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- PDB-2ate: Structure of the complex of PurE with NitroAIR -

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Basic information

Entry
Database: PDB / ID: 2ate
TitleStructure of the complex of PurE with NitroAIR
ComponentsPhosphoribosylaminoimidazole carboxylase catalytic subunit
KeywordsLYASE / PurE / nitroAIR complex
Function / homology
Function and homology information


5-(carboxyamino)imidazole ribonucleotide mutase / 5-(carboxyamino)imidazole ribonucleotide mutase activity / 'de novo' IMP biosynthetic process / identical protein binding / cytosol
Similarity search - Function
Class I PurE / PurE, prokaryotic type / PurE domain / AIR carboxylase / AIR carboxylase / Rossmann fold - #1970 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NIA / N5-carboxyaminoimidazole ribonucleotide mutase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKappock, T.J. / Mathews, I.I. / Zaugg, J.B. / Peng, P. / Hoskins, A.A. / Okamoto, A. / Ealick, S.E. / Stubbe, J.
Citation
Journal: Biochemistry / Year: 2007
Title: N5-CAIR mutase: role of a CO2 binding site and substrate movement in catalysis.
Authors: Hoskins, A.A. / Morar, M. / Kappock, T.J. / Mathews, I.I. / Zaugg, J.B. / Barder, T.E. / Peng, P. / Okamoto, A. / Ealick, S.E. / Stubbe, J.
#1: Journal: Structure / Year: 1999
Title: Crystal structure of Escherichia coli PurE, an unusual mutase in the purine biosynthetic pathway.
Authors: Mathews, I.I. / Kappock, T.J. / Stubbe, J. / Ealick, S.
#2: Journal: Curr.Opin.Chem.Biol. / Year: 2000
Title: Modular evolution of the purine biosynthetic pathway.
Authors: Kappock, T.J. / Ealick, S.E. / Stubbe, J.
History
DepositionAug 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 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_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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoribosylaminoimidazole carboxylase catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3742
Polymers18,0341
Non-polymers3401
Water2,756153
1
A: Phosphoribosylaminoimidazole carboxylase catalytic subunit
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)146,99116
Polymers144,2708
Non-polymers2,7218
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_554-x,y,-z-11
crystal symmetry operation6_554x,-y,-z-11
crystal symmetry operation7_554y,x,-z-11
crystal symmetry operation8_554-y,-x,-z-11
Buried area37650 Å2
ΔGint-160 kcal/mol
Surface area40140 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)112.495, 112.495, 49.796
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-412-

HOH

21A-533-

HOH

31A-553-

HOH

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Components

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


Mass: 18033.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: purE / Plasmid: PNC2 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3)
References: UniProt: P0AG18, phosphoribosylaminoimidazole carboxylase
#2: Chemical ChemComp-NIA / ((2R,3S,4R,5R)-5-(5-AMINO-4-NITRO-1H-IMIDAZOL-1-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL)METHYL DIHYDROGEN PHOSPHATE / 4-NITRO-5-AMINOIMIDAZOLE RIBONUCLEOTIDE / NITRO AIR


Mass: 340.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG400, magnesium chloride, Tris.Hcl., pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å
DetectorType: BRANDEIS / Detector: CCD / Details: monochromator
RadiationMonochromator: Si 111 Channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 13604 / Num. obs: 13604 / % possible obs: 89.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.072
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.249 / % possible all: 69.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QCZ

1qcz


Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.391 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20232 667 5.1 %RANDOM
Rwork0.14897 ---
all0.20232 13024 --
obs0.15163 12357 86.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.888 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å20 Å2
2---0.62 Å20 Å2
3---1.23 Å2
Refine analyzeLuzzati coordinate error free: 0.13 Å
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1197 0 22 153 1372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221244
X-RAY DIFFRACTIONr_bond_other_d0.0010.021148
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.9751699
X-RAY DIFFRACTIONr_angle_other_deg0.88532664
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4425161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.8924.58348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99615190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.983156
X-RAY DIFFRACTIONr_chiral_restr0.0910.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021400
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02227
X-RAY DIFFRACTIONr_nbd_refined0.2070.2248
X-RAY DIFFRACTIONr_nbd_other0.1740.21026
X-RAY DIFFRACTIONr_nbtor_refined0.1650.2605
X-RAY DIFFRACTIONr_nbtor_other0.0850.2659
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.289
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0790.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2060.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.216
X-RAY DIFFRACTIONr_mcbond_it1.1571.5993
X-RAY DIFFRACTIONr_mcbond_other0.2781.5330
X-RAY DIFFRACTIONr_mcangle_it1.3321286
X-RAY DIFFRACTIONr_scbond_it3.2643478
X-RAY DIFFRACTIONr_scangle_it4.2954.5413
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.18 37 -
Rwork0.174 597 -
obs--57.17 %

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