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- PDB-3mjf: Phosphoribosylamine-glycine ligase from Yersinia pestis -

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Basic information

Entry
Database: PDB / ID: 3mjf
TitlePhosphoribosylamine-glycine ligase from Yersinia pestis
ComponentsPhosphoribosylamine--glycine ligase
KeywordsLIGASE / structural genomics / phosphoribosylamine-glycine ligase / Center for Structural Genomics of Infectious Diseases / CSGID
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, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / 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
BETA-MERCAPTOETHANOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Phosphoribosylamine--glycine ligase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.47 Å
AuthorsOsipiuk, J. / Zhou, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: X-ray crystal structure of phosphoribosylamine-glycine ligase from Yersinia pestis.
Authors: Osipiuk, J. / Zhou, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A.
History
DepositionApr 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoribosylamine--glycine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,23113
Polymers46,1471
Non-polymers1,08412
Water9,224512
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.637, 69.151, 95.166
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphoribosylamine--glycine ligase / GARS / Glycinamide ribonucleotide synthetase / Phosphoribosylglycinamide synthetase


Mass: 46147.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: purD, y0501, YPO3729, YP_3092 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8ZAR2, phosphoribosylamine-glycine ligase

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Non-polymers , 8 types, 524 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / 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: 2.45 Å3/Da / Density % sol: 49.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1 M sodium cacodylate, 30% PEG-8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 3, 2010
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.47→30.8 Å / Num. all: 77813 / Num. obs: 77813 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.097 / Χ2: 3.011 / Net I/σ(I): 12.9
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.883 / Mean I/σ(I) obs: 3.05 / Num. unique all: 3850 / Χ2: 1.418 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.47→30.8 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / Occupancy max: 1 / Occupancy min: 0.21 / SU B: 1.952 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.066 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.174 3907 5 %RANDOM
Rwork0.135 ---
all0.137 77708 --
obs0.137 77708 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 114.93 Å2 / Biso mean: 19.157 Å2 / Biso min: 7.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.47→30.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3192 0 63 512 3767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223599
X-RAY DIFFRACTIONr_bond_other_d0.0010.022425
X-RAY DIFFRACTIONr_angle_refined_deg1.741.974933
X-RAY DIFFRACTIONr_angle_other_deg1.0235986
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7445511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22525.291172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87315603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7831521
X-RAY DIFFRACTIONr_chiral_restr0.1120.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214161
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02692
X-RAY DIFFRACTIONr_mcbond_it1.9111.52243
X-RAY DIFFRACTIONr_mcbond_other0.6361.5932
X-RAY DIFFRACTIONr_mcangle_it2.82923627
X-RAY DIFFRACTIONr_scbond_it4.37431356
X-RAY DIFFRACTIONr_scangle_it6.3644.51263
X-RAY DIFFRACTIONr_rigid_bond_restr1.79436024
LS refinement shellResolution: 1.468→1.506 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 287 -
Rwork0.221 5260 -
all-5547 -
obs-5547 97.11 %

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