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- PDB-1gtd: NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG ID TT50) STRUCTURE... -

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Basic information

Entry
Database: PDB / ID: 1gtd
TitleNORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG ID TT50) STRUCTURE OF MTH169, THE PURS SUBUNIT OF FGAM SYNTHETASE
ComponentsMTH169
KeywordsLIGASE / SYNTHETASE / FGAM SYNTHETASE / PURINE SYNTHESIS PATHWAY / PSI / PROTEIN STRUCTURE INITIATIVE / NESG / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM
Function / homology
Function and homology information


phosphoribosylformylglycinamidine synthase / phosphoribosylformylglycinamidine synthase activity / 'de novo' IMP biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Mth169; Chain: A , / Phosphoribosylformylglycinamidine synthase subunit PurS / Phosphoribosylformylglycinamidine synthase subunit PurS / Phosphoribosylformylglycinamidine (FGAM) synthase / Phosphoribosylformylglycinamidine synthase subunit PurS-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoribosylformylglycinamidine synthase subunit PurS
Similarity search - Component
Biological speciesMETHANOBACTERIUM THERMOAUTOTROPHICUM (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.56 Å
AuthorsBatra, R. / Christendat, D. / Saxild, H.H. / Arrowsmith, C. / Tong, L.
Citation
Journal: Proteins: Struct.,Funct., Genet. / Year: 2002
Title: Crystal Structure of Mth169, a Crucial Component of Phosphoribosylformylglycinamidine Synthetase
Authors: Batra, R. / Christendat, D. / Edwards, A. / Arrowsmith, C. / Tong, L.
#1: Journal: Microbiology (Reading, Engl. / Year: 2000
Title: The Yexa Gene Product is Required for Phosphoribosylformylglycinamidine Synthetase Activity in Bacillus Subtilis.
Authors: Saxild, H.H. / Nygaard, P.
History
DepositionJan 14, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2002Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Aug 21, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: pdbx_database_related / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_related / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _pdbx_database_related.db_name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MTH169
B: MTH169


Theoretical massNumber of molelcules
Total (without water)20,1152
Polymers20,1152
Non-polymers00
Water1,49583
1
A: MTH169
B: MTH169

A: MTH169
B: MTH169


Theoretical massNumber of molelcules
Total (without water)40,2304
Polymers40,2304
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+1,y,-z1
Buried area7870 Å2
ΔGint-53.1 kcal/mol
Surface area16690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.800, 53.800, 142.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9881, -0.0032, -0.1536), (-0.0022, -1, 0.0065), (-0.1536, -0.0061, -0.9881)
Vector: 0.3516, 60.9978, 4.1807)

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Components

#1: Protein MTH169


Mass: 10057.487 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOBACTERIUM THERMOAUTOTROPHICUM (archaea)
Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O26271
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE THREE C-TERMINAL RESIDUES ARE PART OF HIS-TAG.

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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: 2.7 Å3/Da / Density % sol: 53.8 %
Crystal growpH: 5.6
Details: 32%(V/V) MPD, 0.1M SODIUM CITRATE (PH 5.6) AND 0.2M AMMONIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793
DetectorDate: Sep 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 7888 / % possible obs: 94 % / Redundancy: 5 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 3.2 / % possible all: 54.2

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.56→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 625704 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.278 882 7.6 %RANDOM
Rwork0.235 ---
obs0.235 11570 90 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.7459 Å2 / ksol: 0.342124 e/Å3
Displacement parametersBiso mean: 31.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.56 Å20 Å20 Å2
2--2.56 Å20 Å2
3----5.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.56→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1318 0 0 83 1401
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.64
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.392
X-RAY DIFFRACTIONc_scbond_it2.632
X-RAY DIFFRACTIONc_scangle_it3.872.5
LS refinement shellResolution: 2.56→2.72 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.422 121 7.5 %
Rwork0.306 1503 -
obs--76.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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