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- PDB-1b6r: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 1b6r
TitleN5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE FROM E. COLI
ComponentsPROTEIN (N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE)
KeywordsLYASE / ATP-GRASP / CARBOXYPHOSPHATE / PURINE BIOSYNTHESIS
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 / ATP-grasp fold, A domain / Rudiment single hybrid motif / 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 / ATP-grasp fold, A domain / Rudiment single hybrid motif / 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
N5-carboxyaminoimidazole ribonucleotide synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.1 Å
AuthorsThoden, J.B. / Kappock, T.J. / Stubbe, J. / Holden, H.M.
CitationJournal: Biochemistry / Year: 1999
Title: Three-dimensional structure of N5-carboxyaminoimidazole ribonucleotide synthetase: a member of the ATP grasp protein superfamily.
Authors: Thoden, J.B. / Kappock, T.J. / Stubbe, J. / Holden, H.M.
History
DepositionJan 17, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 30, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6242
Polymers39,5281
Non-polymers961
Water1,65792
1
A: PROTEIN (N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE)
hetero molecules

A: PROTEIN (N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2484
Polymers79,0562
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-x+1/2,y+1/2,-z+1/21
Unit cell
Length a, b, c (Å)93.400, 95.200, 120.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PROTEIN (N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE) / AIRC / PURK


Mass: 39528.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
References: UniProt: P09029, phosphoribosylaminoimidazole carboxylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 64 %
Crystal growpH: 7.8 / Details: 100MM HEPPS, PH 7.8 0.575 M AMMONIUM SULFATE
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.525 Mammonium sulfate1reservoir
3100 mMHEPPS1reservoir

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: BRUKER / Detector: AREA DETECTOR / Date: Feb 15, 1998 / Details: GOBEL MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 30332 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 24.3
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.292 / % possible all: 78.9
Reflection shell
*PLUS
% possible obs: 78.9 %

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Processing

Software
NameVersionClassification
TNT5Drefinement
SAINTdata reduction
XCALIBREdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.1→30 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rwork0.197 --
all0.197 --
obs-30332 95.6 %
Solvent computationSolvent model: TNT / Bsol: 696.7 Å2 / ksol: 1.032 e/Å3
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2737 0 5 92 2834
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01341940.6
X-RAY DIFFRACTIONt_angle_deg2.3255381
X-RAY DIFFRACTIONt_dihedral_angle_d17.64426840
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.007752.5
X-RAY DIFFRACTIONt_gen_planes0.0117502.75
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.064535
Software
*PLUS
Name: TNT / Version: 5D / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_angle_deg2.33
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.60
X-RAY DIFFRACTIONt_plane_restr0.0112.75

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