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- PDB-3mbi: Crystal structure of the phosphoribosylpyrophosphate (PRPP) synth... -

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Basic information

Entry
Database: PDB / ID: 3mbi
TitleCrystal structure of the phosphoribosylpyrophosphate (PRPP) synthetase from Thermoplasma volcanium in complex with ADP-Mg2+ and ribose 5-phosphate
ComponentsRibose-phosphate pyrophosphokinase
KeywordsTRANSFERASE / Phosphoribosyl transferase / ATP analog binding / Ribose 5-phosphate binding
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 / kinase activity / phosphorylation / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Ribose-phosphate pyrophosphokinase, archaea / N-terminal domain of ribose phosphate pyrophosphokinase / Ribose-phosphate pyrophosphokinase / Ribose-phosphate pyrophosphokinase, N-terminal domain / N-terminal domain of ribose phosphate pyrophosphokinase / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold ...Ribose-phosphate pyrophosphokinase, archaea / N-terminal domain of ribose phosphate pyrophosphokinase / Ribose-phosphate pyrophosphokinase / Ribose-phosphate pyrophosphokinase, N-terminal domain / N-terminal domain of ribose phosphate pyrophosphokinase / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 5-O-phosphono-alpha-D-ribofuranose / PHOSPHATE ION / Ribose-phosphate pyrophosphokinase
Similarity search - Component
Biological speciesThermoplasma volcanium (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCherney, L.T. / Cherney, M.M. / Garen, C.R. / James, M.N.G.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The structures of Thermoplasma volcanium phosphoribosyl pyrophosphate synthetase bound to ribose-5-phosphate and ATP analogs.
Authors: Cherney, M.M. / Cherney, L.T. / Garen, C.R. / James, M.N.
History
DepositionMar 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 25, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_chem_comp_identifier / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 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
C: Ribose-phosphate pyrophosphokinase
D: Ribose-phosphate pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,49916
Polymers129,1784
Non-polymers2,32112
Water22,5911254
1
A: Ribose-phosphate pyrophosphokinase
C: Ribose-phosphate pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6828
Polymers64,5892
Non-polymers1,0936
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-18 kcal/mol
Surface area22440 Å2
MethodPISA
2
B: Ribose-phosphate pyrophosphokinase
D: Ribose-phosphate pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8178
Polymers64,5892
Non-polymers1,2286
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-18 kcal/mol
Surface area22490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.599, 61.841, 127.938
Angle α, β, γ (deg.)90.00, 103.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 5 molecules ABCD

#1: Protein
Ribose-phosphate pyrophosphokinase / RPPK / Phosphoribosyl pyrophosphate synthase / P-Rib-PP synthase / PRPP synthase


Mass: 32294.492 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma volcanium (archaea) / Strain: ATCC51530 / Gene: prs, TV0197, TVG0201915, TVN0197 / Plasmid: pvp16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PlysS
References: UniProt: Q97CA5, ribose-phosphate diphosphokinase
#5: 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.: 1
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 , 4 types, 1265 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1254 / 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: 2.28 Å3/Da / Density % sol: 45.97 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 30% PEG600, 0.1M HEPES, 10% MPD, 0.1% LDAO, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.797→25.471 Å / Num. obs: 105923 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 11.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.71 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_343)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LPN

3lpn


Resolution: 1.8→25.47 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 22.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.219 5260 4.97 %
Rwork0.176 --
obs0.178 105818 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.23 Å2 / ksol: 0.33 e/Å3
Refinement stepCycle: LAST / Resolution: 1.8→25.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9060 0 141 1254 10455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0169391
X-RAY DIFFRACTIONf_angle_d1.00212737
X-RAY DIFFRACTIONf_dihedral_angle_d14.3953625
X-RAY DIFFRACTIONf_chiral_restr0.0741449
X-RAY DIFFRACTIONf_plane_restr0.0041605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.797-1.81760.30641780.26243182X-RAY DIFFRACTION93
1.8176-1.8390.30322040.24223190X-RAY DIFFRACTION96
1.839-1.86140.29191660.2243309X-RAY DIFFRACTION97
1.8614-1.8850.27931860.23343305X-RAY DIFFRACTION97
1.885-1.90980.27551640.22183300X-RAY DIFFRACTION97
1.9098-1.93590.26531690.21843317X-RAY DIFFRACTION97
1.9359-1.96360.30961490.21093350X-RAY DIFFRACTION97
1.9636-1.99290.25971800.20753323X-RAY DIFFRACTION97
1.9929-2.0240.22551730.18663274X-RAY DIFFRACTION97
2.024-2.05720.211560.17773403X-RAY DIFFRACTION97
2.0572-2.09260.22731580.17443289X-RAY DIFFRACTION97
2.0926-2.13060.23361650.17913352X-RAY DIFFRACTION97
2.1306-2.17160.23161670.16943337X-RAY DIFFRACTION97
2.1716-2.21590.21861860.17573323X-RAY DIFFRACTION98
2.2159-2.26410.22981720.17183314X-RAY DIFFRACTION98
2.2641-2.31670.20991870.17193346X-RAY DIFFRACTION98
2.3167-2.37460.2231980.16363362X-RAY DIFFRACTION98
2.3746-2.43870.22621620.17253333X-RAY DIFFRACTION98
2.4387-2.51040.23811810.17663371X-RAY DIFFRACTION98
2.5104-2.59140.23631730.17263378X-RAY DIFFRACTION98
2.5914-2.68390.22071610.1713376X-RAY DIFFRACTION98
2.6839-2.79130.23412020.17883357X-RAY DIFFRACTION98
2.7913-2.91810.24471860.18383384X-RAY DIFFRACTION98
2.9181-3.07170.25121730.18533401X-RAY DIFFRACTION99
3.0717-3.26380.21221770.17363398X-RAY DIFFRACTION99
3.2638-3.51520.21781530.16193441X-RAY DIFFRACTION99
3.5152-3.86790.17361780.14893433X-RAY DIFFRACTION99
3.8679-4.4250.16821920.13383436X-RAY DIFFRACTION99
4.425-5.56550.14561620.14423490X-RAY DIFFRACTION99
5.5655-25.47320.18512020.16713484X-RAY DIFFRACTION98

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