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- PDB-1o1y: Crystal structure of a glutamine amidotransferase (tm1158) from t... -

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Basic information

Entry
Database: PDB / ID: 1o1y
TitleCrystal structure of a glutamine amidotransferase (tm1158) from thermotoga maritima at 1.70 A resolution
Componentsconserved hypothetical protein TM1158
KeywordsTRANSFERASE / Flavodoxin-like fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


glutamine metabolic process / cytosol / cytoplasm
Similarity search - Function
Glutamine amidotransferase class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutamine amidotransferase type-1 domain-containing protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: PROTEINS / Year: 2004
Title: Crystal structure of a putative glutamine amido transferase (TM1158) from Thermotoga maritima at 1.7 A resolution.
Authors: Schwarzenbacher, R. / Deacon, A.M. / Jaroszewski, L. / Brinen, L.S. / Canaves, J.M. / Dai, X. / Elsliger, M.A. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Klock, H.E. / ...Authors: Schwarzenbacher, R. / Deacon, A.M. / Jaroszewski, L. / Brinen, L.S. / Canaves, J.M. / Dai, X. / Elsliger, M.A. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Klock, H.E. / Koesema, E. / Kovarik, J.S. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / McMullan, D. / McPhillips, T.M. / Miller, M.D. / Morse, A. / Moy, K. / Nelson, M.S. / Ouyang, J. / Page, R. / Robb, A. / Quijano, K. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / Vincent, J. / von Delft, F. / Wang, X. / West, B. / Wolf, G. / Hodgson, K.O. / Wooley, J. / Wilson, I.A.
History
DepositionFeb 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: conserved hypothetical protein TM1158
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,61110
Polymers28,7461
Non-polymers8659
Water6,449358
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: conserved hypothetical protein TM1158
hetero molecules

A: conserved hypothetical protein TM1158
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,22120
Polymers57,4922
Non-polymers1,72918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-1/31
Buried area3910 Å2
ΔGint-201 kcal/mol
Surface area21480 Å2
MethodPISA
3
A: conserved hypothetical protein TM1158
hetero molecules

A: conserved hypothetical protein TM1158
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,22120
Polymers57,4922
Non-polymers1,72918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area4280 Å2
ΔGint-196 kcal/mol
Surface area21110 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.362, 92.362, 135.833
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-572-

HOH

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Components

#1: Protein conserved hypothetical protein TM1158


Mass: 28745.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1158 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0P2
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 358 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.5451.21
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, sitting drop, nanodrop92.4 M Ammonium Sulfate; 0.1 M Bicine pH 9.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
2932vapor diffusion, sitting drop, nanodrop52.4 M Ammonium Sulfate; 0.1 M Citric Acid pH 5.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal grow
*PLUS
pH: 7.9 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.4 Mammonium sulfate1reservoir
20.1 MBicine1reservoirpH9.0
320 mMTris1droppH7.9
4150 mM1dropNaCl
50.25 mMTCEP1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONSSRL BL11-110.97931
SYNCHROTRONAPS 19-BM20.979, 0.991
Detector
TypeIDDetectorDateDetails
APS-11CCDOct 26, 2002Flat mirror,single crystal Si(311) bent monochromator
ADSC QUANTUM 3152CCDNov 24, 2002
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979311
20.9791
30.9911
ReflectionResolution: 1.7→39.403 Å / Num. all: 36314 / Num. obs: 36314 / % possible obs: 94.9 % / Redundancy: 8.2 % / Rsym value: 0.086 / Net I/σ(I): 16
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 3969 / Rsym value: 0.643 / % possible all: 72.8
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 79.1 Å / Observed criterion σ(I): 0 / Num. measured all: 314408 / Rmerge(I) obs: 0.087
Reflection shell
*PLUS
% possible obs: 72.8 % / Rmerge(I) obs: 0.643

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
RESOLVEmodel building
SOLVEphasing
XFITdata reduction
REFMACrefinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→39.4 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.878 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The occupancies assigned here to the modelled sulfate groups are inaccurate, as indicated by persistent negative or positive difference density. Hydrogens have been added in the riding ...Details: The occupancies assigned here to the modelled sulfate groups are inaccurate, as indicated by persistent negative or positive difference density. Hydrogens have been added in the riding positions. XFIT/CCP4/TLS was also used in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.17242 1800 5 %RANDOM
Rwork0.14516 ---
obs0.14651 34513 94.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK / Bsol: 370.325 Å2 / ksol: 0.9 e/Å3
Displacement parametersBiso mean: 13.858 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å20.62 Å20 Å2
2--1.23 Å20 Å2
3----1.85 Å2
Refinement stepCycle: LAST / Resolution: 1.7→39.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1922 0 45 358 2325
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212029
X-RAY DIFFRACTIONr_bond_other_d0.0020.021826
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.9882734
X-RAY DIFFRACTIONr_angle_other_deg0.81234249
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8025229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0960.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022177
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02436
X-RAY DIFFRACTIONr_nbd_refined0.210.2368
X-RAY DIFFRACTIONr_nbd_other0.2520.22115
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0820.21191
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.2282
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3250.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2950.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.18721144
X-RAY DIFFRACTIONr_mcangle_it2.17631846
X-RAY DIFFRACTIONr_scbond_it5.0878885
X-RAY DIFFRACTIONr_scangle_it7.9111888
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 86 4.67 %
Rwork0.285 1755 -
Refinement TLS params.Origin x: 15.5977 Å / Origin y: 29.0841 Å / Origin z: -2.2404 Å
111213212223313233
T0.0373 Å2-0.0228 Å2-0.028 Å2-0.0229 Å2-0.004 Å2--0.0704 Å2
L1.0409 °2-0.3576 °20.1355 °2-1.0499 °2-0.0884 °2--1.8487 °2
S-0.0101 Å °-0.0568 Å °0.0549 Å °0.0217 Å °-0.048 Å °0.0032 Å °-0.1446 Å °-0.0302 Å °0.0581 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-2 - 22710 - 239
2X-RAY DIFFRACTION1AB - J401 - 4091
Software
*PLUS
Name: REFMAC / Version: 5.1.24 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 79.1 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor Rfree: 0.172 / Rfactor Rwork: 0.145
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.52
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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