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- PDB-1gph: STRUCTURE OF THE ALLOSTERIC REGULATORY ENZYME OF PURINE BIOSYNTHESIS -

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Entry
Database: PDB / ID: 1gph
TitleSTRUCTURE OF THE ALLOSTERIC REGULATORY ENZYME OF PURINE BIOSYNTHESIS
ComponentsGLUTAMINE PHOSPHORIBOSYL-PYROPHOSPHATE AMIDOTRANSFERASE
KeywordsTRANSFERASE / GLUTAMINE AMIDOTRANSFERASE
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 / 'de novo' IMP biosynthetic process / nucleoside metabolic process / 4 iron, 4 sulfur cluster binding / magnesium ion binding / Amidophosphoribosyltransferase
Function and homology information
Specimen sourceBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / 3 Å resolution
AuthorsSmith, J.L.
CitationJournal: Science / Year: 1994
Title: Structure of the allosteric regulatory enzyme of purine biosynthesis.
Authors: Smith, J.L. / Zaluzec, E.J. / Wery, J.P. / Niu, L. / Switzer, R.L. / Zalkin, H. / Satow, Y.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 20, 1994 / Release: Jul 31, 1994
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 31, 1994Structure modelrepositoryInitial release
1.1Mar 3, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Version format compliance
1.3May 21, 2014Structure modelStructure summary
1.4Nov 29, 2017Structure modelDerived calculations / Otherpdbx_database_status / struct_conf / struct_conf_type_pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: GLUTAMINE PHOSPHORIBOSYL-PYROPHOSPHATE AMIDOTRANSFERASE
2: GLUTAMINE PHOSPHORIBOSYL-PYROPHOSPHATE AMIDOTRANSFERASE
3: GLUTAMINE PHOSPHORIBOSYL-PYROPHOSPHATE AMIDOTRANSFERASE
4: GLUTAMINE PHOSPHORIBOSYL-PYROPHOSPHATE AMIDOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,21316
Polyers202,0294
Non-polymers4,18412
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
1: GLUTAMINE PHOSPHORIBOSYL-PYROPHOSPHATE AMIDOTRANSFERASE
2: GLUTAMINE PHOSPHORIBOSYL-PYROPHOSPHATE AMIDOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,1078
Polyers101,0142
Non-polymers2,0926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)8480
ΔGint (kcal/M)-75
Surface area (Å2)33170
MethodPISA
3
3: GLUTAMINE PHOSPHORIBOSYL-PYROPHOSPHATE AMIDOTRANSFERASE
4: GLUTAMINE PHOSPHORIBOSYL-PYROPHOSPHATE AMIDOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,1078
Polyers101,0142
Non-polymers2,0926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)8490
ΔGint (kcal/M)-79
Surface area (Å2)33200
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)158.800, 75.700, 94.100
Angle α, β, γ (deg.)90.00, 91.40, 90.00
Int Tables number4
Space group name H-MP 1 21 1
Atom site foot note1: CIS PROLINE - PRO 1 86 / 2: CIS PROLINE - PRO 2 86 / 3: CIS PROLINE - PRO 3 86 / 4: CIS PROLINE - PRO 4 86

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Components

#1: Protein/peptide
GLUTAMINE PHOSPHORIBOSYL-PYROPHOSPHATE AMIDOTRANSFERASE


Mass: 50507.203 Da / Num. of mol.: 4 / Source: (gene. exp.) Bacillus subtilis (bacteria) / Genus: Bacillus / References: UniProt: P00497, amidophosphoribosyltransferase
#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Formula: Fe4S4 / Iron–sulfur cluster
#3: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 8 / Formula: C10H14N5O7P / Adenosine monophosphate / Comment: AMP *YM
Nonpolymer detailsTHE FE ATOMS OF THE [4FE-4S] CLUSTER ARE LIGATED BY CYSTEINE S(GAMMA) ATOMS AS FOLLOWS: FE 1 - SG ...THE FE ATOMS OF THE [4FE-4S] CLUSTER ARE LIGATED BY CYSTEINE S(GAMMA) ATOMS AS FOLLOWS: FE 1 - SG CYS 437; FE 2 - SG CYS 236; FE 3 - SG CYS 440; FE 4 - SG CYS 382. THE AMP MOLECULE THAT IS RESIDUE 467 IS BOUND TO THE SITE WHERE THE SUBSTRATE PRPP IS PRESUMED TO BIND. THE AMP MOLECULE THAT IS RESIDUE 468 IS BOUND BETWEEN SUBUNITS IN WHAT IS PRESUMED TO BE AN ALLOSTERIC REGULATORY SITE.
Sequence detailsTHE STRUCTURE DIFFERS FROM THE DEPOSITED SEQUENCE IN TWO PLACES: 1) AN 11-RESIDUE PROPEPTIDE ...THE STRUCTURE DIFFERS FROM THE DEPOSITED SEQUENCE IN TWO PLACES: 1) AN 11-RESIDUE PROPEPTIDE REMOVED POSTTRANSLATIONALLY IS NOT PRESENT IN THE MATURE PROTEIN OR IN THE CRYSTALS, BUT IS INCLUDED IN THE SWISS-PROT ENTRY. RESIDUE NUMBERS IN THE PDB ENTRY ARE WITH RESPECT TO THE MATURE PROTEIN AND THOSE IN THE SWISS-PROT ENTRY ARE WITH RESPECT TO THE UNPROCESSED PROTEIN (I+11). SEQRES RECORDS IN THIS ENTRY CORRESPOND TO THE SEQUENCE OF MATURE PROTEIN. 2) RESIDUE 402 IS REPORTED FROM SEQUENCING TO BE GLYCINE BUT STRONG ELECTRON DENSITY AT THIS POSITION BRIDGES TO AN ARGININE SIDE CHAIN AND IS BEST FIT WITH A SIDE CHAIN OF THREE-ATOM LENGTH. AN ASPARTATE RESIDUE WAS MODELED INTO THIS DENSITY, REFINED, AND INCLUDED IN THE DEPOSITED MODEL. SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: PUR1_BACSU SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE GLY 413 ASP 1 402 GLY 413 ASP 2 402 GLY 413 ASP 3 402 GLY 413 ASP 4 402

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 / Density percent sol: 56.04 %
Crystal grow
*PLUS
pH: 7.9 / Method: batch method
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
17-8 mg/mlprotein11
250 mMTris-HCl11
33-4 mM11MgCl2
45 mMDTE11
52 mMAMP11
612-13 %(w/v)PEG800011
710 mM12MgCl2
85 mMDTE12
92 mMAMP12
1015 %PEG800012
1150 mMTris-HCl12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
D resolution high: 3 Å / Number obs: 41267 / Percent possible obs: 90.1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefineSigma F: 2
Least-squares processR factor R work: 0.182 / R factor obs: 0.182 / Highest resolution: 3 Å / Lowest resolution: 7 Å / Number reflection obs: 37670
Refine hist #LASTHighest resolution: 3 Å / Lowest resolution: 7 Å
Number of atoms included #LASTProtein: 14156 / Nucleic acid: 0 / Ligand: 216 / Solvent: 0 / Total: 14372
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg3.3
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_d
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 / Classification: refinement
Least-squares process
*PLUS
R factor R work: 0.182 / R factor obs: 0.182
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.3

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