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- PDB-5m7h: Crystal structure of Bacillus subtilis EngA in complex with phosp... -

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Basic information

Entry
Database: PDB / ID: 5m7h
TitleCrystal structure of Bacillus subtilis EngA in complex with phosphate ion and GMPPNP
ComponentsGTPase Der
KeywordsHYDROLASE / GTPase / EngA
Function / homology
Function and homology information


ribosome biogenesis / ribosome binding / GTP binding
Similarity search - Function
EngA-type guanine nucleotide-binding (G) domain / EngA-type guanine nucleotide-binding (G) domain profile. / GTP-binding protein EngA / GTPase Der, C-terminal KH-domain-like / KH-domain-like of EngA bacterial GTPase enzymes, C-terminal / K homology (KH) domain / 50S ribosome-binding GTPase / GTP binding domain / GMP Synthetase; Chain A, domain 3 / Small GTP-binding protein domain ...EngA-type guanine nucleotide-binding (G) domain / EngA-type guanine nucleotide-binding (G) domain profile. / GTP-binding protein EngA / GTPase Der, C-terminal KH-domain-like / KH-domain-like of EngA bacterial GTPase enzymes, C-terminal / K homology (KH) domain / 50S ribosome-binding GTPase / GTP binding domain / GMP Synthetase; Chain A, domain 3 / Small GTP-binding protein domain / K homology domain-like, alpha/beta / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / PHOSPHATE ION / GTPase Der
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
Authorsda Silveira Tome, C. / Foucher, A.E. / Jault, J.M. / Housset, D.
CitationJournal: To Be Published
Title: Crystal structure of Bacillus subtilis EngA in complex with phosphate ion and GMPPNP
Authors: da Silveira Tome, C. / Foucher, A.E. / Jault, J.M. / Housset, D.
History
DepositionOct 27, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTPase Der
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5805
Polymers48,8291
Non-polymers7514
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-13 kcal/mol
Surface area22050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.930, 63.880, 62.450
Angle α, β, γ (deg.)90.00, 97.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GTPase Der / GTP-binding protein EngA


Mass: 48828.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: der, engA, yphC, BSU22840 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P50743
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K

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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: 1.98 Å3/Da / Density % sol: 38.02 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M sodium/potassium phosphate 0.1 M Tris pH 6.5 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 3.15→61.94 Å / Num. obs: 6198 / % possible obs: 88.5 % / Redundancy: 2.6 % / Biso Wilson estimate: 66.38 Å2 / CC1/2: 0.987 / Rsym value: 0.114 / Net I/σ(I): 7
Reflection shellResolution: 3.15→3.23 Å / Redundancy: 2.69 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 2.25 / CC1/2: 0.815 / % possible all: 92.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DCU

4dcu


Resolution: 3.15→61.94 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.821 / Cross valid method: THROUGHOUT / ESU R Free: 0.854 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31821 283 4.9 %RANDOM
Rwork0.22121 ---
obs0.2258 5464 82.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.134 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20.02 Å2
2---0.08 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 3.15→61.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 43 0 3365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193423
X-RAY DIFFRACTIONr_bond_other_d00.023275
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.974635
X-RAY DIFFRACTIONr_angle_other_deg3.70237517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9935414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.4124.233163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.22715590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6241524
X-RAY DIFFRACTIONr_chiral_restr0.0620.2520
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213825
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02775
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1266.9051675
X-RAY DIFFRACTIONr_mcbond_other2.1276.9041674
X-RAY DIFFRACTIONr_mcangle_it3.77110.342084
X-RAY DIFFRACTIONr_mcangle_other3.7710.3412085
X-RAY DIFFRACTIONr_scbond_it1.6397.0791748
X-RAY DIFFRACTIONr_scbond_other1.6397.0691741
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.98310.5252543
X-RAY DIFFRACTIONr_long_range_B_refined6.54781.3493815
X-RAY DIFFRACTIONr_long_range_B_other6.5581.333812
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.15→3.232 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.438 18 -
Rwork0.315 373 -
obs--79.47 %

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