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- PDB-6nfe: Crystal Structure of Ribose-phosphate Pyrophosphokinase from Legi... -

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Basic information

Entry
Database: PDB / ID: 6nfe
TitleCrystal Structure of Ribose-phosphate Pyrophosphokinase from Legionella pneumophila with bound AMP, ADP, and Ribose-5-Phosphate
ComponentsRibose-phosphate pyrophosphokinase
KeywordsLIGASE / SSGCID / phosphorylation / AMP / ADP / Ribose-5-Phosphate / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / ribonucleoside monophosphate biosynthetic process / nucleotide biosynthetic process / 5-phosphoribose 1-diphosphate biosynthetic process / nucleoside metabolic process / kinase activity / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Phosphoribosyl pyrophosphate synthetase, conserved site / Phosphoribosyl pyrophosphate synthase signature. / Ribose-phosphate pyrophosphokinase, bacterial-type / Phosphoribosyl synthetase-associated domain / Ribose-phosphate pyrophosphokinase / Ribose-phosphate pyrophosphokinase, N-terminal domain / N-terminal domain of ribose phosphate pyrophosphokinase / Rossmann fold - #2020 / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain ...Phosphoribosyl pyrophosphate synthetase, conserved site / Phosphoribosyl pyrophosphate synthase signature. / Ribose-phosphate pyrophosphokinase, bacterial-type / Phosphoribosyl synthetase-associated domain / Ribose-phosphate pyrophosphokinase / Ribose-phosphate pyrophosphokinase, N-terminal domain / N-terminal domain of ribose phosphate pyrophosphokinase / Rossmann fold - #2020 / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE MONOPHOSPHATE / ETHANOL / 5-O-phosphono-alpha-D-ribofuranose / Ribose-phosphate pyrophosphokinase / Ribose-phosphate pyrophosphokinase
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Ribose-phosphate Pyrophosphokinase from Legionella pneumophila with bound AMP, ADP, and Ribose-5-Phosphate
Authors: Bolejack, M.J. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionDec 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_chem_comp_identifier / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribose-phosphate pyrophosphokinase
B: Ribose-phosphate pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,22922
Polymers70,3992
Non-polymers2,83020
Water9,440524
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint1 kcal/mol
Surface area27200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.000, 109.000, 97.300
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Ribose-phosphate pyrophosphokinase / RPPK / 5-phospho-D-ribosyl alpha-1-diphosphate / Phosphoribosyl diphosphate synthase / ...RPPK / 5-phospho-D-ribosyl alpha-1-diphosphate / Phosphoribosyl diphosphate synthase / Phosphoribosyl pyrophosphate synthase / PRPPase


Mass: 35199.676 Da / Num. of mol.: 2 / Fragment: LepnA.00035.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: prsA, prs, C3927_02005, NCTC12024_00599 / Plasmid: LepnA.00035.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A2S6FBX1, UniProt: Q5ZY30*PLUS, ribose-phosphate diphosphokinase
#4: Sugar ChemComp-HSX / 5-O-phosphono-alpha-D-ribofuranose / 5-O-phosphono-alpha-D-ribose / 5-O-phosphono-D-ribose / 5-O-phosphono-ribose


Type: D-saccharide, alpha linking / Mass: 230.110 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P
IdentifierTypeProgram
a-D-Ribf5PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 542 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: LepnA.00035.a.B1.PS38405 at 19.13 mg/ml was incubated with 4 mM ribose-5-phosphate, 4 mM ATP, and 4 mM MgCl2 then was mixed 1:1 JCSG+(b6): 40% (v/v) reagent alcohol, 100 mM sodium phosphate ...Details: LepnA.00035.a.B1.PS38405 at 19.13 mg/ml was incubated with 4 mM ribose-5-phosphate, 4 mM ATP, and 4 mM MgCl2 then was mixed 1:1 JCSG+(b6): 40% (v/v) reagent alcohol, 100 mM sodium phosphate dibasic/citric acid pH 4.2. Tray: 298764b6, puck: uya9-9.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 12, 2018 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.75→43.245 Å / Num. obs: 67559 / % possible obs: 99.9 % / Redundancy: 7.462 % / Biso Wilson estimate: 26.218 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.077 / Χ2: 1.02 / Net I/σ(I): 18.78 / Num. measured all: 504098
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.75-1.87.4620.4555.3837107497549730.9160.491100
1.8-1.847.4570.3716.435982482648250.9380.401100
1.84-1.97.4760.297.9234995468446810.9620.31399.9
1.9-1.967.4690.2329.5933918454345410.9750.251100
1.96-2.027.4750.19111.133292445444540.9810.207100
2.02-2.097.5030.15713.1231976426442620.9880.169100
2.09-2.177.5010.12415.8731070414241420.9920.133100
2.17-2.267.5160.10417.9429997399239910.9940.112100
2.26-2.367.5060.09119.9528771383538330.9940.09999.9
2.36-2.477.5080.08221.3827470366036590.9950.088100
2.47-2.617.5160.07423.426079347034700.9960.08100
2.61-2.777.5050.06825.4124856331233120.9960.074100
2.77-2.967.4840.06327.723252311031070.9970.06899.9
2.96-3.27.4890.05729.8221718290129000.9970.061100
3.2-3.57.4530.05132.4920018268826860.9980.05599.9
3.5-3.917.4240.04934.2118189245124500.9980.053100
3.91-4.527.3830.04635.9915954216621610.9980.04999.8
4.52-5.537.3560.04536.3113498183718350.9980.04999.9
5.53-7.837.230.04734.8610426145014420.9970.05199.4
7.83-43.2456.6230.04635.4355308568350.9980.0597.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S2U

4s2u


Resolution: 1.75→43.245 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.37
RfactorNum. reflection% reflection
Rfree0.1764 1927 2.85 %
Rwork0.1518 --
obs0.1525 67554 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.36 Å2 / Biso mean: 25.2569 Å2 / Biso min: 8.04 Å2
Refinement stepCycle: final / Resolution: 1.75→43.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4468 0 204 535 5207
Biso mean--45 33.67 -
Num. residues----597
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.79380.23991360.209346374773100
1.7938-1.84230.21161570.180646304787100
1.8423-1.89650.1861170.161946604777100
1.8965-1.95770.17921140.153546444758100
1.9577-2.02770.19271380.157846844822100
2.0277-2.10890.19171360.155246314767100
2.1089-2.20480.15131250.147246744799100
2.2048-2.32110.17671570.146246804837100
2.3211-2.46650.19271550.153146264781100
2.4665-2.65690.1711960.148347424838100
2.6569-2.92420.17291670.1546574824100
2.9242-3.34720.16891420.151347114853100
3.3472-4.21660.14551380.135947544892100
4.2166-43.25780.18851490.15454897504699
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)
11.4440.4730.49551.46070.60961.5162-0.0910.2165-0.1137-0.23910.06370.0143-0.09590.08220.03070.1546-0.00220.02130.13720.00120.097317.040944.57951.21
21.98950.18030.26081.27020.05771.4532-0.0220.21030.1437-0.1778-0.0433-0.0138-0.11910.11010.03130.1411-0.00610.00570.11890.00110.07915.254950.40944.3785
31.23710.32550.02671.83990.01451.0636-0.00690.07210.077-0.1023-0.04520.039-0.10890.06010.04270.12140.0054-0.00070.1145-0.00470.082412.328952.16069.3538
41.4385-0.1749-0.41721.26890.78413.60790.0748-0.2536-0.15060.2317-0.03230.04710.2249-0.19860.09430.1221-0.0042-0.00150.13570.03270.10252.932239.619126.0123
51.29880.1284-0.09833.38610.81631.18930.001-0.0055-0.0254-0.1418-0.04220.0661-0.0614-0.04350.03090.09850.01780.00920.10610.00290.08190.795545.002713.3862
60.83490.49390.12964.21381.40441.2867-0.17120.2031-0.4026-0.13030.09580.27980.252-0.30140.07660.1698-0.04190.04340.2237-0.08560.4223-1.673818.38255.4173
72.5158-1.34412.00215.2243-0.86527.4691-0.1747-0.01130.3063-0.2210.12110.06820.0341-0.590.06070.1591-0.03920.07160.2674-0.00580.4043-8.230121.216313.8775
81.1169-1.80310.09162.9890.14760.9585-0.4034-0.3104-0.72270.34290.0824-0.19540.6404-0.56570.00650.3577-0.11110.15390.22670.02060.5536-3.08213.830819.5873
90.50651.02610.34593.527-0.88622.04150.0435-0.6056-0.51040.4349-0.22030.36660.3285-0.42020.0750.274-0.06420.10250.25110.11470.38275.129817.618620.2201
101.80461.63720.89923.5597-0.7822.9504-0.0143-0.015-0.58850.3-0.00250.20520.46060.0667-0.00710.2080.02680.07650.1184-0.00690.28938.563519.012414.6055
113.08130.63870.77836.3566-2.26513.0575-0.0949-0.0835-0.61830.12950.02850.01530.24020.06060.06070.1330.02210.05980.116-0.00280.195114.043421.255510.1792
127.2351-7.42974.37258.8653-6.4916.21510.03610.25080.04840.0009-0.13860.0484-0.1519-0.16350.13870.1181-0.00710.00720.1349-0.0290.0964.8136.1357-0.8988
130.69670.26190.01991.08370.02370.56490.0093-0.15190.01380.1472-0.01250.0149-0.0041-0.03460.00650.13140.011-0.01730.14860.01540.075916.676953.633231.3141
144.0039-0.16790.94862.4096-1.08773.80370.1153-0.47460.03650.402-0.0858-0.3649-0.21080.4548-0.07240.2012-0.0513-0.06560.25310.00130.19744.690466.024536.0771
156.27330.60210.0685.1054-1.97571.95130.42010.40230.10370.1145-0.09930.4646-0.12650.0355-0.34050.22320.02470.0160.19480.00410.292942.129370.685223.9295
163.14690.6931-0.8091.2069-0.28951.34370.0251-0.0748-0.12630.0199-0.048-0.2459-0.0510.19780.02630.13570.0061-0.05370.19220.02980.152640.970657.293130.078
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 39 )A2 - 39
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 62 )A40 - 62
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 89 )A63 - 89
4X-RAY DIFFRACTION4chain 'A' and (resid 90 through 108 )A90 - 108
5X-RAY DIFFRACTION5chain 'A' and (resid 109 through 148 )A109 - 148
6X-RAY DIFFRACTION6chain 'A' and (resid 149 through 170 )A149 - 170
7X-RAY DIFFRACTION7chain 'A' and (resid 171 through 195 )A171 - 195
8X-RAY DIFFRACTION8chain 'A' and (resid 196 through 220 )A196 - 220
9X-RAY DIFFRACTION9chain 'A' and (resid 221 through 238 )A221 - 238
10X-RAY DIFFRACTION10chain 'A' and (resid 239 through 262 )A239 - 262
11X-RAY DIFFRACTION11chain 'A' and (resid 263 through 286 )A263 - 286
12X-RAY DIFFRACTION12chain 'A' and (resid 287 through 305 )A287 - 305
13X-RAY DIFFRACTION13chain 'B' and (resid 2 through 148 )B2 - 148
14X-RAY DIFFRACTION14chain 'B' and (resid 149 through 170 )B149 - 170
15X-RAY DIFFRACTION15chain 'B' and (resid 171 through 206 )B171 - 206
16X-RAY DIFFRACTION16chain 'B' and (resid 207 through 305 )B207 - 305

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