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- PDB-2ji4: Human phosphoribosylpyrophosphate synthetase - associated protein... -

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Basic information

Entry
Database: PDB / ID: 2ji4
TitleHuman phosphoribosylpyrophosphate synthetase - associated protein 41 (PAP41)
ComponentsPHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE-ASSOCIATED PROTEIN 2
KeywordsTRANSFERASE / PHOSPHORYLATION / NUCLEOTIDE BIOSYNTHESIS
Function / homology
Function and homology information


5-phosphoribose 1-diphosphate biosynthetic process / purine nucleotide biosynthetic process / nucleobase-containing compound metabolic process / enzyme inhibitor activity / enzyme regulator activity / bone development / magnesium ion binding / identical protein binding / cytoplasm
Similarity search - Function
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
Phosphoribosyl pyrophosphate synthase-associated protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsMoche, M. / Lehtio, L. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. ...Moche, M. / Lehtio, L. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg-Schiavone, L. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Nordlund, P.
CitationJournal: To be Published
Title: Human Phosphoribosylpyrophosphate Synthetase -Associated Protein 41 (Pap41)
Authors: Moche, M. / Lehtio, L. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / ...Authors: Moche, M. / Lehtio, L. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg-Schiavone, L. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Nordlund, P.
History
DepositionFeb 26, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE-ASSOCIATED PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2303
Polymers42,1591
Non-polymers712
Water68538
1
A: PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE-ASSOCIATED PROTEIN 2
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)253,37818
Polymers252,9536
Non-polymers42512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation6_555-x,-x+y,-z1
crystal symmetry operation5_555x-y,-y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)104.400, 104.400, 192.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE-ASSOCIATED PROTEIN 2 / PHOSPHORIBOSYLPYROPHOSPHATE SYNTHETASE-ASSOCIATED PROTEIN 41 - PAP41 / PRPP SYNTHETASE-ASSOCIATED ...PHOSPHORIBOSYLPYROPHOSPHATE SYNTHETASE-ASSOCIATED PROTEIN 41 - PAP41 / PRPP SYNTHETASE-ASSOCIATED PROTEIN 2 / 41 KDA PHOSPHORIBOSYPYROPHOSPHATE SYNTHETASE-ASSOCIATED PROTEIN / PAP41


Mass: 42158.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O60256
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsOUR CONSTRUCT CONTAINS 1. AN N-TERMINAL HEXAHISTIDINE TAG 2. A NUMBER OF LINKER RESIDUES 3. M13-D369 OF O60256

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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: 3.03 Å3/Da / Density % sol: 48.47 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 19, 2006 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 14119 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 24.8
Reflection shellResolution: 2.5→2.7 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 7.4 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.3.0021refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C4K

2c4k


Resolution: 2.55→19.73 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.904 / SU B: 12.206 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R: 0.465 / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.273 659 4.9 %RANDOM
Rwork0.206 ---
obs0.21 12664 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.55→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2336 0 2 38 2376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222368
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.9733197
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0295299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56224.31695
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.23715442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7581515
X-RAY DIFFRACTIONr_chiral_restr0.1390.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021705
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2340.21100
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3330.51651
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.3143
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0480.35
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.36521527
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.66232441
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4532902
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.513756
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.62 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.414 50
Rwork0.329 901

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