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- PDB-1kjj: Crystal structure of glycniamide ribonucleotide transformylase in... -

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Basic information

Entry
Database: PDB / ID: 1kjj
TitleCrystal structure of glycniamide ribonucleotide transformylase in complex with Mg-ATP-gamma-S
Componentsphosphoribosylglycinamide formyltransferase 2
KeywordsTRANSFERASE / ATP-grasp / purine biosynthesis / nucleotide
Function / homology
Function and homology information


phosphoribosylglycinamide formyltransferase 2 / phosphoribosylglycinamide formyltransferase 2 activity / acetate kinase activity / phosphoribosylglycinamide formyltransferase activity / 'de novo' IMP biosynthetic process / ligase activity / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
: / PurT, C-terminal / Formate-dependent phosphoribosylglycinamide formyltransferase / ATP-grasp fold, ATP-dependent carboxylate-amine ligase-type / ATP-grasp domain / Rossmann fold - #20 / Rudiment single hybrid motif / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 ...: / PurT, C-terminal / Formate-dependent phosphoribosylglycinamide formyltransferase / ATP-grasp fold, ATP-dependent carboxylate-amine ligase-type / ATP-grasp domain / Rossmann fold - #20 / Rudiment single hybrid motif / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Formate-dependent phosphoribosylglycinamide formyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.75 Å
AuthorsThoden, J.B. / Firestine, S.M. / Benkovic, S.J. / Holden, H.M.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: PurT-encoded glycinamide ribonucleotide transformylase. Accommodation of adenosine nucleotide analogs within the active site.
Authors: Thoden, J.B. / Firestine, S.M. / Benkovic, S.J. / Holden, H.M.
History
DepositionDec 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: phosphoribosylglycinamide formyltransferase 2
B: phosphoribosylglycinamide formyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,11011
Polymers84,6992
Non-polymers1,4119
Water12,142674
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7390 Å2
ΔGint-77 kcal/mol
Surface area27480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.900, 179.300, 76.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein phosphoribosylglycinamide formyltransferase 2 / / E.C.2.1.2.- / GART 2 / GAR TRANSFORMYLASE 2 / 5'-PHOSPHORIBOSYLGLYCINAMIDE


Mass: 42349.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PURT / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P33221, Transferases; Transferring one-carbon groups; Hydroxymethyl-, formyl- and related transferases

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Non-polymers , 6 types, 683 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID / MOPS


Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 674 / 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: 2.49 Å3/Da / Density % sol: 50.64 %
Crystal growTemperature: 277 K / Method: batch / pH: 6.7
Details: PEG 5000, NaCl, MgCl2, MOPS, ATP-gamma-S, pH 6.7, batch at 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: batch method / Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15 mMATPgammaS1drop
210 mM1dropMgCl2
3250 mM1dropNaCl
420 mMprotein1drop
516-24 %(w/v)PEG5000 ME1reservoir
6100 mMMOPS1reservoirpH6.7
7100 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Nov 6, 2000 / Details: goebel optics
RadiationMonochromator: goebel optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. all: 82695 / Num. obs: 82695 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.2
Reflection shellResolution: 1.75→1.87 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 4.4 / Num. unique all: 9407 / % possible all: 88
Reflection
*PLUS
Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 88 % / Num. unique obs: 9407 / Rmerge(I) obs: 0.215

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Processing

Software
NameClassification
TNTrefinement
FRAMBOdata collection
SAINTdata scaling
TNTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1EYZ

1eyz


Resolution: 1.75→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 8270 10 %RANDOM
Rwork0.184 ---
all0.187 82695 --
obs0.187 82695 96 %-
Refinement stepCycle: LAST / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5892 0 81 674 6647
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.6
X-RAY DIFFRACTIONt_bond_d0.014
Refinement
*PLUS
Rfactor all: 0.187 / Rfactor Rfree: 0.233 / Rfactor Rwork: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg16.7
X-RAY DIFFRACTIONt_planar_d0.009
X-RAY DIFFRACTIONt_plane_restr0.013

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