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- PDB-3gar: A PH-DEPENDENT STABLIZATION OF AN ACTIVE SITE LOOP OBSERVED FROM ... -

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Basic information

Entry
Database: PDB / ID: 3gar
TitleA PH-DEPENDENT STABLIZATION OF AN ACTIVE SITE LOOP OBSERVED FROM LOW AND HIGH PH CRYSTAL STRUCTURES OF MUTANT MONOMERIC GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE
ComponentsGLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE
KeywordsPURINE BIOSYNTHESIS / FOLATE COFACTORS / LOOP FLEXIBILITY / MONOMER-DIMER ASSOCIATION / ENZYME MECHANISM / ANTI-CANCER AGENTS
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
PHOSPHATE ION / Phosphoribosylglycinamide formyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSu, Y. / Yamashita, M.M. / Greasley, S.E. / Mullen, C.A. / Shim, J.H. / Jennings, P.A. / Benkovic, S.J. / Wilson, I.A.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: A pH-dependent stabilization of an active site loop observed from low and high pH crystal structures of mutant monomeric glycinamide ribonucleotide transformylase at 1.8 to 1.9 A.
Authors: Su, Y. / Yamashita, M.M. / Greasley, S.E. / Mullen, C.A. / Shim, J.H. / Jennings, P.A. / Benkovic, S.J. / Wilson, I.A.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Towards Structure-Based Drug Design: Crystal Structure of a Multisubstrate Adduct Complex of Glycinamide Ribonucleotide Transformylase at 1.96 A Resolution
Authors: Klein, C. / Chen, P. / Arevalo, J.H. / Stura, E.A. / Marolewski, A. / Warren, M.S. / Benkovic, S.J. / Wilson, I.A.
#2: 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.
#3: 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.
History
DepositionMay 13, 1998Processing site: BNL
Revision 1.0Aug 12, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3032
Polymers23,2081
Non-polymers951
Water2,666148
1
A: GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE
hetero molecules

A: GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6064
Polymers46,4162
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_766-x+2,-x+y+1,-z+5/31
Unit cell
Length a, b, c (Å)50.400, 50.400, 275.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE / GARTFASE


Mass: 23208.217 Da / Num. of mol.: 1 / Mutation: E70A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P08179, phosphoribosylglycinamide formyltransferase 1
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growpH: 7.5
Details: CRYSTAL GREW FROM A SOLUTION OF 2%(V/V) PEG 400. 2.0M AMMONIUM SULFATE, 0.1M HEPES, PH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 22 R.T. / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
22 %(v/v)PEG4001reservoir
32.0 Mammonium sulfate1reservoir
40.1 Msodium HEPES1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 16340 / % possible obs: 92.8 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 22.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.331 / % possible all: 81.8
Reflection
*PLUS
Num. measured all: 67156
Reflection shell
*PLUS
% possible obs: 81.8 %

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GAR

1gar


Resolution: 1.9→50 Å / Rfactor Rfree error: 0.0002 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1484 10.2 %RANDOM
Rwork0.215 ---
obs0.215 14555 92.8 %-
Displacement parametersBiso mean: 31 Å2
Baniso -1Baniso -2Baniso -3
1-13 Å20 Å20 Å2
2--13 Å20 Å2
3---19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1619 0 0 148 1767
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.8
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.99 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.303 139 12.9 %
Rwork0.284 1074 -
obs--63 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PO4.PARPO4.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.8

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