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- PDB-1vq3: Crystal structure of Phosphoribosylformylglycinamidine synthase, ... -

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Basic information

Entry
Database: PDB / ID: 1vq3
TitleCrystal structure of Phosphoribosylformylglycinamidine synthase, purS subunit (EC 6.3.5.3) (TM1244) from Thermotoga maritima at 1.90 A resolution
ComponentsPhosphoribosylformylglycinamidine synthase, purS subunit
KeywordsLIGASE / TM1244 / phosphoribosylformylglycinamidine synthase / purs subunit (EC 6.3.5.3) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
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 speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of phosphoribosylformyl-glycinamidine synthase II, PurS subunit (TM1244) from Thermotoga maritima at 1.90 A resolution.
Authors: Mathews, I.I. / Krishna, S.S. / Schwarzenbacher, R. / McMullan, D. / Jaroszewski, L. / Miller, M.D. / Abdubek, P. / Agarwalla, S. / Ambing, E. / Axelrod, H.L. / Canaves, J.M. / Carlton, D. / ...Authors: Mathews, I.I. / Krishna, S.S. / Schwarzenbacher, R. / McMullan, D. / Jaroszewski, L. / Miller, M.D. / Abdubek, P. / Agarwalla, S. / Ambing, E. / Axelrod, H.L. / Canaves, J.M. / Carlton, D. / Chiu, H.J. / Clayton, T. / DiDonato, M. / Duan, L. / Elsliger, M.A. / Grzechnik, S.K. / Hale, J. / Hampton, E. / Haugen, J. / Jin, K.K. / Klock, H.E. / Koesema, E. / Kovarik, J.S. / Kreusch, A. / Kuhn, P. / Levin, I. / Morse, A.T. / Nigoghossian, E. / Okach, L. / Oommachen, S. / Paulsen, J. / Quijano, K. / Reyes, R. / Rife, C.L. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / White, A. / Wolf, G. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionDec 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 999 SEQUENCE CLONING ARTIFACT: THIS GENE USES AN ALTERNATE INITIATION CODON THAT RESULTS IN A LEUCINE ... SEQUENCE CLONING ARTIFACT: THIS GENE USES AN ALTERNATE INITIATION CODON THAT RESULTS IN A LEUCINE AT POSITION 1 WHEN EXPRESSED AS A FUSION WITH THE PURIFICATION TAG

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoribosylformylglycinamidine synthase, purS subunit
B: Phosphoribosylformylglycinamidine synthase, purS subunit
C: Phosphoribosylformylglycinamidine synthase, purS subunit
D: Phosphoribosylformylglycinamidine synthase, purS subunit


Theoretical massNumber of molelcules
Total (without water)44,3994
Polymers44,3994
Non-polymers00
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: Phosphoribosylformylglycinamidine synthase, purS subunit
D: Phosphoribosylformylglycinamidine synthase, purS subunit


Theoretical massNumber of molelcules
Total (without water)22,2002
Polymers22,2002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-23 kcal/mol
Surface area10490 Å2
MethodPISA
3
A: Phosphoribosylformylglycinamidine synthase, purS subunit
B: Phosphoribosylformylglycinamidine synthase, purS subunit


Theoretical massNumber of molelcules
Total (without water)22,2002
Polymers22,2002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-18 kcal/mol
Surface area10390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.270, 73.433, 92.567
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 4 - 82 / Label seq-ID: 16 - 94

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Phosphoribosylformylglycinamidine synthase, purS subunit /


Mass: 11099.803 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM1244 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9X0X1, phosphoribosylformylglycinamidine synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.29 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 20.0% Glycerol, 24.0% PEG-1500,, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9865
DetectorType: ADSC / Detector: CCD / Date: Dec 13, 2003
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9865 Å / Relative weight: 1
ReflectionResolution: 1.9→49.31 Å / Num. obs: 29272 / % possible obs: 91.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 33.83 Å2 / Rsym value: 0.056 / Net I/σ(I): 16.3
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 1434 / Rsym value: 0.467 / % possible all: 62.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
REFMAC5.2.0001refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T4A

1t4a


Resolution: 1.9→49.31 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.272 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 957 3.3 %RANDOM
Rwork0.17783 ---
obs0.1799 28282 91.35 %-
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: 24.155 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å20 Å2
2--1.7 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 1.9→49.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2789 0 0 301 3090
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212837
X-RAY DIFFRACTIONr_bond_other_d0.0020.022696
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.9753822
X-RAY DIFFRACTIONr_angle_other_deg0.79636264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7395337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.18423.786140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9815550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1711526
X-RAY DIFFRACTIONr_chiral_restr0.0990.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023080
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02542
X-RAY DIFFRACTIONr_nbd_refined0.1970.2460
X-RAY DIFFRACTIONr_nbd_other0.1850.22622
X-RAY DIFFRACTIONr_nbtor_other0.0860.21820
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3070.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.212
X-RAY DIFFRACTIONr_mcbond_it2.76531846
X-RAY DIFFRACTIONr_mcbond_other1.0323686
X-RAY DIFFRACTIONr_mcangle_it3.17852777
X-RAY DIFFRACTIONr_scbond_it5.44681200
X-RAY DIFFRACTIONr_scangle_it7.142111045
Refine LS restraints NCS

Ens-ID: 1 / Number: 1222 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.70.5
2Bmedium positional0.670.5
3Cmedium positional0.60.5
4Dmedium positional0.630.5
1Amedium thermal1.522
2Bmedium thermal1.712
3Cmedium thermal1.552
4Dmedium thermal1.482
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 22 1.54 %
Rwork0.229 1406 -
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)
11.0209-0.0234-0.13860.0165-0.03290.5202-0.0262-0.01610.01480.00830.0081-0.0026-0.0149-0.01040.01820.0012-0.00070.0055-0.03910.0131-0.015441.89289.147218.8705
20.8055-0.10050.03930.05040.09480.55280.0240.016-0.040.0049-0.00330.01320.0604-0.0143-0.0208-0.0048-0.0054-0.0052-0.03390.0076-0.009128.4752-3.093-2.6562
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 1 - 82 / Label seq-ID: 13 - 94

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
21BB
32CC
42DD

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