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- PDB-5x4b: Crystal Structure of N-terminal G-domain of EngA from Bacillus su... -

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Basic information

Entry
Database: PDB / ID: 5x4b
TitleCrystal Structure of N-terminal G-domain of EngA from Bacillus subtilis
ComponentsGTPase Der
KeywordsHYDROLASE / Ribosome biogenesis / Rossmann fold / GTPase / GDP
Function / homology
Function and homology information


ribosome biogenesis / ribosome binding / GTP binding
Similarity search - Function
GTP-binding protein EngA / EngA-type guanine nucleotide-binding (G) domain / EngA-type guanine nucleotide-binding (G) domain profile. / GTPase Der, C-terminal KH-domain-like / KH-domain-like of EngA bacterial GTPase enzymes, C-terminal / 50S ribosome-binding GTPase / GTP binding domain / K homology domain-like, alpha/beta / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases ...GTP-binding protein EngA / EngA-type guanine nucleotide-binding (G) domain / EngA-type guanine nucleotide-binding (G) domain profile. / GTPase Der, C-terminal KH-domain-like / KH-domain-like of EngA bacterial GTPase enzymes, C-terminal / 50S ribosome-binding GTPase / GTP binding domain / K homology domain-like, alpha/beta / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / : / GTPase Der
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSingh, V. / Prakash, B.
CitationJournal: To Be Published
Title: Crystal Structure of N-terminal G-domain of EngA from Bacillus subtilis
Authors: Singh, V. / Prakash, B.
History
DepositionFeb 11, 2017Deposition site: PDBJ / Processing site: PDBJ
SupersessionMay 31, 2017ID: 4KYU
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rrim_I_all
Revision 1.2Apr 27, 2022Group: Database references / Derived calculations / Category: database_2 / pdbx_struct_conn_angle / struct_conn
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_asym_id / _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_asym_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTPase Der
B: GTPase Der
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,63110
Polymers35,5562
Non-polymers1,0758
Water4,612256
1
A: GTPase Der
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3636
Polymers17,7781
Non-polymers5855
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-6 kcal/mol
Surface area7030 Å2
MethodPISA
2
B: GTPase Der
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2694
Polymers17,7781
Non-polymers4903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-6 kcal/mol
Surface area6970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.260, 43.750, 50.710
Angle α, β, γ (deg.)66.880, 79.880, 70.820
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 17778.025 Da / Num. of mol.: 2 / Fragment: UNP residues 2-163
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: der, engA, yphC, BSU22840 / Plasmid: PQE2 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: P50743

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Non-polymers , 5 types, 264 molecules

#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.49 Å3/Da / Density % sol: 50.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG3350, NH4Cl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→19.65 Å / Num. obs: 46098 / % possible obs: 91.2 % / Observed criterion σ(I): -3 / Redundancy: 4.649 % / Biso Wilson estimate: 20.947 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.02 / Rrim(I) all: 0.025 / Χ2: 0.995 / Net I/σ(I): 45.45 / Num. measured all: 214315 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.84.7150.06224.218784621290186300.9970.06987.5
1.8-24.6870.03142.4733917796172360.9990.03490.9
2-2.24.6570.02353.8722805528348970.9990.02692.7
2.2-2.64.5880.0261.5227298631759500.9990.02294.2
2.6-2.84.5570.01867.1384081939184510.0295.2
2.8-34.5440.01768.816321145013910.9990.0295.9
3-3.74.5160.01674.24128992949285610.01896.8
3.7-3.84.5320.01580.49112424924810.01799.6
3.8-3.94.5510.01485.25110625524310.01695.3
3.9-44.4980.01483.7691320820310.01697.6
4-4.54.5280.01486.56349678277210.01698.7
4.5-64.4910.01483.8448141092107210.01698.2
6-84.4340.01681.28197345344510.01898.2
8-104.5470.01380.2277317417010.01597.7
10-124.5520.01183.92305696710.01397.1
12-154.370.01777.15201474610.01997.9
15-204.2960.01477.1116282710.01696.4
19.65-2023

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→19.65 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.951 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1809 2305 5 %RANDOM
Rwork0.1528 ---
obs0.1542 43793 91.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.09 Å2 / Biso mean: 15.674 Å2 / Biso min: 1.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å2-0.17 Å2-0.32 Å2
2---0.42 Å20.25 Å2
3---0.13 Å2
Refinement stepCycle: final / Resolution: 1.5→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2224 0 62 256 2542
Biso mean--11.91 27.38 -
Num. residues----296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0192339
X-RAY DIFFRACTIONr_bond_other_d0.0020.022112
X-RAY DIFFRACTIONr_angle_refined_deg2.4421.9883195
X-RAY DIFFRACTIONr_angle_other_deg1.16434869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.615298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8924.554101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.28915348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1131512
X-RAY DIFFRACTIONr_chiral_restr0.1480.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212627
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02477
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.197 157 -
Rwork0.156 2991 -
all-3148 -
obs--85.17 %

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