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- PDB-1ecf: ESCHERICHIA COLI GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE (PRPP) AMI... -

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Basic information

Entry
Database: PDB / ID: 1ecf
TitleESCHERICHIA COLI GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE (PRPP) AMIDOTRANSFERASE
ComponentsGLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE
KeywordsTRANSFERASE (GLUTAMINE AMIDOTRANSFERASE) / PURINE BIOSYNTHESIS / TRANSFERASE / GLYCOSYLTRANSFERASE / GLUTAMINE AMIDOTRANSFERASE
Function / homology
Function and homology information


amidophosphoribosyltransferase / amidophosphoribosyltransferase activity / purine nucleobase biosynthetic process / glutamine metabolic process / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / guanosine tetraphosphate binding / glycosyltransferase activity / magnesium ion binding / identical protein binding ...amidophosphoribosyltransferase / amidophosphoribosyltransferase activity / purine nucleobase biosynthetic process / glutamine metabolic process / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / guanosine tetraphosphate binding / glycosyltransferase activity / magnesium ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Amidophosphoribosyltransferase / Amidophosphoribosyltransferase, N-terminal / Glutamine amidotransferase domain / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / Purine/pyrimidine phosphoribosyl transferases signature. / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain ...Amidophosphoribosyltransferase / Amidophosphoribosyltransferase, N-terminal / Glutamine amidotransferase domain / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / Purine/pyrimidine phosphoribosyl transferases signature. / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Amidophosphoribosyltransferase / Amidophosphoribosyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT, SIR PHASES FROM SEMET PROTEIN / Resolution: 2 Å
AuthorsKrahn, J.M.
CitationJournal: Protein Sci. / Year: 1998
Title: Crystal structure of glutamine phosphoribosylpyrophosphate amidotransferase from Escherichia coli.
Authors: Muchmore, C.R. / Krahn, J.M. / Kim, J.H. / Zalkin, H. / Smith, J.L.
History
DepositionApr 23, 1996Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 9, 2023Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_validate_polymer_linkage / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_polymer_linkage.dist / _pdbx_validate_polymer_linkage.label_alt_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_distant_solvent_atoms / pdbx_entry_details / struct_conn
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE
B: GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,6608
Polymers112,8452
Non-polymers1,8146
Water17,763986
1
A: GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE
B: GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE
hetero molecules

A: GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE
B: GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,31916
Polymers225,6914
Non-polymers3,62812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area23030 Å2
ΔGint18 kcal/mol
Surface area68450 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)116.900, 157.500, 106.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-509-

HOH

21A-510-

HOH

31A-511-

HOH

41B-509-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.0809, -0.0094, 0.9967), (-0.0056, -0.9999, -0.0089), (0.9967, -0.0049, -0.0806)
Vector: 27.406, 79.413, -29.552)
DetailsPHE B 88 - SER B 92 EXISTS IN TWO DISTINCT CONFORMATIONS AS A RESULT OF THE BINDING OF PIPES BUFFER ALONG THE CRYSTALLOGRAPHIC MOLECULAR TWO-FOLD AXIS, AND IS THEREFORE POORLY DEFINED. APPLICATION OF THE CRYSTALLOGRAPHIC SYMMETRY OPERATOR TO THE SECOND SET OF RESIDUES WILL GENERATE A COMPLETE ASYMMETRIC MODEL OF THIS SITE.

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Components

#1: Protein GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE


Mass: 56422.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Description: T7 PHI10 PROMOTER / Cell line: BL21 / Gene: PURF / Plasmid: PT7F1 / Species (production host): Escherichia coli / Gene (production host): PURF / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P00496, UniProt: P0AG16*PLUS, amidophosphoribosyltransferase
#2: Chemical
ChemComp-PIN / PIPERAZINE-N,N'-BIS(2-ETHANESULFONIC ACID) / PIPES / 1,4-PIPERAZINEDIETHANESULFONIC ACID


Mass: 302.368 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18N2O6S2 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 986 / Source method: isolated from a natural source / Formula: H2O
Compound detailsGLU A 303 AND GLU B 303 ARE CIS-GLUTAMINE - PART OF A PHOSPHATE BINDING SITE INVOLVED IN BINDING ...GLU A 303 AND GLU B 303 ARE CIS-GLUTAMINE - PART OF A PHOSPHATE BINDING SITE INVOLVED IN BINDING BOTH SUBSTRATE AND INHIBITORS.
Has protein modificationN

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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: 2.17 Å3/Da / Density % sol: 40 %
Description: ORIGINAL MOLECULAR REPLACEMENT SOLUTION WAS OBTAINED IN A DIFFERENT CRYSTAL FORM.
Crystal growpH: 5.6 / Details: pH 5.6
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
215 %(w/v)PEG33501reservoir
35 %2-propanol1reservoir
4100 mMPIPES1reservoir
54 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 18, 1995
RadiationMonochromator: MSC DOUBLE MIRROR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 65480 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 24.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 4.5 / % possible all: 92.7
Reflection
*PLUS
Num. measured all: 268969
Reflection shell
*PLUS
% possible obs: 92.7 %

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Processing

Software
NameVersionClassification
SHARPphasing
X-PLOR3.1model building
X-PLOR3.1refinement
HKL(DENZO)data reduction
HKLdata scaling
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, SIR PHASES FROM SEMET PROTEIN
Starting model: 1GPH

1gph


Resolution: 2→30 Å / σ(F): 0
Details: TYR 94 IN EACH CHAIN HAS PHI/PSI VALUES THAT ARE NORMALLY DISALLOWED. IT FORMS A SHARP BETA-TURN WITH PRO 93, A CIS-PROLINE. THE DISTANCE BETWEEN X982 AND X230 IS ARTIFICIALLY SHORT DUE TO ...Details: TYR 94 IN EACH CHAIN HAS PHI/PSI VALUES THAT ARE NORMALLY DISALLOWED. IT FORMS A SHARP BETA-TURN WITH PRO 93, A CIS-PROLINE. THE DISTANCE BETWEEN X982 AND X230 IS ARTIFICIALLY SHORT DUE TO UNMODELLED HETEROGENEITY AT A SPECIAL POSITION NEAR X230. ADDITIONAL UNMODELED ELECTRON DENSITY IS PRESENT NEAR THE CYS 1 SULFUR. IT APPEARS TO REPRESENT A HETEROGENEOUS OXIDATION BY OXYGEN AND SULFUR COMPOUNDS.
RfactorNum. reflection% reflection
Rfree0.23 -5 %
Rwork0.175 --
obs0.175 65066 98.2 %
Displacement parametersBiso mean: 24.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7786 0 88 986 8860
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.893
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.97
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.51
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 65453
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.73
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.51

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