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- PDB-3etj: Crystal structure E. coli Purk in complex with Mg, ADP, and Pi -

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Basic information

Entry
Database: PDB / ID: 3etj
TitleCrystal structure E. coli Purk in complex with Mg, ADP, and Pi
ComponentsPhosphoribosylaminoimidazole carboxylase ATPase subunit
KeywordsLYASE / ATP-grasp / purine biosynthesis / antimicrobial / ATP-binding / Decarboxylase / Nucleotide-binding
Function / homology
Function and homology information


5-(carboxyamino)imidazole ribonucleotide synthase / 5-(carboxyamino)imidazole ribonucleotide synthase activity / phosphoribosylaminoimidazole carboxylase activity / 'de novo' IMP biosynthetic process / ATP binding / metal ion binding / cytosol
Similarity search - Function
Phosphoribosylaminoimidazole carboxylase, ATPase subunit / Phosphoribosylaminoimidazole carboxylase, C-terminal domain / Phosphoribosylaminoimidazole carboxylase C-terminal domain / ATP-grasp fold, ATP-dependent carboxylate-amine ligase-type / ATP-grasp domain / Rossmann fold - #20 / Rudiment single hybrid motif / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 ...Phosphoribosylaminoimidazole carboxylase, ATPase subunit / Phosphoribosylaminoimidazole carboxylase, C-terminal domain / Phosphoribosylaminoimidazole carboxylase C-terminal domain / ATP-grasp fold, ATP-dependent carboxylate-amine ligase-type / ATP-grasp domain / Rossmann fold - #20 / Rudiment single hybrid motif / 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'-DIPHOSPHATE / HYDROGENPHOSPHATE ION / N5-carboxyaminoimidazole ribonucleotide synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsHolden, H.M. / Thoden, J.B.
CitationJournal: Biochemistry / Year: 2008
Title: Structural analysis of the active site geometry of N(5)-Carboxyaminoimidazole ribonucleotide synthetase from Escherichia coli.
Authors: Thoden, J.B. / Holden, H.M. / Firestine, S.M.
History
DepositionOct 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoribosylaminoimidazole carboxylase ATPase subunit
B: Phosphoribosylaminoimidazole carboxylase ATPase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,23511
Polymers79,0562
Non-polymers1,1799
Water12,268681
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-88 kcal/mol
Surface area26900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.800, 70.500, 88.700
Angle α, β, γ (deg.)90.000, 124.300, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Phosphoribosylaminoimidazole carboxylase ATPase subunit / AIR carboxylase / AIRC


Mass: 39528.000 Da / Num. of mol.: 2 / Mutation: E61Q, Q205R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0522, JW0511, purK, PURK_ECOLI / Plasmid: pET31 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3)
References: UniProt: P09029, phosphoribosylaminoimidazole carboxylase

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Non-polymers , 5 types, 690 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PI / HYDROGENPHOSPHATE ION / Phosphate


Mass: 95.979 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO4P
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 681 / 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: 2.1 Å3/Da / Density % sol: 41.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: monomethylether poly(ethylene glycol) 5000, MgATP, 5-aminoimidazole ribonucleotide, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: SBC-3 / Detector: CCD / Date: Dec 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 80957 / Num. obs: 80957 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 28.6
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 2.6 / Num. unique all: 6164 / Rsym value: 0.207 / % possible all: 71.1

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Processing

Software
NameVersionClassificationNB
TNTrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementStarting model: pdb entry 3ETH

3eth


Resolution: 1.6→30 Å / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 6164 -random
Rwork0.158 ---
all0.16 80952 --
obs0.16 80952 93.6 %-
Displacement parametersBiso max: 99.88 Å2 / Biso mean: 28.274 Å2 / Biso min: 6.39 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5555 0 69 681 6305

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