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- PDB-5avm: Crystal structures of 5-aminoimidazole ribonucleotide (AIR) synth... -

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Basic information

Entry
Database: PDB / ID: 5avm
TitleCrystal structures of 5-aminoimidazole ribonucleotide (AIR) synthetase, PurM, from Thermus thermophilus
ComponentsPhosphoribosylformylglycinamidine cyclo-ligase
KeywordsLIGASE / PURINE BIOSYNTHESIS / ATP BINDING / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


phosphoribosylformylglycinamidine cyclo-ligase / phosphoribosylformylglycinamidine cyclo-ligase activity / 'de novo' IMP biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / Phosphoribosylformylglycinamidine cyclo-ligase / 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 ...Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / Phosphoribosylformylglycinamidine cyclo-ligase / 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 Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoribosylformylglycinamidine cyclo-ligase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKanagawa, M. / Baba, S. / Watanabe, Y. / Nakagawa, N. / Ebihara, A. / Sampei, G. / Kawai, G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biochem. / Year: 2016
Title: Crystal structures and ligand binding of PurM proteins from Thermus thermophilus and Geobacillus kaustophilus
Authors: Kanagawa, M. / Baba, S. / Watanabe, Y. / Nakagawa, N. / Ebihara, A. / Kuramitsu, S. / Yokoyama, S. / Sampei, G. / Kawai, G.
History
DepositionJun 23, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoribosylformylglycinamidine cyclo-ligase
B: Phosphoribosylformylglycinamidine cyclo-ligase
C: Phosphoribosylformylglycinamidine cyclo-ligase
D: Phosphoribosylformylglycinamidine cyclo-ligase
E: Phosphoribosylformylglycinamidine cyclo-ligase
F: Phosphoribosylformylglycinamidine cyclo-ligase
G: Phosphoribosylformylglycinamidine cyclo-ligase
H: Phosphoribosylformylglycinamidine cyclo-ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,16625
Polymers283,5338
Non-polymers1,63317
Water31,8331767
1
A: Phosphoribosylformylglycinamidine cyclo-ligase
B: Phosphoribosylformylglycinamidine cyclo-ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3647
Polymers70,8832
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-102 kcal/mol
Surface area21980 Å2
MethodPISA
2
C: Phosphoribosylformylglycinamidine cyclo-ligase
D: Phosphoribosylformylglycinamidine cyclo-ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2686
Polymers70,8832
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-88 kcal/mol
Surface area22120 Å2
MethodPISA
3
E: Phosphoribosylformylglycinamidine cyclo-ligase
F: Phosphoribosylformylglycinamidine cyclo-ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1725
Polymers70,8832
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-66 kcal/mol
Surface area22600 Å2
MethodPISA
4
G: Phosphoribosylformylglycinamidine cyclo-ligase
H: Phosphoribosylformylglycinamidine cyclo-ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3647
Polymers70,8832
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-82 kcal/mol
Surface area22520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.328, 142.630, 218.616
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Phosphoribosylformylglycinamidine cyclo-ligase / 5-aminoimidazole ribonucleotide synthetase / AIR synthase / AIRS / Phosphoribosyl-aminoimidazole synthetase


Mass: 35441.672 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / Gene: purM, TTHA0367 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli)
References: UniProt: Q5SLC6, phosphoribosylformylglycinamidine cyclo-ligase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1767 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.92 Å3/Da / Density % sol: 68.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.0 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 9, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 224495 / % possible obs: 99.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 17.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 4.5 / % possible all: 98.5

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Processing

Software
NameVersionClassification
CNS1.3refinement
HKL-2000data processing
HKL-2000data scaling
AMoREphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BTU

2btu


Resolution: 2.2→50 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.215 20886 9.3 %RANDOM
Rwork0.163 ---
obs0.163 217248 96.6 %-
Solvent computationBsol: 70.73 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 30.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.114 Å20 Å20 Å2
2---0.391 Å20 Å2
3---0.504 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16868 0 85 1767 18720
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d1.318
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.68
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.889
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.0651.5
X-RAY DIFFRACTIONc_mcangle_it1.7652
X-RAY DIFFRACTIONc_scbond_it1.7912
X-RAY DIFFRACTIONc_scangle_it2.7252.5
LS refinement shellResolution: 2.2→2.28 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2534 1885 9.43 %
Rwork0.2286 18096 -
all-19981 -
obs--89.84 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR/PROTEIN_REP.PARAMCNS_TOPPAR/PROTEIN.TOP
X-RAY DIFFRACTION2CNS_TOPPAR/DNA-RNA_REP.PARAMCNS_TOPPAR/DNA-RNA.TOP
X-RAY DIFFRACTION3CNS_TOPPAR/WATER_REP.PARAMCNS_TOPPAR/WATER.TOP
X-RAY DIFFRACTION4CNS_TOPPAR/ION.PARAMCNS_TOPPAR/ION.TOP
X-RAY DIFFRACTION5CNS_TOPPAR/CARBOHYDRATE.PARAMCNS_TOPPAR/CARBOHYDRATE.TOP

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