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- PDB-2nsh: E. coli PurE H45Q mutant complexed with nitro-AIR -

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Basic information

Entry
Database: PDB / ID: 2nsh
TitleE. coli PurE H45Q mutant complexed with nitro-AIR
ComponentsPhosphoribosylaminoimidazole carboxylase catalytic subunit
KeywordsLYASE / central three-layer alpha-beta-alpha sandwich / kinked C-terminal helix
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
AuthorsEalick, S.E. / Morar, M.
CitationJournal: Biochemistry / Year: 2007
Title: N(5)-CAIR Mutase: Role of a CO(2) 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.
History
DepositionNov 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)18,1292
Polymers17,7891
Non-polymers3401
Water2,216123
1
A: Phosphoribosylaminoimidazole carboxylase catalytic subunit
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)145,03516
Polymers142,3148
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 area37810 Å2
ΔGint-150 kcal/mol
Surface area39920 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)111.688, 111.688, 49.412
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-312-

HOH

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Components

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


Mass: 17789.252 Da / Num. of mol.: 1 / Mutation: H45Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: purE / Production host: Escherichia coli (E. coli)
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.: 123 / 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: 2.16 Å3/Da / Density % sol: 43.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25% PEG400, 0.2M magnesium chloride, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→39.5 Å / Num. all: 14561 / Num. obs: 12061 / % possible obs: 91.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.8→1.91 Å / % possible all: 77.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→39.5 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.886 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21095 1347 10 %RANDOM
Rwork0.17386 ---
all0.178 14561 --
obs0.178 12061 91.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.332 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--0.41 Å20 Å2
3----0.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.8→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1202 0 22 123 1347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221258
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9761721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1685166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.49224.89849
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57715192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.574156
X-RAY DIFFRACTIONr_chiral_restr0.1080.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02948
X-RAY DIFFRACTIONr_nbd_refined0.2240.2578
X-RAY DIFFRACTIONr_nbtor_refined0.310.2889
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.275
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.219
X-RAY DIFFRACTIONr_mcbond_it0.9721.5842
X-RAY DIFFRACTIONr_mcangle_it1.50721317
X-RAY DIFFRACTIONr_scbond_it2.6793461
X-RAY DIFFRACTIONr_scangle_it4.1944.5402
LS refinement shellResolution: 1.8→1.91 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 156 -
Rwork0.237 629 -
obs--77.1 %
Refinement TLS params.Method: refined / Origin x: 3.0094 Å / Origin y: -24.7703 Å / Origin z: -15.9583 Å
111213212223313233
T-0.0631 Å20.0236 Å2-0.031 Å2--0.1393 Å20.0089 Å2---0.1189 Å2
L1.03 °20.0796 °2-0.1958 °2-0.0826 °2-0.077 °2--0.2103 °2
S0.0433 Å °-0.0491 Å °-0.0702 Å °0.0398 Å °0.0187 Å °-0.0327 Å °0.1117 Å °0.038 Å °-0.062 Å °

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