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- PDB-2c4k: Crystal structure of human phosphoribosylpyrophosphate synthetase... -

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Basic information

Entry
Database: PDB / ID: 2c4k
TitleCrystal structure of human phosphoribosylpyrophosphate synthetase- associated protein 39 (PAP39)
ComponentsPHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE-ASSOCIATED PROTEIN 1
KeywordsREGULATORY PROTEIN / NUCLEOTIDE BIOSYNTHESIS / SYNTHETASE / LIGASE
Function / homology
Function and homology information


ribose phosphate diphosphokinase complex / ribose phosphate diphosphokinase activity / nucleotide biosynthetic process / 5-phosphoribose 1-diphosphate biosynthetic process / purine nucleotide biosynthetic process / enzyme inhibitor activity / nucleobase-containing compound metabolic process / magnesium ion binding / identical protein binding / cytoplasm
Similarity search - Function
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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoribosyl pyrophosphate synthase-associated protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsKursula, P. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Edwards, A. / Ehn, M. / Flodin, S. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. ...Kursula, P. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Edwards, A. / Ehn, M. / Flodin, S. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg Schiavone, L. / Kotenyova, T. / Nilsson-Ehle, P. / Ogg, D. / Persson, C. / Sagemark, J. / Schuler, H. / Sundstrom, M. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Nordlund, P.
CitationJournal: To be Published
Title: Crystal Structure of Human Phosphoribosylpyrophosphate Synthetase-Associated Protein 39 (Pap39)
Authors: Kursula, P. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Edwards, A. / Ehn, M. / Flodin, S. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg Schiavone, L. / Kotenyova, T. / ...Authors: Kursula, P. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Edwards, A. / Ehn, M. / Flodin, S. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg Schiavone, L. / Kotenyova, T. / Nilsson-Ehle, P. / Ogg, D. / Persson, C. / Sagemark, J. / Schuler, H. / Sundstrom, M. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Nordlund, P.
History
DepositionOct 20, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE-ASSOCIATED PROTEIN 1
B: PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE-ASSOCIATED PROTEIN 1
C: PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE-ASSOCIATED PROTEIN 1
D: PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE-ASSOCIATED PROTEIN 1
E: PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE-ASSOCIATED PROTEIN 1
F: PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE-ASSOCIATED PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,05114
Polymers247,2156
Non-polymers8368
Water1,36976
1
A: PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE-ASSOCIATED PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)41,2031
Polymers41,2031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE-ASSOCIATED PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5584
Polymers41,2031
Non-polymers3553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE-ASSOCIATED PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2992
Polymers41,2031
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE-ASSOCIATED PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2992
Polymers41,2031
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE-ASSOCIATED PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3953
Polymers41,2031
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE-ASSOCIATED PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2992
Polymers41,2031
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)180.055, 103.875, 127.161
Angle α, β, γ (deg.)90.00, 97.63, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2005-

HOH

21B-2008-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 4 / Auth seq-ID: 9 - 349 / Label seq-ID: 28 - 368

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

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Components

#1: Protein
PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE-ASSOCIATED PROTEIN 1 / 39 KDA PHOSPHORIBOSYPYROPHOSPHATE SYNTHETASE-ASSOCIATED PROTEIN / PRPSAP1


Mass: 41202.582 Da / Num. of mol.: 6 / Fragment: RESIDUES 5-351
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PG-TF2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q14558
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE / Tris


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.6 Å3/Da / Density % sol: 52 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.092
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.092 Å / Relative weight: 1
ReflectionResolution: 2.65→20 Å / Num. obs: 67352 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.23 / Net I/σ(I): 7.4
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DKU

1dku


Resolution: 2.65→20 Å / Cor.coef. Fo:Fc: 0.866 / Cor.coef. Fo:Fc free: 0.835 / Cross valid method: THROUGHOUT / ESU R: 1.082 / ESU R Free: 0.382 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.299 3371 5 %RANDOM
Rwork0.269 ---
obs0.271 63978 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.24 Å2
Baniso -1Baniso -2Baniso -3
1--2.98 Å20 Å2-0.21 Å2
2---3.65 Å20 Å2
3---6.57 Å2
Refinement stepCycle: LAST / Resolution: 2.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14256 0 46 76 14378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02214510
X-RAY DIFFRACTIONr_bond_other_d00.0213939
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.97519620
X-RAY DIFFRACTIONr_angle_other_deg3.703332293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.53151818
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.85923.4600
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.53152646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.26315120
X-RAY DIFFRACTIONr_chiral_restr0.0730.22329
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215810
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022838
X-RAY DIFFRACTIONr_nbd_refined0.2180.23795
X-RAY DIFFRACTIONr_nbd_other0.2390.215413
X-RAY DIFFRACTIONr_nbtor_refined0.1760.27214
X-RAY DIFFRACTIONr_nbtor_other0.1180.27400
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2411
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1230.261
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2530.2328
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.71429118
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.289314796
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.28645392
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.08854824
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 4644 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.020.05
2Bmedium positional0.020.05
3Cmedium positional0.020.05
4Dmedium positional0.020.05
5Emedium positional0.020.05
6Fmedium positional0.020.05
1Amedium thermal2.2120
2Bmedium thermal2.8220
3Cmedium thermal2.1420
4Dmedium thermal2.1720
5Emedium thermal2.0420
6Fmedium thermal2.1120
LS refinement shellResolution: 2.65→2.72 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.446 241
Rwork0.412 4634

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