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- PDB-1cde: STRUCTURES OF APO AND COMPLEXED ESCHERICHIA COLI GLYCINAMIDE RIBO... -

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Basic information

Entry
Database: PDB / ID: 1cde
TitleSTRUCTURES OF APO AND COMPLEXED ESCHERICHIA COLI GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE
ComponentsPHOSPHORIBOSYL-GLYCINAMIDE FORMYLTRANSFERASE
KeywordsTRANSFERASE(FORMYL)
Function / homology
Function and homology information


phosphoribosylglycinamide formyltransferase 1 / phosphoribosylglycinamide formyltransferase activity / 'de novo' IMP biosynthetic process / DNA damage response / cytosol / cytoplasm
Similarity search - Function
Phosphoribosylglycinamide formyltransferase / Formyl transferase, N-terminal domain / Phosphoribosylglycinamide formyltransferase, active site / Phosphoribosylglycinamide formyltransferase active site. / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5-DEAZAFOLIC ACID / GLYCINAMIDE RIBONUCLEOTIDE / Phosphoribosylglycinamide formyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsAlmassy, R.J. / Janson, C.A. / Kan, C.-C. / Hostomska, Z.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Structures of apo and complexed Escherichia coli glycinamide ribonucleotide transformylase.
Authors: Almassy, R.J. / Janson, C.A. / Kan, C.C. / Hostomska, Z.
#1: Journal: Nucleic Acids Res. / Year: 1990
Title: De Novo Purine Nucleotide Biosynthesis: Cloning of Human and Avian Cdna'S Encoding the Trifunctional Glycinamide Ribonucleotide Synthetase-Aminoimidazole Ribonucleotide Synthetase-Glycinamide ...Title: De Novo Purine Nucleotide Biosynthesis: Cloning of Human and Avian Cdna'S Encoding the Trifunctional Glycinamide Ribonucleotide Synthetase-Aminoimidazole Ribonucleotide Synthetase-Glycinamide Ribonucleotide Transformylase by Functional Complementation in E. Coli
Authors: Aimi, J. / Qiu, H. / Williams, J. / Zalkin, H. / Dixon, J.E.
#2: Journal: J.Biol.Chem. / Year: 1987
Title: Identification and Nucleotide Sequence of a Gene Encoding 5'-Phosphoribosylglycinamide Transformylase in Escherichia Coli K12
Authors: Smith, J.M. / Daum /III, H.A.
History
DepositionMay 15, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHORIBOSYL-GLYCINAMIDE FORMYLTRANSFERASE
B: PHOSPHORIBOSYL-GLYCINAMIDE FORMYLTRANSFERASE
C: PHOSPHORIBOSYL-GLYCINAMIDE FORMYLTRANSFERASE
D: PHOSPHORIBOSYL-GLYCINAMIDE FORMYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,96312
Polymers93,0654
Non-polymers2,8988
Water0
1
A: PHOSPHORIBOSYL-GLYCINAMIDE FORMYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9913
Polymers23,2661
Non-polymers7252
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PHOSPHORIBOSYL-GLYCINAMIDE FORMYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9913
Polymers23,2661
Non-polymers7252
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PHOSPHORIBOSYL-GLYCINAMIDE FORMYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9913
Polymers23,2661
Non-polymers7252
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PHOSPHORIBOSYL-GLYCINAMIDE FORMYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9913
Polymers23,2661
Non-polymers7252
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.700, 72.600, 57.000
Angle α, β, γ (deg.)111.50, 82.80, 62.60
Int Tables number1
Space group name H-MP1
Atom site foot note1: CIS PROLINE - PRO 113
2: THE GLUTAMATE PORTION OF THE INHIBITOR DZF IS DISORDERED.
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.992314, 0.094951, 0.079358), (-0.085925, 0.990177, -0.110297), (-0.089052, 0.102631, 0.990725)73.9969, 49.8837, 22.2637
2given(-0.643066, 0.315166, 0.697951), (0.338554, -0.700492, 0.628245), (0.686911, 0.640297, 0.343762)78.1289, 3.1336, 37.917
3given(-0.574509, 0.286038, 0.766891), (0.298183, -0.799419, 0.521551), (0.762251, 0.52831, 0.373981)37.2142, 17.6869, 14.7499
DetailsTHE TRANSFORMATIONS GIVEN ON *MTRIX* RECORDS BELOW WILL GENERATE THE OTHER THREE MOLECULES OF THE ASYMMETRIC UNIT.

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Components

#1: Protein
PHOSPHORIBOSYL-GLYCINAMIDE FORMYLTRANSFERASE


Mass: 23266.254 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain (production host): K12
References: UniProt: P08179, phosphoribosylglycinamide formyltransferase 1
#2: Chemical
ChemComp-GAR / GLYCINAMIDE RIBONUCLEOTIDE / Glycineamide ribonucleotide


Mass: 284.160 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H13N2O8P
#3: Chemical
ChemComp-DZF / 5-DEAZAFOLIC ACID


Mass: 440.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H20N6O6
Nonpolymer detailsTHE GLUTAMATE PORTION OF THE INHIBITOR DZF IS DISORDERED

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.26 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mg/mlenzyme1drop
4154 mM1reservoirCaCl2
577 mMMops1reservoir
619 %(w/v)PEG34001reservoir
74 %(v/v)MPD1reservoir
2GAR1drop
35dTHF1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 8 Å / Num. all: 69765 / Num. obs: 28188 / Rmerge(I) obs: 0.123

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.25 / Rfactor obs: 0.25 / Highest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6468 0 200 0 6668
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg3.5
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_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
Refinement
*PLUS
Highest resolution: 2.5 Å / Num. reflection obs: 25408 / σ(F): 0.5 / Rfactor obs: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.5

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