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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 / homologyGlutamine amidotransferase domain / Glutamine amidotransferase type 2 domain / Glutamine amidotransferase type 2 domain profile. / Purine/pyrimidine phosphoribosyl transferases signature. / Phosphoribosyl transferase domain / Amidophosphoribosyltransferase, N-terminal / Phosphoribosyltransferase-like / Nucleophile aminohydrolases, N-terminal / Amidophosphoribosyltransferase / Phosphoribosyltransferase domain ...Glutamine amidotransferase domain / Glutamine amidotransferase type 2 domain / Glutamine amidotransferase type 2 domain profile. / Purine/pyrimidine phosphoribosyl transferases signature. / Phosphoribosyl transferase domain / Amidophosphoribosyltransferase, N-terminal / Phosphoribosyltransferase-like / Nucleophile aminohydrolases, N-terminal / Amidophosphoribosyltransferase / Phosphoribosyltransferase domain / amidophosphoribosyltransferase activity / amidophosphoribosyltransferase / purine nucleobase biosynthetic process / glutamine metabolic process / nucleoside metabolic process / 'de novo' IMP biosynthetic process / 4 iron, 4 sulfur cluster binding / magnesium ion binding / Amidophosphoribosyltransferase
Function and homology information
Specimen sourceBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 2.8 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 15, 1997 / Release: Nov 12, 1997
RevisionDateData content typeGroupProviderType
1.0Nov 12, 1997Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Polyers199,5144
Non-polymers4,66516
Water724
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)21400
ΔGint (kcal/M)-219
Surface area (Å2)60520
MethodPISA
Unit cell
γ
α
β
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-MP 21 21 21
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/peptide , 1 types, 4 molecules ABCD

#1: Protein/peptide
GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE


Mass: 49878.469 Da / Num. of mol.: 4 / Source: (gene. exp.) Bacillus subtilis (bacteria) / Genus: Bacillus / Gene: PURF / Plasmid name: PGZ1 (PURF+ FRAGMENT INSERTED INTO PUC18) / Genus (production host): Escherichia / 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 / Formula: Mg / Magnesium
#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Formula: Fe4S4 / Iron–sulfur cluster
#4: Chemical
ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 4 / Formula: C10H14N5O8P / Guanosine monophosphate
#5: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Formula: H2O / Water

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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 / Density percent sol: 4 %
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
IDConcCommon 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
SourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Collection date: Jan 1, 1995
RadiationMonochromator: MSC DOUBLE MIRROR / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 / Relative weight: 1
ReflectionB iso Wilson estimate: 47 / D resolution high: 2.8 / D resolution low: 15 / Number obs: 46771 / Observed criterion sigma I: -3 / Rsym value: 0.08 / NetI over sigmaI: 20.2 / Redundancy: 4.2 % / Percent possible obs: 91
Reflection
*PLUS
Number 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
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GPH
R Free selection details: RANDOM FROM ALL DATA / Data cutoff high absF: 1 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0
Displacement parametersB iso mean: 32.5
Least-squares processR factor R free: 0.264 / R factor R work: 0.214 / R factor obs: 0.214 / Highest resolution: 2.8 / Lowest resolution: 15 / Number reflection obs: 46771 / Percent reflection R free: 5 / Percent reflection obs: 91
Refine hist #LASTHighest resolution: 2.8 / Lowest resolution: 15
Number of atoms included #LASTProtein: 13908 / Nucleic acid: 204 / Ligand: 36 / Solvent: 4 / Total: 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_deg2.50
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
Refine LS shellHighest resolution: 2.8 / R factor R free: 0.3823 / R factor R work: 0.2881 / Lowest resolution: 2.88 / Number reflection R free: 184 / Number reflection R work: 3409 / Total number of bins used: 10 / Percent reflection R free: 5
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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