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- PDB-2ip4: Crystal Structure of Glycinamide Ribonucleotide Synthetase from T... -

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Basic information

Entry
Database: PDB / ID: 2ip4
TitleCrystal Structure of Glycinamide Ribonucleotide Synthetase from Thermus thermophilus HB8
ComponentsPhosphoribosylamine--glycine ligase
KeywordsLIGASE / GAR synthetase / PurD / thermus thermophilus / purine nucleotide / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


purine nucleobase biosynthetic process / phosphoribosylamine-glycine ligase / phosphoribosylamine-glycine ligase activity / 'de novo' IMP biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Phosphoribosylglycinamide synthetase, C-terminal domain / Glycinamide Ribonucleotide Synthetase; Chain A, domain 4 / Phosphoribosylglycinamide synthetase / Phosphoribosylglycinamide synthetase, conserved site / Phosphoribosylglycinamide synthetase, C-domain / Phosphoribosylglycinamide synthetase, N-terminal / Phosphoribosylglycinamide synthetase, C-domain superfamily / Phosphoribosylglycinamide synthetase, C domain / Phosphoribosylglycinamide synthetase, N domain / Phosphoribosylglycinamide synthetase signature. ...Phosphoribosylglycinamide synthetase, C-terminal domain / Glycinamide Ribonucleotide Synthetase; Chain A, domain 4 / Phosphoribosylglycinamide synthetase / Phosphoribosylglycinamide synthetase, conserved site / Phosphoribosylglycinamide synthetase, C-domain / Phosphoribosylglycinamide synthetase, N-terminal / Phosphoribosylglycinamide synthetase, C-domain superfamily / Phosphoribosylglycinamide synthetase, C domain / Phosphoribosylglycinamide synthetase, N domain / Phosphoribosylglycinamide synthetase signature. / Phosphoribosylglycinamide synthetase, C domain / Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / Rossmann fold - #20 / ATP-grasp fold, A domain / Rudiment single hybrid motif / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold, B domain / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Alpha-Beta Complex / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoribosylamine--glycine ligase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSampei, G. / Baba, S. / Kanagawa, M. / Yanai, H. / Ishii, T. / Kawai, H. / Fukai, Y. / Ebihara, A. / Nakagawa, N. / Kawai, G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biochem. / Year: 2010
Title: Crystal structures of glycinamide ribonucleotide synthetase, PurD, from thermophilic eubacteria
Authors: Sampei, G. / Baba, S. / Kanagawa, M. / Yanai, H. / Ishii, T. / Kawai, H. / Fukai, Y. / Ebihara, A. / Nakagawa, N. / Kawai, G.
History
DepositionOct 11, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoribosylamine--glycine ligase
B: Phosphoribosylamine--glycine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1616
Polymers89,7772
Non-polymers3844
Water43224
1
A: Phosphoribosylamine--glycine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0803
Polymers44,8881
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphoribosylamine--glycine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0803
Polymers44,8881
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.308, 98.068, 121.142
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 Phosphoribosylamine--glycine ligase / PurD


Mass: 44888.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0811 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: Q5SK40, phosphoribosylamine-glycine ligase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.39 Å3/Da / Density % sol: 48.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M ammonium sulfate, 0.1M MES, 30% PEGMME5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9843 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 6, 2004
RadiationMonochromator: SI 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9843 Å / Relative weight: 1
ReflectionResolution: 2.8→60 Å / Num. all: 30609 / Num. obs: 29262 / % possible obs: 95.6 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Rmerge(I) obs: 0.1
Reflection shellResolution: 2.8→2.9 Å / % possible all: 96.8

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Processing

Software
NameClassification
HKL-2000data collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GSO

1gso


Resolution: 2.8→60 Å / Cross valid method: FREE R / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.238 2086 RANDOM
Rwork0.2185 --
obs0.225 20976 -
all-21844 -
Refinement stepCycle: LAST / Resolution: 2.8→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6224 0 20 24 6268

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