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- PDB-8ewh: Salmonella typhimurium GTPase BIPA -

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Basic information

Entry
Database: PDB / ID: 8ewh
TitleSalmonella typhimurium GTPase BIPA
Components50S ribosomal subunit assembly factor BipA
KeywordsTRANSLATION / virulence factor / 50S ribosome subunit / stress response / GTPase
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / ribosome binding / ribosomal large subunit assembly / tRNA binding / rRNA binding / ribonucleoprotein complex / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
GTP-binding protein TypA / BipA, domain V / GTP-binding protein TypA/BipA, C-terminal / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 ...GTP-binding protein TypA / BipA, domain V / GTP-binding protein TypA/BipA, C-terminal / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
50S ribosomal subunit assembly factor BipA
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.33 Å
AuthorsBrown, R.S. / deLivron, M.A. / Robinson, V.L.
Funding support United States, 1items
OrganizationGrant numberCountry
American Heart Association0635519T United States
CitationJournal: J Biomol Struct Dyn. / Year: 2007
Title: Crystallographic and Biochemical Characterization of the GTPase and Ribosome Binding Properties of Salmonella typhimuirum BipA
Authors: Brown, R.S. / deLivron, M.A. / Robinson, V.L.
History
DepositionOct 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 50S ribosomal subunit assembly factor BipA
B: 50S ribosomal subunit assembly factor BipA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,0136
Polymers134,9212
Non-polymers924
Water1,982110
1
A: 50S ribosomal subunit assembly factor BipA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5063
Polymers67,4601
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 50S ribosomal subunit assembly factor BipA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5063
Polymers67,4601
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.414, 83.702, 95.408
Angle α, β, γ (deg.)90.000, 105.770, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 2 - 601 / Label seq-ID: 2 - 601

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein 50S ribosomal subunit assembly factor BipA / GTP-BINDING PROTEIN / RIBOSOME-DEPENDENT GTPASE


Mass: 67460.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: bipA, STM4009 / Plasmid: PET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: H9L427, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 16-18% PEG 3350, 100 MM NA/K TARTRATE, 20 MM TRIS, PH 7.5. CRYO SOLVENT 20% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2007
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.33→29.8 Å / Num. obs: 52682 / % possible obs: 90.8 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 35.1 Å2 / CC1/2: 0.983 / R split: 0.093 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.059 / Rrim(I) all: 0.112 / Rsym value: 0.087 / Χ2: 1 / Net I/av σ(I): 15.9 / Net I/σ(I): 10.29
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 3.35 / Num. unique obs: 2609 / CC1/2: 0.868 / R split: 0.24 / Rpim(I) all: 0.167 / Rrim(I) all: 0.264 / Rsym value: 0.195 / Χ2: 1 / % possible all: 54.1

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Processing

Software
NameVersionClassification
REFMACv5.8.0267refinement
DENZOdata reduction
SCALEPACKv1.97.2data scaling
SOLVEphasing
RESOLVEmodel building
Cootv0.8.9.2model building
RefinementMethod to determine structure: SAD / Resolution: 2.33→29.78 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.855 / SU B: 15.963 / SU ML: 0.194 / SU R Cruickshank DPI: 0.2837 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2551 4.8 %RANDOM
Rwork0.2312 ---
obs0.2337 50131 90.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK / Bsol: 70 Å2 / ksol: 0.864 e/Å3
Displacement parametersBiso max: 110.71 Å2 / Biso mean: 34.062 Å2 / Biso min: 8.81 Å2
Baniso -1Baniso -2Baniso -3
1--4.76 Å2-0 Å2-0.11 Å2
2---0.13 Å20 Å2
3---4.89 Å2
Refine analyzeLuzzati coordinate error obs: 0.3546 Å / Luzzati d res low obs: 29.8 Å
Refinement stepCycle: final / Resolution: 2.33→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9044 0 4 110 9158
Biso mean--31.99 23.3 -
Num. residues----1162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0139186
X-RAY DIFFRACTIONr_bond_other_d0.0040.0158874
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.63912426
X-RAY DIFFRACTIONr_angle_other_deg0.4531.58420398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.24951156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.47322.462520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.717151622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3071574
X-RAY DIFFRACTIONr_chiral_restr0.0660.21214
X-RAY DIFFRACTIONr_gen_planes_refined0.0530.0210498
X-RAY DIFFRACTIONr_gen_planes_other0.0460.022066
Refine LS restraints NCS

Ens-ID: 1 / Number: 17177 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.33→2.39 Å
RfactorNum. reflection% reflection
Rfree0.266 108 -
Rwork0.233 2236 -
obs--54.69 %
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)
13.71771.3432-0.90853.09710.38442.0448-0.0241-0.0528-0.03930.25760.00090.54490.0025-0.48980.02320.09070.0190.03880.18430.0220.177618.815847.507866.7483
20.4305-0.42620.03690.49630.0150.03950.0146-0.1224-0.20670.23550.0990.05680.1882-0.0364-0.11361.19840.0104-0.10040.92780.14920.94798.716355.319561.3522
31.91920.4583-0.47512.31230.41191.8555-0.0531-0.0499-0.20620.0799-0.01690.10920.2097-0.0750.070.08530.01790.04360.03670.0160.052828.298746.341562.2517
42.92730.1558-0.56833.3013-0.26452.1021-0.0476-0.3981-0.22120.31870.0240.08520.1980.03010.02360.18420.00230.05510.20340.02110.034824.400156.23188.0705
52.4274-0.8568-0.21244.1498-0.11831.8848-0.0549-0.2818-0.14960.36020.05670.01270.1944-0.0977-0.00180.1556-0.01420.06050.15960.00240.053424.541585.120374.7707
61.60660.08960.22693.3180.43642.9089-0.0727-0.2240.22270.20530.0816-0.4119-0.22730.2977-0.00890.07020.01750.0060.1097-0.00060.145245.217270.668165.3887
72.3119-0.2049-0.01223.5055-0.9383.53-0.0611-0.01570.20360.0524-0.0323-0.254-0.22030.37380.09340.0718-0.02030.01530.0771-0.01130.054134.8089100.870459.6288
84.34841.10770.90013.13180.61862.2053-0.0608-0.06630.07520.20260.0704-0.37550.00540.3655-0.00960.076-0.0047-0.03650.11010.03160.098288.795378.045166.5758
90.1274-0.5160.54264.3456-5.52847.24190.2219-0.01670.15490.281-0.389-0.21-0.75370.71270.16710.9246-0.08120.04180.8012-0.13840.841299.453470.541162.2213
101.95530.64390.57992.3456-0.01412.1344-0.0637-0.02690.0670.0203-0.00330.041-0.19820.06110.0670.06230.0169-0.05020.0297-0.00890.05879.746779.065162.2207
113.48060.0356-0.52342.9711-0.0713.2498-0.035-0.2760.09450.18650.01880.1791-0.1331-0.03960.01620.13660.0076-0.00240.1425-0.00520.015183.815769.87588.5406
122.3431-0.98540.45193.6514-0.18391.8574-0.0432-0.31640.09850.67740.1122-0.3545-0.04640.1307-0.06890.27990.0184-0.09850.2387-0.02140.318682.783840.62875.2394
132.0696-0.1288-0.35032.9707-0.2193.5193-0.0485-0.2479-0.20720.14210.03770.27540.2817-0.19540.01090.04380.0016-0.02620.0875-0.00970.197962.895155.20765.2583
142.367-0.3633-0.41834.37230.9993.2017-0.0638-0.0266-0.06920.1994-0.01850.30390.1727-0.37920.08230.0834-0.0163-0.03090.09570.02710.125572.841924.962259.9403
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 33
2X-RAY DIFFRACTION2A34 - 56
3X-RAY DIFFRACTION3A57 - 197
4X-RAY DIFFRACTION4A198 - 306
5X-RAY DIFFRACTION5A307 - 385
6X-RAY DIFFRACTION6A386 - 481
7X-RAY DIFFRACTION7A482 - 601
8X-RAY DIFFRACTION8B2 - 32
9X-RAY DIFFRACTION9B33 - 56
10X-RAY DIFFRACTION10B57 - 197
11X-RAY DIFFRACTION11B198 - 303
12X-RAY DIFFRACTION12B304 - 386
13X-RAY DIFFRACTION13B387 - 477
14X-RAY DIFFRACTION14B478 - 601

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