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- PDB-1ao0: GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE (PRPP) AMIDOTRANSFERASE FRO... -

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Basic information

Entry
Database: PDB / ID: 1ao0
TitleGLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE (PRPP) AMIDOTRANSFERASE FROM B. SUBTILIS COMPLEXED WITH ADP AND GMP
ComponentsGLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE
KeywordsGLUTAMINE AMIDOTRANSFERASE / TRANSFERASE / PRTASE / PURINE BIOSYNTHESIS / PHOSPHORIBOSYLTRANSFERASE / GLYCOSYLTRANSFERASE
Function / homology
Function and homology information


amidophosphoribosyltransferase / amidophosphoribosyltransferase activity / purine nucleobase biosynthetic process / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / 4 iron, 4 sulfur cluster binding / magnesium ion binding
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 / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Aminohydrolase, N-terminal nucleophile (Ntn) 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 / 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
GUANOSINE-5'-MONOPHOSPHATE / ADENOSINE-5'-DIPHOSPHATE / IRON/SULFUR CLUSTER / Amidophosphoribosyltransferase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTomchick, D.R. / Smith, J.L.
CitationJournal: Biochemistry / Year: 1997
Title: Mechanism of the synergistic end-product regulation of Bacillus subtilis glutamine phosphoribosylpyrophosphate amidotransferase by nucleotides.
Authors: Chen, S. / Tomchick, D.R. / Wolle, D. / Hu, P. / Smith, J.L. / Switzer, R.L. / Zalkin, H.
History
DepositionJul 15, 1997Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / 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 / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 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)204,17920
Polymers199,5144
Non-polymers4,66516
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21400 Å2
ΔGint-219 kcal/mol
Surface area60520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.300, 70.400, 182.700
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(0.96687, -0.24296, 0.07829), (-0.24324, -0.96995, -0.00616), (0.07743, -0.01308, -0.99691)-3.9642, 12.048, 136.39999
2given(-0.99667, -0.01904, -0.07928), (0.02097, -0.9995, -0.02354), (-0.0788, -0.02513, 0.99657)86.068, 2.137, 3.339
3given(-0.96022, 0.27892, 0.0135), (0.27924, 0.95948, 0.03767), (-0.00244, 0.03994, -0.9992)78.19, -13.636, 139.44
DetailsTHE AMIDOTRANSFERASE MOLECULE IS A HOMOTETRAMER IN THE CRYSTALLINE STATE, BUT THE AGGREGATION STATE IN SOLUTION IS CONCENTRATION DEPENDENT. CRYSTALS CONTAIN 1 TETRAMER PER ASYMMETRIC UNIT AND COORDINATES FOR THE ENTIRE TETRAMER ARE INCLUDED IN THE ENTRY. THE SUBUNITS HAVE CHAIN IDENTIFIERS A, B, C, AND D. EACH "CHAIN" INCLUDES 455 AMINO ACID RESIDUES, ONE [4FE-4S] CLUSTER (RESIDUE 466), ONE GMP MOLECULE (RESIDUE 467), ONE ADP MOLECULE (RESIDUE 468), ONE MAGNESIUM ION (RESIDUE 469) AND ONE WATER MOLECULE LIGATED TO THE MAGNESIUM (CHAIN IDENTIFIER S). MOLECULAR P, Q AND R AXES RELATING SUBUNITS B, D, AND C, RESPECTIVELY, TO SUBUNIT A ARE SPECIFIED IN THE MTRIX RECORDS. THE FIRST MATRIX PRESENTED IN *MTRIX* RECORDS BELOW IS A MOLECULAR P AXIS MATRIX. THE SECOND IS A MOLECULAR R AXIS MATRIX, AND THE THIRD IS A MOLECULAR Q AXIS MATRIX.

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE


Mass: 49878.469 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: PURF / Plasmid: PGZ1 (PURF+ FRAGMENT INSERTED INTO PUC18) / Production host: Escherichia coli (E. coli) / Strain (production host): TX158 / References: UniProt: P00497, amidophosphoribosyltransferase

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Non-polymers , 5 types, 20 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical
ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O8P
#5: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsPRO 86 IN ALL CHAINS IS A CIS-PROLINE. ASP 282 IN ALL CHAINS IS A CIS-ASPARTATE, PART OF A ...PRO 86 IN ALL CHAINS IS A CIS-PROLINE. ASP 282 IN ALL CHAINS IS A CIS-ASPARTATE, PART OF A PHOSPHATE BINDING SITE INVOLVED IN BINDING BOTH SUBSTRATE AND INHIBITORS.

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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: 2.58 Å3/Da / Density % sol: 40 %
Crystal growpH: 7.9
Details: 24% PEG8000, 200MM KCL, 50MM EPPS PH 7.9,2 MM ADP, 2 MM GMP, 10 MM MGCL2
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein11
21 mMADP11
31 mMGMP11
45 mM11MgCl2
524 %PEG800012
6200 mM12KCl
750 mMEPPS12
81 mMADP12
91 mMGMP12
105 mM12MgCl2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 1995
RadiationMonochromator: MSC DOUBLE MIRROR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→15 Å / Num. obs: 46771 / % possible obs: 91 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 47 Å2 / Rsym value: 0.08 / Net I/σ(I): 20.2
Reflection
*PLUS
Num. measured all: 195956 / Rmerge(I) obs: 0.08

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
HKL(DENZO)data reduction
HKLdata scaling
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GPH

1gph


Resolution: 2.8→15 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.264 -5 %RANDOM FROM ALL DATA
Rwork0.214 ---
obs0.214 46771 91 %-
Displacement parametersBiso mean: 32.5 Å2
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13908 204 36 4 14152
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg2.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.39
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
LS refinement shellResolution: 2.8→2.88 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3823 184 5 %
Rwork0.2881 3409 -
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.39

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