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- PDB-1vk3: Crystal structure of Phosphoribosylformylglycinamidine synthase I... -

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Basic information

Entry
Database: PDB / ID: 1vk3
TitleCrystal structure of Phosphoribosylformylglycinamidine synthase II (TM1246) from Thermotoga maritima at 2.15 A resolution
ComponentsPhosphoribosylformylglycinamidine synthase II
KeywordsLIGASE / TM1246 / PHOSPHORIBOSYLFORMYLGLYCINAMIDINE SYNTHASE II / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


phosphoribosylformylglycinamidine synthase / phosphoribosylformylglycinamidine synthase activity / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Formylglycinamide ribonucleotide amidotransferase, C-terminal domain / Phosphoribosylformylglycinamidine subunit PurL, C-terminal / PurL, C-terminal domain superfamily / Phosphoribosylformylglycinamidine synthase II C-terminus / Phosphoribosylformylglycinamidine subunit PurL / Phosphoribosylformylglycinamidine synthase, linker domain / Formylglycinamide ribonucleotide amidotransferase linker domain / Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain ...Formylglycinamide ribonucleotide amidotransferase, C-terminal domain / Phosphoribosylformylglycinamidine subunit PurL, C-terminal / PurL, C-terminal domain superfamily / Phosphoribosylformylglycinamidine synthase II C-terminus / Phosphoribosylformylglycinamidine subunit PurL / Phosphoribosylformylglycinamidine synthase, linker domain / Formylglycinamide ribonucleotide amidotransferase linker domain / Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / 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 Plaits / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoribosylformylglycinamidine synthase subunit PurL
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 A resolution.
Authors: Mathews, I.I. / Krishna, S.S. / Schwarzenbacher, R. / McMullan, D. / Abdubek, P. / Ambing, E. / Canaves, J.M. / Chiu, H.J. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Godzik, A. / ...Authors: Mathews, I.I. / Krishna, S.S. / Schwarzenbacher, R. / McMullan, D. / Abdubek, P. / Ambing, E. / Canaves, J.M. / Chiu, H.J. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Hale, J. / Hampton, E. / Han, G.W. / Haugen, J. / Jaroszewski, L. / Klock, H.E. / Koesema, E. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / Levin, I. / Miller, M.D. / Moy, K. / Nigoghossian, E. / Paulsen, J. / Quijano, K. / Reyes, R. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / White, A. / Wolf, G. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Wilson, I.A.
History
DepositionApr 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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_ref_seq_dif.details
Remark 650HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoribosylformylglycinamidine synthase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3382
Polymers68,3021
Non-polymers351
Water3,981221
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.775, 72.689, 128.418
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 Phosphoribosylformylglycinamidine synthase II / FGAM synthase II


Mass: 68302.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: PURL, TM1246 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9X0X3, phosphoribosylformylglycinamidine synthase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.14 Å3/Da / Density % sol: 41.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 8
Details: 30.00% PEG 200, 0.10M Tris pH 8.0, 7% NP_PEG 4000 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0035, 0.9796
DetectorType: ADSC / Detector: CCD / Date: Dec 12, 2003
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.00351
20.97961
ReflectionResolution: 2.15→72.69 Å / Num. obs: 28272 / % possible obs: 90.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 38.5 Å2 / Rsym value: 0.089 / Net I/σ(I): 10.2
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.3 / Num. unique all: 1292 / Rsym value: 0.554 / % possible all: 56.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
SOLVEphasing
RESOLVEmodel building
REFMAC5.2.0001refinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.15→63.26 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.91 / SU B: 13.207 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.318 / ESU R Free: 0.239
RfactorNum. reflection% reflectionSelection details
Rfree0.25423 1368 4.8 %RANDOM
Rwork0.18645 ---
obs0.18974 26869 90.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.896 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---1.52 Å20 Å2
3---1.66 Å2
Refinement stepCycle: LAST / Resolution: 2.15→63.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4444 0 1 221 4666
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224535
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.9596164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0445584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56323.966179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.93415751
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3621527
X-RAY DIFFRACTIONr_chiral_restr0.0890.2712
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023402
X-RAY DIFFRACTIONr_nbd_refined0.2010.22070
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2263
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.210
X-RAY DIFFRACTIONr_mcbond_it1.75832988
X-RAY DIFFRACTIONr_mcangle_it2.59754700
X-RAY DIFFRACTIONr_scbond_it5.42381736
X-RAY DIFFRACTIONr_scangle_it7.269111464
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 62 4.82 %
Rwork0.253 1225 -
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)
11.0952-0.07161.02281.2122-0.05081.5736-0.0203-0.0192-0.0819-0.00510.036-0.02370.1253-0.0415-0.01570.0030.01380.0120.026-0.0156-0.034118.78942.21636.226
20.70480.0230.350.8631-0.12180.68760.0237-0.01330.02370.0082-0.03030.05650.0294-0.00440.00670.01130.00290.02640.0311-0.0236-0.015917.03264.67451.616
32.12020.083802.701-0.61452.9703-0.0633-0.17050.13420.0922-0.0477-0.0106-0.18110.05810.111-0.0558-0.0075-0.0145-0.0266-0.0651-0.03423.18783.04365.32
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
112 - 3414 - 46
21163 - 341175 - 353
3235 - 16247 - 174
42342 - 506354 - 518
53507 - 603519 - 615

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