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- PDB-3dah: 2.3 A crystal structure of ribose-phosphate pyrophosphokinase fro... -

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Basic information

Entry
Database: PDB / ID: 3dah
Title2.3 A crystal structure of ribose-phosphate pyrophosphokinase from Burkholderia pseudomallei
ComponentsRibose-phosphate pyrophosphokinase
KeywordsTRANSFERASE / BURKHOLDERIA / PSEUDOMALLEI / RIBOSE / PHOSPHATE / PYROPHOSPHOKINASE / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / SSGCID / Magnesium / Metal binding / Nucleotide biosynthesis
Function / homology
Function and homology information


ribose phosphate diphosphokinase complex / ribonucleoside monophosphate biosynthetic process / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / 5-phosphoribose 1-diphosphate biosynthetic process / purine nucleotide biosynthetic 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 / 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 / Phosphoribosyltransferase-like ...Phosphoribosyl pyrophosphate synthetase, conserved site / Phosphoribosyl pyrophosphate synthase signature. / Ribose-phosphate pyrophosphokinase, bacterial-type / Phosphoribosyl synthetase-associated domain / 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 / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / PHOSPHATE ION / Ribose-phosphate pyrophosphokinase / Ribose-phosphate pyrophosphokinase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionMay 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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: Ribose-phosphate pyrophosphokinase
B: Ribose-phosphate pyrophosphokinase
C: Ribose-phosphate pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,71413
Polymers103,0073
Non-polymers1,70610
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ribose-phosphate pyrophosphokinase
B: Ribose-phosphate pyrophosphokinase
C: Ribose-phosphate pyrophosphokinase
hetero molecules

A: Ribose-phosphate pyrophosphokinase
B: Ribose-phosphate pyrophosphokinase
C: Ribose-phosphate pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,42726
Polymers206,0146
Non-polymers3,41320
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area22970 Å2
ΔGint-51.4 kcal/mol
Surface area62650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.966, 123.242, 197.364
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Ribose-phosphate pyrophosphokinase


Mass: 34335.734 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: prsA, BURPS1710b_0753 / Plasmid: Ava0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q3JW86, UniProt: Q63XL8*PLUS, ribose-phosphate diphosphokinase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.3 Å3/Da / Density % sol: 46.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5.9
Details: 20% PEG 3350, 0.2M Magnesium formate, pH 5.9, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 2, 2008 / Details: ADJUSTABLE FOCUSING MIRRORS
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 41722 / % possible obs: 98 % / Redundancy: 6 % / Rmerge(I) obs: 0.09 / Χ2: 0.926 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.384.40.4936480.875187.1
2.38-2.484.90.46139800.914194.7
2.48-2.595.40.40141400.954198.3
2.59-2.736.10.36842300.9531100
2.73-2.96.40.27742060.9521100
2.9-3.126.60.21442391.0071100
3.12-3.446.70.13642460.9721100
3.44-3.936.70.07742660.8351100
3.93-4.956.60.05442920.9341100
4.95-506.40.03344750.8471100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.55 Å49.34 Å
Translation2.55 Å49.34 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1DKU

1dku


Resolution: 2.3→46.93 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / SU B: 8.489 / SU ML: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.367 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2110 5.1 %RANDOM
Rwork0.206 ---
obs0.208 41695 97.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.513 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20 Å2
2---1.11 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6637 0 104 138 6879
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226817
X-RAY DIFFRACTIONr_angle_refined_deg1.32429242
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4325878
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72723.704270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.779151184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8491562
X-RAY DIFFRACTIONr_chiral_restr0.090.21109
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024978
X-RAY DIFFRACTIONr_nbd_refined0.1970.23084
X-RAY DIFFRACTIONr_nbtor_refined0.2990.24645
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2288
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.2103
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.223
X-RAY DIFFRACTIONr_mcbond_it0.5191.54548
X-RAY DIFFRACTIONr_mcangle_it0.89427051
X-RAY DIFFRACTIONr_scbond_it1.25432537
X-RAY DIFFRACTIONr_scangle_it2.14.52191
LS refinement shellResolution: 2.3→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 125 -
Rwork0.279 2527 -
all-2652 -
obs--84.19 %

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