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

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Basic information

Entry
Database: PDB / ID: 1cdd
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 / cytoplasm / cytosol
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
PHOSPHATE ION / Phosphoribosylglycinamide formyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.8 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7224
Polymers46,5332
Non-polymers1902
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-23 kcal/mol
Surface area17790 Å2
MethodPISA
2
A: PHOSPHORIBOSYL-GLYCINAMIDE FORMYLTRANSFERASE
hetero molecules

B: PHOSPHORIBOSYL-GLYCINAMIDE FORMYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7224
Polymers46,5332
Non-polymers1902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645-x+3/2,y-1/2,-z+1/21
Buried area2280 Å2
ΔGint-26 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.900, 97.600, 102.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: PRO B 204 - PRO B 205 OMEGA =212.30 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.19391, 0.33875, 0.92068), (0.43494, -0.81152, 0.3902), (0.87933, 0.47611, 0.01002)
Vector: 112.79, 1.83, -101.45)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR MOLECULE 1 (CHAIN A) WHEN APPLIED TO MOLECULE 2 (CHAIN B) WITH AN RMS DEVIATION OF 0.83 ANGSTROMS FOR 189 CA COORDINATES (APPROXIMATELY A TWO-FOLD ROTATION, 184 DEGREES).

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Components

#1: Protein PHOSPHORIBOSYL-GLYCINAMIDE FORMYLTRANSFERASE


Mass: 23266.254 Da / Num. of mol.: 2
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.78 Å3/Da / Density % sol: 67.47 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
250 mMTris1drop
31 mMdithiothreitol1drop
40.8 MNa+/K+ phosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 8 Å / Num. all: 124304 / Num. obs: 16623 / Rmerge(I) obs: 0.074

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor obs: 0.225 / Highest resolution: 2.8 Å
Details: RESIDUES 210 - 212 IN CHAIN A HAVE HIGH TEMPERATURE FACTORS, ARE IN WEAK DENSITY, AND HAVE SIGNIFICANT DISORDER.
Refinement stepCycle: LAST / Highest resolution: 2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2908 0 10 0 2918
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d4.1
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 8 Å / Num. reflection obs: 15431 / σ(F): 0.5 / Rfactor obs: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg4.1

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