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- PDB-2r87: Crystal structure of PurP from Pyrococcus furiosus complexed with ADP -

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Basic information

Entry
Database: PDB / ID: 2r87
TitleCrystal structure of PurP from Pyrococcus furiosus complexed with ADP
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, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold, B domain ...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, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold, B domain / 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'-DIPHOSPHATE / 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: 2.3 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 / 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 / _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

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Assembly

Deposited unit
A: PurP protein PF1517
B: PurP protein PF1517
C: PurP protein PF1517
D: PurP protein PF1517
E: PurP protein PF1517
F: PurP protein PF1517
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,45731
Polymers230,0896
Non-polymers4,36825
Water9,746541
1
A: PurP protein PF1517
B: PurP protein PF1517
C: PurP protein PF1517
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,27616
Polymers115,0443
Non-polymers2,23113
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16940 Å2
MethodPISA
2
D: PurP protein PF1517
E: PurP protein PF1517
F: PurP protein PF1517
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,18115
Polymers115,0443
Non-polymers2,13612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.095, 127.222, 121.673
Angle α, β, γ (deg.)90.000, 102.850, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71A
81B
91C
101D
111E
121F
12A
22D
32F
13C
23B
33E

NCS domain segments:

Refine code: 5

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETGLYGLYAA1 - 1601 - 160
211METMETGLYGLYBB1 - 1601 - 160
311METMETGLYGLYCC1 - 1601 - 160
411METMETGLYGLYDD1 - 1601 - 160
511METMETGLYGLYEE1 - 1601 - 160
611METMETGLYGLYFF1 - 1601 - 160
721ILEILETHRTHRAA170 - 334170 - 334
821ILEILETHRTHRBB170 - 334170 - 334
921ILEILETHRTHRCC170 - 334170 - 334
1021ILEILETHRTHRDD170 - 334170 - 334
1121ILEILETHRTHREE170 - 334170 - 334
1221ILEILETHRTHRFF170 - 334170 - 334
112ILEILEASNASNAA161 - 169161 - 169
212ILEILEASNASNDD161 - 169161 - 169
312ILEILEASNASNFF161 - 169161 - 169
113ILEILEASNASNCC161 - 169161 - 169
213ILEILEASNASNBB161 - 169161 - 169
313ILEILEASNASNEE161 - 169161 - 169

NCS ensembles :
ID
1
2
3
Detailsbiological assembly is a hexamer or a trimer from the asymmetric unit

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Components

#1: Protein
PurP protein PF1517


Mass: 38348.148 Da / Num. of mol.: 6
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
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 541 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 10% 2-propanol, 200 mM Li2SO4, 100 mM Na phosphate-citrate, pH 4.2, vapor diffusion, hanging drop, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONCHESS F110.9177
ROTATING ANODERIGAKU21.54178
Detector
TypeIDDetectorDate
ADSC QUANTUM 2701CCDJan 1, 2007
RIGAKU RAXIS IV2IMAGE PLATEMay 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91771
21.541781
ReflectionResolution: 2.3→50 Å / Num. all: 98989 / Num. obs: 98928 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.138 / Χ2: 1.678 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.382.90.26498600.88698.5
2.38-2.482.90.20697880.92898.4
2.48-2.593.80.27498371.27298.7
2.59-2.734.70.28398731.46799
2.73-2.94.90.23399021.6599
2.9-3.1250.18899521.78599.5
3.12-3.445.10.151100201.84499.9
3.44-3.934.40.12295552.18995.6
3.93-4.955.20.1100552.194100
4.95-505.10.085101471.64599.6

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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: 2.3→42.64 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.897 / SU B: 6.766 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.382 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.244 4941 5 %RANDOM
Rwork0.201 ---
all0.203 98989 --
obs0.203 98928 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.251 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å2-1.66 Å2
2--0 Å20 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 2.3→42.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16230 0 257 541 17028
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02216858
X-RAY DIFFRACTIONr_angle_refined_deg1.0671.99422848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.71151998
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.62723.721774
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87152988
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.2315120
X-RAY DIFFRACTIONr_chiral_restr0.0740.22460
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212630
X-RAY DIFFRACTIONr_nbd_refined0.1750.27872
X-RAY DIFFRACTIONr_nbtor_refined0.3020.211525
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2918
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.219
X-RAY DIFFRACTIONr_mcbond_it0.4191.510376
X-RAY DIFFRACTIONr_mcangle_it0.735216212
X-RAY DIFFRACTIONr_scbond_it0.82737541
X-RAY DIFFRACTIONr_scangle_it1.4144.56636
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1300MEDIUM POSITIONAL0.210.5
11B1300MEDIUM POSITIONAL0.190
11C1300MEDIUM POSITIONAL0.180
11D1300MEDIUM POSITIONAL0.150
11E1300MEDIUM POSITIONAL0.250
11F1300MEDIUM POSITIONAL0.180
11A1326LOOSE POSITIONAL0.585
11B1326LOOSE POSITIONAL0.480
11C1326LOOSE POSITIONAL0.580
11D1326LOOSE POSITIONAL0.440
11E1326LOOSE POSITIONAL0.580
11F1326LOOSE POSITIONAL0.480
11A1300MEDIUM THERMAL1.32
11B1300MEDIUM THERMAL0.850
11C1300MEDIUM THERMAL1.940
11D1300MEDIUM THERMAL1.480
11E1300MEDIUM THERMAL1.760
11F1300MEDIUM THERMAL1.390
11A1326LOOSE THERMAL1.510
11B1326LOOSE THERMAL1.040.01
11C1326LOOSE THERMAL2.110
11D1326LOOSE THERMAL1.60
11E1326LOOSE THERMAL1.810
11F1326LOOSE THERMAL1.460
22A36MEDIUM POSITIONAL0.130.5
22B36MEDIUM POSITIONAL0.150.01
22C36MEDIUM POSITIONAL0.140
22D43LOOSE POSITIONAL0.585
22E43LOOSE POSITIONAL0.760.12
22F43LOOSE POSITIONAL0.60
22A36MEDIUM THERMAL0.112
22B36MEDIUM THERMAL0.170.06
22C36MEDIUM THERMAL0.080
22D43LOOSE THERMAL0.1210
22E43LOOSE THERMAL0.140.23
22F43LOOSE THERMAL0.120.01
33A36MEDIUM POSITIONAL0.150.5
33B36MEDIUM POSITIONAL0.150.01
33C36MEDIUM POSITIONAL0.150
33D43LOOSE POSITIONAL0.395
33E43LOOSE POSITIONAL0.380.12
33F43LOOSE POSITIONAL0.350
33A36MEDIUM THERMAL0.312
33B36MEDIUM THERMAL0.230.06
33C36MEDIUM THERMAL0.120
33D43LOOSE THERMAL0.2310
33E43LOOSE THERMAL0.210.23
33F43LOOSE THERMAL0.140.01
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 329 -
Rwork0.238 6810 -
all-7139 -
obs--96.73 %

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