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- PDB-1d7a: CRYSTAL STRUCTURE OF E. COLI PURE-MONONUCLEOTIDE COMPLEX. -

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Basic information

Entry
Database: PDB / ID: 1d7a
TitleCRYSTAL STRUCTURE OF E. COLI PURE-MONONUCLEOTIDE COMPLEX.
ComponentsPHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE
KeywordsLYASE / THREE-LAYER (ALPHA-BETA-ALPHA) SANDWICH N5-CAIR MUTASE (PURE) / AMINOIMIDAZOLE RIBONUCLEOTIDE (AIR)
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
5-AMINOIMIDAZOLE RIBONUCLEOTIDE / N5-carboxyaminoimidazole ribonucleotide mutase / N5-carboxyaminoimidazole ribonucleotide mutase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsMathews, I.I. / Kappock, T.J. / Stubbe, J. / Ealick, S.E.
Citation
Journal: Structure Fold.Des. / 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.E.
#1: Journal: Biochemistry / Year: 1999
Title: Evidence for the Direct Transfer of the Carboxylate of N5-Carboxyaminoimidazole Ribonucleotide (N5-Cair) to Generate 4-Carboxy-5- Aminoimidazole Ribonucleotide Catalyzed by Escherichia Coli Pure, an N5-Cair Mutase
Authors: Meyer, E. / Kappock, T.J. / Osuji, C. / Stubbe, J.
#2: Journal: Biochemistry / Year: 1994
Title: Reactions Catalyzed by 5-Aminoimidazole Ribonucleotide Carboxylases from Escherichia Coli and Gallus Gallus: A Case for Divergent Catalytic Mechanisms
Authors: Firestine, S.M. / Poon, S.W. / Mueller, E.J. / Stubbe, J. / Davisson, V.J.
#3: Journal: Biochemistry / Year: 1994
Title: N5-Carboxyaminoimidazole Ribonucleotide: Evidence for a New Intermediate and Two New Enzymatic Activities in the De Novo Purine Biosynthetic Pathway of Escherichia Coli
Authors: Mueller, E.J. / Meyer, E. / Rudolph, J. / Davisson, V.J. / Stubbe, J.
#4: Journal: J.Bacteriol. / Year: 1989
Title: Nucleotide Sequence Analysis of the Purek Operon Encoding 5'-Phosphoribosyl-5-Aminoimidazole Carboxylase of Escherichia Coli K-12
Authors: Tiedeman, A.A. / Keyhani, J. / Kamholz, J. / Daum III, H.A. / Gots, J.S. / Smith, J.M.
#5: Journal: J.Bacteriol. / Year: 1989
Title: Identification and Sequence Analysis of Escherichia Coli Pure and Purk Genes Encoding 5'-Phosphoribosyl-5-Amino-4-Imidazole Carboxylase for De Novo Purine Biosynthesis
Authors: Watanabe, W. / Sampei, G. / Aiba, A. / Mizobuchi, K.
History
DepositionOct 16, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE
B: PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE
C: PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE
D: PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE
L: PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE
M: PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE
N: PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE
O: PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,09212
Polymers136,9118
Non-polymers1,1814
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35430 Å2
ΔGint-175 kcal/mol
Surface area39060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.92, 94.55, 149.96
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE


Mass: 17113.875 Da / Num. of mol.: 8 / Fragment: CATALYTIC SUBUNIT / Mutation: M14(MSE), M23(MSE), M79(MSE), M110(MSE)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PNC2 / Production host: Escherichia coli (E. coli)
References: UniProt: P09028, UniProt: P0AG18*PLUS, phosphoribosylaminoimidazole carboxylase
#2: Chemical
ChemComp-AIR / 5-AMINOIMIDAZOLE RIBONUCLEOTIDE


Mass: 295.186 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H14N3O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.25 Å3/Da / Density % sol: 45.31 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG4000, Ammonium Acetate, TRIS.HCl, 4-CARBOXY AMINOIMIDAZOLE RIBONUCLEOTIDE (CAIR), pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120-22 %PEG40001reservoir
20.2 Mammonium acetate1reservoir
30.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 9, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. all: 37498 / Num. obs: 37498 / % possible obs: 87.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 7.2
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.277 / Num. unique all: 5182 / % possible all: 83.6
Reflection
*PLUS
Num. measured all: 99859
Reflection shell
*PLUS
% possible obs: 83.6 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.843refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
RefinementResolution: 2.5→25 Å / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 5 -RANDOM
Rwork0.203 ---
all0.2 36925 --
obs0.2 36925 82 %-
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9528 0 76 120 9724
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.24
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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