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

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Basic information

Entry
Database: PDB / ID: 1ecj
TitleESCHERICHIA COLI GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE (PRPP) AMIDOTRANSFERASE COMPLEXED WITH 2 AMP PER TETRAMER
ComponentsGLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE
KeywordsTRANSFERASE / GLUTAMINE AMIDOTRANSFERASE / PURINE BIOSYNTHESIS / GLYCOSYLTRANSFERASE / AMP / ADENINE 5'-MONOPHOSPHATE
Function / homology
Function and homology information


amidophosphoribosyltransferase / amidophosphoribosyltransferase activity / purine nucleobase biosynthetic process / purine nucleotide biosynthetic process / glutamine metabolic process / 'de novo' IMP biosynthetic process / guanosine tetraphosphate binding / glycosyltransferase activity / magnesium ion binding / identical protein binding ...amidophosphoribosyltransferase / amidophosphoribosyltransferase activity / purine nucleobase biosynthetic process / purine nucleotide biosynthetic process / glutamine metabolic 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
ADENOSINE MONOPHOSPHATE / Amidophosphoribosyltransferase / Amidophosphoribosyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMuchmore, C.R. / Krahn, J.M. / Smith, J.L.
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
DepositionJul 16, 1997Processing site: BNL
Revision 1.0Apr 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
C: GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE
D: GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,3856
Polymers225,6914
Non-polymers6942
Water3,207178
1
A: GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE
B: GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,1933
Polymers112,8452
Non-polymers3471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-14 kcal/mol
Surface area37510 Å2
MethodPISA
2
C: GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE
D: GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,1933
Polymers112,8452
Non-polymers3471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-14 kcal/mol
Surface area37580 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16560 Å2
ΔGint-32 kcal/mol
Surface area70040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.800, 156.000, 106.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.073983, 0.010528, 0.997204), (0.015553, -0.999835, 0.009402), (0.997138, 0.014814, -0.074135)0.3232, 76.6064, -1.4012
2given(-0.999659, -0.025431, -0.005879), (-0.025428, 0.999676, -0.00065), (0.005893, -0.0005, -0.999982)60.55825, 0.84042, 53.33965
3given(-0.070798, 0.012665, -0.99741), (0.017544, -0.999749, -0.01394), (-0.997336, -0.018485, 0.070558)58.0906, 77.253, 55.091

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Components

#1: Protein
GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE


Mass: 56422.684 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PURF / Plasmid: PT7F1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P00496, UniProt: P0AG16*PLUS, amidophosphoribosyltransferase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 10

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 47.6 %
Description: THE SYNCHROTRON DATA DESCRIBED BY THE PREVIOUS STATISTICS WAS SUPPLEMENTED WITH LOW RESOLUTION DATA COLLECTED WITH A RIGAKU ROTATING ANODE COPPER K(ALPHA) SOURCE AND A XUONG-HAMLIN ...Description: THE SYNCHROTRON DATA DESCRIBED BY THE PREVIOUS STATISTICS WAS SUPPLEMENTED WITH LOW RESOLUTION DATA COLLECTED WITH A RIGAKU ROTATING ANODE COPPER K(ALPHA) SOURCE AND A XUONG-HAMLIN MULTIWIRE AREA DETECTOR. THIS DATA WAS PROCESSED WITH XDS (KABSCH) ADAPTED FOR THE XUONG-HAMLIN DETECTOR (D. DIGGS, K. WATKINS).
Crystal growpH: 6.3
Details: 100MM MES, 50MM TRIS, 2MM AMP, 4MM EDTA, 15-18% PEG-3350, PH 6.3
Crystal grow
*PLUS
Temperature: 27 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMMES1reservoir
250 mMTris1reservoir
32 mMAMP1reservoir
44 mMEDTA1reservoir
515-18 %(w/v)PEG33501reservoir
650 mMMES1drop
725 mMTris1drop
81 mMAMP1drop
92 mMEDTA1drop
107.5-9 %(w/v)PEG33501drop
113.5-17.5 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 279 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Feb 1, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 55291 / % possible obs: 77.8 % / Redundancy: 3.6 % / Rsym value: 0.065 / Net I/σ(I): 37
Reflection shellResolution: 2.5→2.61 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 4.3 / Rsym value: 0.215 / % possible all: 56.1
Reflection
*PLUS
Num. measured all: 199847 / Rmerge(I) obs: 0.065

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Processing

Software
NameVersionClassification
GLRFphasing
X-PLOR3.1model building
X-PLOR3.1refinement
WEISdata reduction
Agrovatadata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GPH

1gph


Resolution: 2.5→30 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Cross valid method: FREE R, THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2686 5 %RANDOM SELECTION FROM ALL DATA
Rwork0.181 ---
obs0.181 55291 77.8 %-
Displacement parametersBiso mean: 32 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15476 46 0 178 15700
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.32
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.326
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Refine LS restraints NCSNCS model details: RESTRAINTS BETWEEN SUBUNIT FRAGMENTS
LS refinement shellResolution: 2.5→2.61 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.388 250 5.6 %
Rwork0.315 4454 -
obs--56.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11X.DNATOPH11.DNA
X-RAY DIFFRACTION3AMP.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 54315
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.32
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.326

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