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- PDB-2hru: T. maritima PurL complexed with ADP -

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Basic information

Entry
Database: PDB / ID: 2hru
TitleT. maritima PurL complexed with ADP
ComponentsPhosphoribosylformylglycinamidine synthase II
KeywordsLIGASE / beta barrel / alpha-beta structure
Function / homology
Function and homology information


phosphoribosylformylglycinamidine synthase / phosphoribosylformylglycinamidine synthase activity / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Formylglycinamide ribonucleotide amidotransferase, C-terminal domain / Phosphoribosylformylglycinamidine subunit PurL, C-terminal / PurL, C-terminal domain superfamily / Phosphoribosylformylglycinamidine synthase II C-terminus / Phosphoribosylformylglycinamidine subunit PurL / Phosphoribosylformylglycinamidine synthase, linker domain / Formylglycinamide ribonucleotide amidotransferase linker domain / Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain ...Formylglycinamide ribonucleotide amidotransferase, C-terminal domain / Phosphoribosylformylglycinamidine subunit PurL, C-terminal / PurL, C-terminal domain superfamily / Phosphoribosylformylglycinamidine synthase II C-terminus / Phosphoribosylformylglycinamidine subunit PurL / Phosphoribosylformylglycinamidine synthase, linker domain / Formylglycinamide ribonucleotide amidotransferase linker domain / Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain / 60s Ribosomal Protein L30; Chain: A; / Alpha-Beta Plaits / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Phosphoribosylformylglycinamidine synthase subunit PurL
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsEalick, S.E. / Morar, M.
CitationJournal: Biochemistry / Year: 2006
Title: Complexed Structures of Formylglycinamide Ribonucleotide Amidotransferase from Thermotoga maritima Describe a Novel ATP Binding Protein Superfamily
Authors: Morar, M. / Anand, R. / Hoskins, A.A. / Stubbe, J. / Ealick, S.E.
History
DepositionJul 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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_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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoribosylformylglycinamidine synthase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4775
Polymers65,9761
Non-polymers5004
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.626, 70.960, 136.953
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphoribosylformylglycinamidine synthase II / / E.C.6.3.5.3 / PurL / formylglycinamide ribonucleotide amidotransferase / FGAM synthase II


Mass: 65976.469 Da / Num. of mol.: 1 / Mutation: His72Ala
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: purL / Plasmid: pET-24a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3)
References: UniProt: Q9X0X3, phosphoribosylformylglycinamidine synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.08 Å3/Da / Density % sol: 40.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 17% PEG 4000, 8% isopropanol, 0.1M HEPES, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→38.39 Å / Num. all: 14120 / Num. obs: 12175 / % possible obs: 85.9 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 51.1 Å2
Reflection shellResolution: 2.8→2.98 Å

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→38.39 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 492765.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.295 616 5.1 %RANDOM
Rwork0.205 ---
all0.2051 14120 --
obs0.2051 12175 85.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.1815 Å2 / ksol: 0.296407 e/Å3
Displacement parametersBiso mean: 45.6 Å2
Baniso -1Baniso -2Baniso -3
1--2 Å20 Å20 Å2
2--8.49 Å20 Å2
3----6.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.8→38.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4476 0 30 120 4626
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_mcbond_it6.171.5
X-RAY DIFFRACTIONc_mcangle_it9.782
X-RAY DIFFRACTIONc_scbond_it10.422
X-RAY DIFFRACTIONc_scangle_it14.072.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.368 99 4.9 %
Rwork0.292 1940 -
obs--87.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2adp.paramwater.top
X-RAY DIFFRACTION3ion.paramrealadp.top
X-RAY DIFFRACTION4water.param

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