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- PDB-2yx5: Crystal Structure of Methanocaldococcus jannaschii PurS, One of t... -

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Basic information

Entry
Database: PDB / ID: 2yx5
TitleCrystal Structure of Methanocaldococcus jannaschii PurS, One of the Subunits of Formylglycinamide Ribonucleotide Amidotransferase in the Purine Biosynthetic Pathway
ComponentsUPF0062 protein MJ1593
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / anti parallel beta sheet / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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 speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKanagawa, M. / Baba, S. / Agari, Y. / Chen, L.Q. / Fu, Z.-Q. / Chrzas, J. / Wang, B.C. / Kuramitsu, S. / Yokoyama, S. / Kawai, G. ...Kanagawa, M. / Baba, S. / Agari, Y. / Chen, L.Q. / Fu, Z.-Q. / Chrzas, J. / Wang, B.C. / Kuramitsu, S. / Yokoyama, S. / Kawai, G. / Sampei, G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of Methanocaldococcus jannaschii PurS, One of the Subunits of Formylglycinamide Ribonucleotide Amidotransferase in the Purine Biosynthetic Pathway
Authors: Kanagawa, M. / Baba, S. / Agari, Y. / Chen, L.Q. / Fu, Z.-Q. / Chrzas, J. / Wang, B.C. / Kuramitsu, S. / Yokoyama, S. / Kawai, G. / Sampei, G.
History
DepositionApr 24, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 25, 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

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Assembly

Deposited unit
A: UPF0062 protein MJ1593


Theoretical massNumber of molelcules
Total (without water)9,7111
Polymers9,7111
Non-polymers00
Water19811
1
A: UPF0062 protein MJ1593

A: UPF0062 protein MJ1593

A: UPF0062 protein MJ1593

A: UPF0062 protein MJ1593


Theoretical massNumber of molelcules
Total (without water)38,8464
Polymers38,8464
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area8830 Å2
ΔGint-79 kcal/mol
Surface area16490 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)96.251, 96.251, 48.257
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein UPF0062 protein MJ1593 / hypothetical protein PurS


Mass: 9711.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / References: UniProt: Q58988
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.32 Å3/Da / Density % sol: 62.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.9
Details: 25% 1,2-propanediol, 10% glycerol, phosphate-citrate, 5% PEG 3000, pH 4.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 31, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 6252 / % possible obs: 99.9 % / Redundancy: 20.7 % / Biso Wilson estimate: 36.8 Å2 / Rmerge(I) obs: 0.051
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 21 % / Rmerge(I) obs: 0.355 / Num. unique all: 593 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T4A

1t4a


Resolution: 2.3→31.54 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 237174.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.284 663 11.1 %RANDOM
Rwork0.24 ---
obs0.24 6000 96.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.7779 Å2 / ksol: 0.364558 e/Å3
Displacement parametersBiso mean: 58.1 Å2
Baniso -1Baniso -2Baniso -3
1-5.86 Å23.13 Å20 Å2
2--5.86 Å20 Å2
3----11.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.3→31.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms674 0 0 11 685
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
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_deg1.5
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_d0.93
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it51.5
X-RAY DIFFRACTIONc_mcangle_it6.352
X-RAY DIFFRACTIONc_scbond_it8.42
X-RAY DIFFRACTIONc_scangle_it11.462.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.314 114 12.4 %
Rwork0.33 809 -
obs--92.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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