
26THRTHRLEULEUDD6 - 28731 - 312

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Quinolinate phosphoribosyltransferase


Mass: 34425.902 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M49 (strain NZ131) (bacteria)
Strain: NZ131 / Gene: Spy49_0176 / Plasmid: pjExpress411 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: A0A0H3BVM1, nicotinate-nucleotide diphosphorylase (carboxylating)
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.51 Å3/Da / Density % sol: 64.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 1 M Ammonium Phosphate, 0.1 M Sodium citrate tribasic/ Citric acid, 0.2 M Sodium Chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.73
11K, H, -L20.27
ReflectionResolution: 2.85→40 Å / Num. obs: 44917 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 24.1
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.815 / Mean I/σ(I) obs: 2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KWV

4kwv


Resolution: 2.855→39.2 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / SU B: 23.922 / SU ML: 0.261 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.057 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20518 2270 5.1 %RANDOM
Rwork0.16991 ---
obs0.17169 42645 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 154.782 Å2
Baniso -1Baniso -2Baniso -3
1--152.64 Å2-103.21 Å2-106.36 Å2
2--48.02 Å2-39.72 Å2
3---104.61 Å2
Refinement stepCycle: 1 / Resolution: 2.855→39.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8573 0 95 3 8671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0198770
X-RAY DIFFRACTIONr_bond_other_d0.0090.028314
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.96611888
X-RAY DIFFRACTIONr_angle_other_deg1.87319011
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.51251129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.69624.158380
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.051151450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.921556
X-RAY DIFFRACTIONr_chiral_restr0.0880.21406
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029976
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021982
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_it11.33713.3614531
X-RAY DIFFRACTIONr_mcbond_other11.33613.364530
X-RAY DIFFRACTIONr_mcangle_it13.83920.0895655
X-RAY DIFFRACTIONr_mcangle_other13.83820.0915656
X-RAY DIFFRACTIONr_scbond_it12.48913.8534239
X-RAY DIFFRACTIONr_scbond_other12.14813.8044161
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other15.72720.5026119
X-RAY DIFFRACTIONr_long_range_B_refined17.4559249
X-RAY DIFFRACTIONr_long_range_B_other17.4559250
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A323200.09
12B323200.09
21A319800.09
22C319800.09
31A321440.09
32D321440.09
41B325760.09
42C325760.09
51B326280.09
52D326280.09
61C318660.1
62D318660.1
LS refinement shellResolution: 2.855→2.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.457 159 -
Rwork0.373 3086 -
obs--99.57 %
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)
11.8664-0.478-0.979711.8702-5.43563.31360.3370.583-0.3022-0.38530.07291.47650.0477-0.3725-0.40980.57250.10320.08020.487-0.09180.507948.46246.83630.95
20.9297-0.32960.62880.7872-0.41430.9585-0.03340.2256-0.1937-0.091-0.05-0.01640.10980.10380.08340.12640.0120.02510.0724-0.08060.14169.01533.06736.286
35.0148-0.8866-1.95210.60790.20880.88780.0329-0.1010.0566-0.01020.03080.05650.01380.1692-0.06370.2097-0.0046-0.02340.2203-0.00980.135452.12364.79747.43
40.65060.1794-0.40361.767-1.09960.82470.0156-0.04240.1079-0.11710.26240.40780.0583-0.1067-0.27790.0116-0.0321-0.03070.14340.04850.13429.89468.28457.104
52.1992-1.16871.6323.0957-3.15586.01520.18780.1817-0.3783-0.1838-0.0742-0.21510.10940.6862-0.11360.21460.0485-0.03710.385-0.07730.2285129.15832.98646.631
61.813-0.75050.87561.1598-0.28030.93830.05810.3897-0.282-0.04330.08260.19890.19230.1776-0.14070.163-0.0216-0.02670.157-0.03450.0534109.72539.1531.943
70.1555-0.2690.14480.4891-0.41452.9113-0.049-0.0455-0.03770.09190.03940.0210.0952-0.22750.00960.1186-0.0272-0.05430.24110.10120.1934131.68166.44854.237
81.01931.37850.71232.03750.6081.457-0.33950.2195-0.0419-0.50260.4081-0.0339-0.18640.0717-0.06860.1404-0.1055-0.00040.18980.00520.0113123.39570.36331.602
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 40
2X-RAY DIFFRACTION2A41 - 288
3X-RAY DIFFRACTION3B6 - 38
4X-RAY DIFFRACTION4B40 - 288
5X-RAY DIFFRACTION5C6 - 40
6X-RAY DIFFRACTION6C41 - 288
7X-RAY DIFFRACTION7D5 - 39
8X-RAY DIFFRACTION8D40 - 288

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