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- PDB-3cb4: The Crystal Structure of LepA -

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Basic information

Entry
Database: PDB / ID: 3cb4
TitleThe Crystal Structure of LepA
ComponentsGTP-binding protein lepA
KeywordsTRANSLATION / GTPAse / OB-fold / GTP-binding / Membrane / Nucleotide-binding
Function / homology
Function and homology information


: / response to pH / guanosine tetraphosphate binding / ribosomal large subunit binding / ribosomal small subunit binding / translation elongation factor activity / response to salt stress / response to cold / positive regulation of translation / ribosome binding ...: / response to pH / guanosine tetraphosphate binding / ribosomal large subunit binding / ribosomal small subunit binding / translation elongation factor activity / response to salt stress / response to cold / positive regulation of translation / ribosome binding / ribosomal small subunit biogenesis / GTPase activity / GTP binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Elongation factor 4, C-terminal domain / Elongation factor 4 / GTP-binding protein LepA, C-terminal / Elongation factor 4, domain IV / LepA, C-terminal domain superfamily / GTP-binding protein LepA C-terminus / Elongation Factor G (Translational Gtpase), domain 3 / Alpha-Beta Plaits - #240 / Translation factors / Elongation factor EFG, domain V-like ...Elongation factor 4, C-terminal domain / Elongation factor 4 / GTP-binding protein LepA, C-terminal / Elongation factor 4, domain IV / LepA, C-terminal domain superfamily / GTP-binding protein LepA C-terminus / Elongation Factor G (Translational Gtpase), domain 3 / Alpha-Beta Plaits - #240 / Translation factors / 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 / Elongation Factor Tu (Ef-tu); domain 3 / 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 / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Plaits / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.8 Å
AuthorsEvans, R.N. / Blaha, G. / Bailey, S. / Steitz, T.A.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: The structure of LepA, the ribosomal back translocase.
Authors: Evans, R.N. / Blaha, G. / Bailey, S. / Steitz, T.A.
History
DepositionFeb 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: GTP-binding protein lepA
A: GTP-binding protein lepA
B: GTP-binding protein lepA
C: GTP-binding protein lepA
E: GTP-binding protein lepA
F: GTP-binding protein lepA


Theoretical massNumber of molelcules
Total (without water)399,9136
Polymers399,9136
Non-polymers00
Water543
1
A: GTP-binding protein lepA


Theoretical massNumber of molelcules
Total (without water)66,6521
Polymers66,6521
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTP-binding protein lepA


Theoretical massNumber of molelcules
Total (without water)66,6521
Polymers66,6521
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GTP-binding protein lepA


Theoretical massNumber of molelcules
Total (without water)66,6521
Polymers66,6521
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: GTP-binding protein lepA


Theoretical massNumber of molelcules
Total (without water)66,6521
Polymers66,6521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: GTP-binding protein lepA


Theoretical massNumber of molelcules
Total (without water)66,6521
Polymers66,6521
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: GTP-binding protein lepA


Theoretical massNumber of molelcules
Total (without water)66,6521
Polymers66,6521
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.960, 146.243, 139.317
Angle α, β, γ (deg.)90.00, 100.60, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a monomer. There are 6 biological units in the asymmetric unit (chains A, B, C, D, E, and F). The 6 biological units are arranged as a trimer of dimers.

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Components

#1: Protein
GTP-binding protein lepA


Mass: 66652.094 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: lepA / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P60785
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM Tris-HCl pH 8.0 10% Peg 2000MME, 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2510.979
SYNCHROTRONALS 8.2.220.979
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDSep 28, 2007
ADSC QUANTUM 3152CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 92895 / Num. obs: 88629 / % possible obs: 94.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rmerge(I) obs: 0.117 / Rsym value: 0.088 / Net I/σ(I): 9.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 1.4 / Num. unique all: 6070 / Rsym value: 0.494 / % possible all: 64.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CBASSdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.855 / SU B: 46.615 / SU ML: 0.396 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.46 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29455 4590 5.2 %RANDOM
Rwork0.24644 ---
obs0.24896 84039 95.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.18 Å2
Baniso -1Baniso -2Baniso -3
1-1.53 Å20 Å20.42 Å2
2--1.64 Å20 Å2
3----3.02 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24492 0 0 3 24495
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02224909
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0881.97533762
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.56753132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68124.3921134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.304154344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.50415180
X-RAY DIFFRACTIONr_chiral_restr0.0730.23900
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0218726
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.210787
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.216785
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2678
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.282
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2390.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2061.516049
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.371225320
X-RAY DIFFRACTIONr_scbond_it0.46639790
X-RAY DIFFRACTIONr_scangle_it0.8124.58442
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 163 -
Rwork0.401 3062 -
obs--64.46 %
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)
14.61130.70410.25712.16420.38793.117-0.07140.1603-0.0429-0.34320.2163-0.34240.13290.4409-0.1449-0.1413-0.043-0.0037-0.13470.0547-0.232430.9432110.7694146.8033
23.1426-1.1721-0.07114.6356-0.47623.3763-0.04550.03420.07310.4412-0.08830.4243-0.2745-0.34110.1338-0.0987-0.1322-0.1259-0.0322-0.0285-0.239979.272392.2992139.7363
35.4656-0.68741.18291.4714-0.59494.7835-0.08370.64890.9801-0.17250.07030.5348-0.7853-0.33210.01340.018-0.0695-0.062-0.01320.02340.142145.694859.0578101.229
44.3446-0.25471.02831.97990.4073.1762-0.2213-0.36810.13570.36120.1385-0.0681-0.08730.24320.08280.02860.00870.1033-0.09680.1535-0.143658.266758.672140.8229
52.0164-0.2639-0.27124.44820.72983.2075-0.01810.3155-0.4878-0.33870.05460.1480.7179-0.1688-0.03650.12660.0090.09610.054-0.01270.060395.022489.961864.3688
63.32441.1028-0.58452.73820.162.53850.0794-0.41-0.43720.085-0.1017-0.01450.4266-0.3070.0223-0.05170.00880.05310.1776-0.0262-0.13640.379108.999284.8798
70.4344-0.7454-0.7724.1571-0.97374.4062-0.00670.20220.20270.25660.0116-0.0206-0.13370.2208-0.0049-0.33480.01060.0164-0.1497-0.0114-0.085424.286976.4601139.7182
83.34021.49790.21260.7370.42754.7637-0.14770.15340.0367-0.00570.0504-0.1306-0.38580.25840.0973-0.1518-0.00910.0304-0.1939-0.0047-0.155761.639561.9864142.1917
92.04021.8435-1.07452.77771.06454.29210.1027-0.14220.20120.162-0.2020.2236-0.1684-0.20490.0992-0.2470.05680.0025-0.17570.006-0.205279.593569.4796103.1206
101.75031.081-0.6923.7911-0.6632.5807-0.008-0.0996-0.17790.0901-0.0586-0.09310.20920.25110.0667-0.1930.0425-0.0433-0.07610.0101-0.223139.875989.004943.3086
114.3764-0.068-1.07170.0886-0.39665.0332-0.1703-0.2972-0.45090.07570.0530.01760.2907-0.05760.1173-0.1521-0.03850.0038-0.2765-0.0346-0.174569.8235113.865153.8436
123.0148-1.467-0.45941.206-0.18663.4539-0.00890.2664-0.0172-0.1373-0.02060.01630.0727-0.21020.0295-0.1103-0.0821-0.0069-0.1908-0.0228-0.169573.9336109.054197.2294
130.0111-0.1072-0.0143.682-0.98610.49230.15960.24550.0639-0.2855-0.1564-0.2942-0.0780.1069-0.0032-0.01740.01960.07450.12710.0248-0.074533.942878.8115124.015
142.5221.97170.92941.67031.02621.0393-0.0611-0.31720.31390.01540.00380.3684-0.292-0.06290.0574-0.03280.06710.0695-0.0114-0.0238-0.108554.74868.3139158.1526
151.26421.72510.59372.49740.35231.7407-0.120.11330.4489-0.22980.16050.2654-0.0252-0.3806-0.04060.0490.01260.0595-0.09750.038-0.103278.072173.671285.0655
160.0307-0.26210.1383.6304-0.79540.7261-0.0248-0.20590.0580.22060.0117-0.26280.14270.14920.01310.009-0.06370.00090.20160.0229-0.123343.661588.802361.3062
173.6999-0.5874-0.38190.09320.06161.1166-0.07920.16-0.47250.06210.06110.19320.35090.05940.01810.0061-0.04640.0407-0.0538-0.0796-0.146471.6691107.26936.8421
184.6705-1.7081-0.28360.7234-0.15630.7020.0027-0.1555-0.42590.15270.06490.08840.1279-0.2167-0.06760.0347-0.05280.0348-0.07560.0124-0.175366.9436102.9943113.2461
193.23530.45950.62025.1698-0.39585.1086-0.0281-0.14430.0758-0.04380.03410.47260.0898-0.2053-0.006-0.4537-0.0144-0.0679-0.3257-0.0061-0.25848.034699.8679150.6475
204.70780.20511.60983.20310.65385.1298-0.09110.1089-0.31180.0911-0.0374-0.59980.48820.37240.1286-0.2108-0.0896-0.0426-0.16630.0757-0.164890.062169.8009133.7751
213.8150.9735-0.10314.5980.53054.1139-0.0332-0.2351-0.55940.07950.0459-0.04870.50040.2807-0.0127-0.23180.01860.0424-0.2003-0.0131-0.236663.465845.9242114.2713
224.14370.4183-1.26014.5515-1.84273.71190.07050.0628-0.2777-0.2819-0.06130.20870.1543-0.5282-0.0092-0.2478-0.10090.0326-0.16910.0171-0.163936.240262.315328.3368
234.9493-0.0361-0.28852.23170.01123.79890.0871-0.17870.60890.16620.1019-0.458-0.47170.1561-0.189-0.1221-0.01810.0292-0.22130.0082-0.095394.2005114.248472.398
245.2113-0.1236-1.31543.8421.68084.49390.11790.20440.6194-0.0871-0.1057-0.0101-0.53970.0652-0.0123-0.11670.04010.0241-0.1670.0129-0.194557.0704127.824279.8477
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AB1 - 1851 - 185
2X-RAY DIFFRACTION2BC1 - 1851 - 185
3X-RAY DIFFRACTION3CD1 - 1851 - 185
4X-RAY DIFFRACTION4DA1 - 1851 - 185
5X-RAY DIFFRACTION5EE1 - 1851 - 185
6X-RAY DIFFRACTION6FF1 - 1851 - 185
7X-RAY DIFFRACTION7AB290 - 375290 - 375
8X-RAY DIFFRACTION8BC290 - 375290 - 375
9X-RAY DIFFRACTION9CD290 - 375290 - 375
10X-RAY DIFFRACTION10DA290 - 375290 - 375
11X-RAY DIFFRACTION11EE290 - 375290 - 375
12X-RAY DIFFRACTION12FF290 - 375290 - 375
13X-RAY DIFFRACTION13AB376 - 555376 - 555
14X-RAY DIFFRACTION14BC376 - 555376 - 555
15X-RAY DIFFRACTION15CD376 - 555376 - 555
16X-RAY DIFFRACTION16DA376 - 555376 - 555
17X-RAY DIFFRACTION17EE376 - 555376 - 555
18X-RAY DIFFRACTION18FF376 - 555376 - 555
19X-RAY DIFFRACTION19AB186 - 289186 - 289
20X-RAY DIFFRACTION20BC186 - 289186 - 289
21X-RAY DIFFRACTION21CD186 - 289186 - 289
22X-RAY DIFFRACTION22DA186 - 289186 - 289
23X-RAY DIFFRACTION23EE186 - 289186 - 289
24X-RAY DIFFRACTION24FF186 - 289186 - 289

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