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- PDB-1grc: CRYSTAL STRUCTURE OF GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE FR... -

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Basic information

Entry
Database: PDB / ID: 1grc
TitleCRYSTAL STRUCTURE OF GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE FROM ESCHERICHIA COLI AT 3.0 ANGSTROMS RESOLUTION: A TARGET ENZYME FOR CHEMOTHERAPY
ComponentsGLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE
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: 3 Å
AuthorsChen, P. / Wilson, I.A.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Crystal structure of glycinamide ribonucleotide transformylase from Escherichia coli at 3.0 A resolution. A target enzyme for chemotherapy.
Authors: Chen, P. / Schulze-Gahmen, U. / Stura, E.A. / Inglese, J. / Johnson, D.L. / Marolewski, A. / Benkovic, S.J. / Wilson, I.A.
#1: Journal: J.Biol.Chem. / Year: 1989
Title: Preliminary Crystallographic Investigations of Glycinamide Ribonucleotide Transformylase in Escherichia Coli K12
Authors: Stura, E.A. / Johnson, D.L. / Inglese, J. / Smith, J.M. / Benkovic, S.J. / Wilson, I.A.
#2: Journal: J.Biol.Chem. / Year: 1987
Title: Identification and Nucleotide Sequence of a Gene Encoding 5'-Phosphoribosyl-Glycinamide Transformylase in Escherichia Coli K12
Authors: Smith, J.M. / Daum III, H.A.
History
DepositionJul 21, 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

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Assembly

Deposited unit
A: GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE
B: GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE
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 area2060 Å2
ΔGint-22 kcal/mol
Surface area17450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.500, 98.200, 103.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: RESIDUE 113 OF CHAIN B IS A CIS PROLINE.
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.197721, 0.401817, 0.894119), (0.355059, -0.820833, 0.447398), (0.913695, 0.405925, 0.019627)6.56252, 125.12114, -58.6362
2given(-0.197721, 0.355059, 0.913695), (0.401817, -0.820833, 0.405925), (0.894119, 0.447398, 0.019627)10.44778, 123.86861, -60.6958
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. (KABSCH ROTATION MATRIX) THE TRANSFORMATION PRESENTED ON *MTRIX 2* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*. (KABSCH ROTATION MATRIX)

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Components

#1: Protein GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE


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: 3.83 Å3/Da / Density % sol: 67.86 %
Crystal grow
*PLUS
pH: 6.75 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.9-1.0 Msodium potassium phosphate1reservoir
21-3 %ethanol1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3 Å / Num. obs: 13910 / % possible obs: 94.7 % / Num. measured all: 75626 / Rmerge(I) obs: 0.103

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.19 / Rfactor obs: 0.19 / Highest resolution: 3 Å
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2955 0 10 0 2965
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_deg3.55
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: 3 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.55
LS refinement shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.1 Å / Rfactor obs: 0.27

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