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- PDB-1t9h: The crystal structure of YloQ, a circularly permuted GTPase. -

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Basic information

Entry
Database: PDB / ID: 1t9h
TitleThe crystal structure of YloQ, a circularly permuted GTPase.
ComponentsProbable GTPase engC
KeywordsHYDROLASE / N-terminal beta-barrel domain with Oligonucleotide Binding fold / central GTP binding domain / C-terminal zinc-binding domain
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / ribosomal small subunit biogenesis / rRNA binding / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
Ribosome biogenesis GTPase RsgA, N-terminal / RsgA N-terminal domain / Probable gtpase engc; domain 3 / Ribosome biogenesis GTPase RsgA / RsgA GTPase domain / RsgA GTPase / EngC GTPase domain profile. / Ribonucleotide Reductase Protein R1; domain 1 / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. ...Ribosome biogenesis GTPase RsgA, N-terminal / RsgA N-terminal domain / Probable gtpase engc; domain 3 / Ribosome biogenesis GTPase RsgA / RsgA GTPase domain / RsgA GTPase / EngC GTPase domain profile. / Ribonucleotide Reductase Protein R1; domain 1 / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / P-loop containing nucleotide triphosphate hydrolases / Nucleic acid-binding, OB-fold / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / URANYL (VI) ION / Small ribosomal subunit biogenesis GTPase RsgA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.6 Å
AuthorsLevdikov, V.M. / Blagova, E.V. / Brannigan, J.A. / Cladiere, L. / Antson, A.A. / Isupov, M.N. / Seror, S.J. / Wilkinson, A.J.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: The Crystal Structure of YloQ, a Circularly Permuted GTPase Essential for Bacillus Subtilis Viability.
Authors: Levdikov, V.M. / Blagova, E.V. / Brannigan, J.A. / Cladiere, L. / Antson, A.A. / Isupov, M.N. / Seror, S.J. / Wilkinson, A.J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization of YloQ, a GTPase of unknown function essential for Bacillus subtilis viability.
Authors: Cladiere, L. / Blagova, E.V. / Levdikov, V.M. / Brannigan, J.A. / Seror, S.J. / Wilkinson, A.J.
History
DepositionMay 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: Probable GTPase engC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,59117
Polymers35,0271
Non-polymers2,56316
Water5,459303
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.970, 47.970, 279.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Probable GTPase engC / YloQ


Mass: 35027.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ENGC, BSU15780 / Plasmid: pOMG201 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a
References: UniProt: O34530, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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Non-polymers , 5 types, 319 molecules

#2: Chemical
ChemComp-IUM / URANYL (VI) ION


Mass: 270.028 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: O2U
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.3 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 5000, calcium acetate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 11, 2003 / Details: Si mirror
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.6→22 Å / Num. all: 44626 / Num. obs: 44626 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 6.3
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.7 / Num. unique all: 4339 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: MIR / Resolution: 1.6→20.5 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.904 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17801 2243 5 %RANDOM
Rwork0.14396 ---
all0.14565 42211 --
obs0.14565 42211 100 %-
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: 22.801 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2322 0 41 303 2666
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222394
X-RAY DIFFRACTIONr_bond_other_d0.0020.022128
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.9553213
X-RAY DIFFRACTIONr_angle_other_deg0.96734975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1115283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.76224.25120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6415429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3641516
X-RAY DIFFRACTIONr_chiral_restr0.0740.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022625
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02475
X-RAY DIFFRACTIONr_nbd_refined0.2240.2525
X-RAY DIFFRACTIONr_nbd_other0.1870.22219
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0810.21378
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2230.2226
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.3380.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.241
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.2120
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2680.242
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.34541496
X-RAY DIFFRACTIONr_mcbond_other0.9664580
X-RAY DIFFRACTIONr_mcangle_it3.1862331
X-RAY DIFFRACTIONr_scbond_it3.39881015
X-RAY DIFFRACTIONr_scangle_it4.56810882
X-RAY DIFFRACTIONr_rigid_bond_restr2.06334912
X-RAY DIFFRACTIONr_sphericity_free4.3473308
X-RAY DIFFRACTIONr_sphericity_bonded1.95234486
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.239 152
Rwork0.162 2983
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)
11.26530.1162-0.24071.37652.11373.3855-0.0240.1386-0.0159-0.15620.0534-0.0206-0.20460.1288-0.02940.1090.0001-0.0185-0.05160.0136-0.013920.524-12.4213.283
21.0137-0.4205-0.58272.68320.52031.71890.0050.0147-0.0659-0.06230.02220.30710.0861-0.3032-0.0272-0.0129-0.0067-0.0103-0.03290.0307-0.032610.3312.64121.064
32.972.63721.11263.79932.06872.33130.1446-0.1591-0.22740.2171-0.1535-0.0440.2634-0.170.00880.04910.027-0.0076-0.09860.014-0.027616.8740.83419.478
42.5152-0.91750.88621.7636-0.93192.1745-0.0584-0.02990.18390.0768-0.0633-0.246-0.15320.25980.12170.0033-0.0293-0.0167-0.05790.0149-0.021630.0225.26624.888
50.14060.5036-0.05292.34220.84482.00430.04240.01440.0836-0.43160.0465-0.1338-0.08510.0308-0.08890.01780.03410.032-0.11540.0252-0.119323.33618.0749.125
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-7 - 672 - 76
2X-RAY DIFFRACTION2AA68 - 18677 - 195
3X-RAY DIFFRACTION3AA206 - 233215 - 242
4X-RAY DIFFRACTION4AA234 - 298243 - 307
5X-RAY DIFFRACTION5AB - I401 - 4081

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