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- PDB-2r86: Crystal structure of PurP from Pyrococcus furiosus complexed with ATP -

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Basic information

Entry
Database: PDB / ID: 2r86
TitleCrystal structure of PurP from Pyrococcus furiosus complexed with ATP
ComponentsPurP protein PF1517
KeywordsUNKNOWN FUNCTION / ATP-grasp superfamily
Function / homology
Function and homology information


formate-phosphoribosylaminoimidazolecarboxamide ligase / ligase activity, forming carbon-nitrogen bonds / 'de novo' IMP biosynthetic process / magnesium ion binding / ATP binding
Similarity search - Function
IMP biosynthesis enzyme PurP, C-terminal / IMP biosynthesis enzyme PurP, N-terminal / IMP biosynthesis enzyme PurP / Protein of unknown function (DUF1246) / Domain of unknown function (DUF1297) / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily ...IMP biosynthesis enzyme PurP, C-terminal / IMP biosynthesis enzyme PurP, N-terminal / IMP biosynthesis enzyme PurP / Protein of unknown function (DUF1246) / Domain of unknown function (DUF1297) / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsZhang, Y. / White, R.H. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2008
Title: Crystal structure and function of 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase from Methanocaldococcus jannaschii.
Authors: Zhang, Y. / White, R.H. / Ealick, S.E.
History
DepositionSep 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr1_label_seq_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: PurP protein PF1517
B: PurP protein PF1517
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,37312
Polymers76,6962
Non-polymers1,67710
Water2,396133
1
A: PurP protein PF1517
hetero molecules

A: PurP protein PF1517
hetero molecules

A: PurP protein PF1517
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,91421
Polymers115,0443
Non-polymers2,86918
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area19440 Å2
MethodPISA
2
B: PurP protein PF1517
hetero molecules

B: PurP protein PF1517
hetero molecules

B: PurP protein PF1517
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,20515
Polymers115,0443
Non-polymers2,16012
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area16210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.477, 122.477, 560.925
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-676-

HOH

21A-688-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 5 / Auth seq-ID: 1 - 334 / Label seq-ID: 1 - 334

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
Detailsbiological assembly is a hexamer or a trimer from the asymmetric unit by the operations: (x,y,z), (-y,x-y,z +(1 1 0)), (-x+y,-x,z)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PurP protein PF1517


Mass: 38348.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: T7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8U0R7

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Non-polymers , 5 types, 143 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 5.28 Å3/Da / Density % sol: 76.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 30% MPD, 100 mM Na/K phosphate, pH 6.1, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 8, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 55984 / Num. obs: 55970 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.057 / Χ2: 0.95 / Net I/σ(I): 11.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.596.10.28345880.50181.9
2.59-2.696.70.25655150.51697.6
2.69-2.827.50.18556440.556100
2.82-2.967.70.14356660.594100
2.96-3.157.80.10456890.645100
3.15-3.397.90.07656730.827100
3.39-3.737.90.0657311.171100
3.73-4.277.80.05657171.754100
4.27-5.387.60.04357771.631100
5.38-507.60.02559841.01599.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.3.0026refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2R7K

2r7k


Resolution: 2.5→39.97 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.915 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.235 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2874 5.1 %RANDOM
Rwork0.218 ---
all0.219 55984 --
obs0.219 55970 97.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.904 Å2
Baniso -1Baniso -2Baniso -3
1-1.86 Å20.93 Å20 Å2
2--1.86 Å20 Å2
3----2.8 Å2
Refinement stepCycle: LAST / Resolution: 2.5→39.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5302 0 84 149 5535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225522
X-RAY DIFFRACTIONr_angle_refined_deg1.0241.9977491
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6285650
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09923.661254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79515971
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6421540
X-RAY DIFFRACTIONr_chiral_restr0.070.2809
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024128
X-RAY DIFFRACTIONr_nbd_refined0.180.22224
X-RAY DIFFRACTIONr_nbtor_refined0.3050.23764
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.2237
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.2150
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.246
X-RAY DIFFRACTIONr_mcbond_it0.4631.53258
X-RAY DIFFRACTIONr_mcangle_it0.8725293
X-RAY DIFFRACTIONr_scbond_it0.9432354
X-RAY DIFFRACTIONr_scangle_it1.6764.52198
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1268MEDIUM POSITIONAL0.150.5
1B1307LOOSE POSITIONAL0.375
2A1268MEDIUM THERMAL7.812
2B1307LOOSE THERMAL7.8720
LS refinement shellResolution: 2.5→2.558 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 168 -
Rwork0.301 3032 -
all-3200 -
obs--77.26 %

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