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- PDB-3m84: Crystal Structure of Phosphoribosylaminoimidazole Synthetase from... -

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Basic information

Entry
Database: PDB / ID: 3m84
TitleCrystal Structure of Phosphoribosylaminoimidazole Synthetase from Francisella tularensis
ComponentsPhosphoribosylformylglycinamidine cyclo-ligaseAIR synthetase (FGAM cyclase)
KeywordsLIGASE / alpha-beta fold / CSGID / ATP-binding / Nucleotide-binding / Purine biosynthesis / Center for Structural Genomics of Infectious Diseases
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
ACETIC ACID / ADENOSINE MONOPHOSPHATE / FORMIC ACID / Phosphoribosylformylglycinamidine cyclo-ligase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.699 Å
AuthorsMaltseva, N. / Kim, Y. / Hasseman, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Phosphoribosylaminoimidazole Synthetase from Francisella tularensis
Authors: Maltseva, N. / Kim, Y. / Hasseman, J. / Anderson, W.F. / Joachimiak, A.
History
DepositionMar 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 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

Downloads & links

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Assembly

Deposited unit
A: Phosphoribosylformylglycinamidine cyclo-ligase
B: Phosphoribosylformylglycinamidine cyclo-ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,58423
Polymers77,4982
Non-polymers2,08621
Water14,700816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-208 kcal/mol
Surface area29270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.708, 90.560, 118.989
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Phosphoribosylformylglycinamidine cyclo-ligase / AIR synthetase (FGAM cyclase)


Mass: 38748.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: SCHU S4 / Gene: purM / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic / References: UniProt: Q5NGF2

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Non-polymers , 6 types, 837 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 816 / 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: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M Litium Sulfate; 0.1M Tris pH 7.0; 2M Ammonium Sulfate, 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: 0.97915 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 21, 2010 / Details: Mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.699→50 Å / Num. all: 72851 / Num. obs: 72851 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 17.14 Å2 / Rsym value: 0.076 / Net I/σ(I): 18.3
Reflection shellResolution: 1.699→1.73 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 2798 / Rsym value: 0.23 / % possible all: 75.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXmodel building
MLPHAREphasing
DMmodel building
SOLVEphasing
RESOLVEmodel building
PHENIX(phenix.refine: 1.6_289)refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.699→28.751 Å / SU ML: 0.16 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.183 3669 5.05 %random
Rwork0.154 ---
obs0.155 72676 96.45 %-
all-72676 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.568 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso mean: 23 Å2
Baniso -1Baniso -2Baniso -3
1-2.1124 Å2-0 Å2-0 Å2
2---1.5902 Å20 Å2
3----0.5222 Å2
Refinement stepCycle: LAST / Resolution: 1.699→28.751 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5324 0 119 816 6259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096071
X-RAY DIFFRACTIONf_angle_d1.2088276
X-RAY DIFFRACTIONf_dihedral_angle_d18.0042295
X-RAY DIFFRACTIONf_chiral_restr0.088903
X-RAY DIFFRACTIONf_plane_restr0.0051096
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.6987-1.75940.21463010.1725477577878
1.7594-1.82990.2123440.16356436678091
1.8299-1.91310.19643960.15687015741199
1.9131-2.0140.1893800.1570717451100
2.014-2.14010.18343770.146270767453100
2.1401-2.30530.18843380.145171277465100
2.3053-2.53710.18983840.155571167500100
2.5371-2.9040.19363960.163471207516100
2.904-3.65750.16923700.146872297599100
3.6575-28.75470.16263830.14697340772398
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.01530.001-0.08160.1807-0.00190.0640.0127-0.00680.00450.01710.0006-0.01060.011-0.0074-0.01020.03170.0007-0.00210.03140.00210.01547.24726.402824.087
20.2012-0.0768-0.09080.3770.05680.2454-0.0047-0.0110.0004-0.01080.00980.0171-0.026-0.0116-0.00340.03470.00750.00070.038-0.00130.025319.586149.51728.6192
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 347
2X-RAY DIFFRACTION2B-2 - 347

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