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- PDB-4j0q: Crystal structure of Pseudomonas putida elongation factor Tu (EF-Tu) -

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Basic information

Entry
Database: PDB / ID: 4j0q
TitleCrystal structure of Pseudomonas putida elongation factor Tu (EF-Tu)
ComponentsElongation factor Tu-A
KeywordsTRANSLATION / GDP / GTP / GTPase / elongation / pseudomonas
Function / homology
Function and homology information


guanosine tetraphosphate binding / translation elongation factor activity / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 ...Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / 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. / Elongation Factor Tu (Ef-tu); domain 3 / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Elongation factor Tu-A
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.294 Å
AuthorsScotti, J.S. / McDonough, M.A. / Schofield, C.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Human oxygen sensing may have origins in prokaryotic elongation factor Tu prolyl-hydroxylation
Authors: Scotti, J.S. / Leung, I.K.H. / Ge, W. / Bentley, M.A. / Paps, J. / Kramer, H.B. / Lee, J. / Aik, W. / Choi, H. / Paulsen, S.M. / Bowman, L.A.H. / Loik, N.D. / Horita, S. / Ho, C.H. / ...Authors: Scotti, J.S. / Leung, I.K.H. / Ge, W. / Bentley, M.A. / Paps, J. / Kramer, H.B. / Lee, J. / Aik, W. / Choi, H. / Paulsen, S.M. / Bowman, L.A.H. / Loik, N.D. / Horita, S. / Ho, C.H. / Kershaw, N.J. / Tang, C.M. / Claridge, T.D.W. / Preston, G.M. / McDonough, M.A. / Schofield, C.J.
History
DepositionJan 31, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.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.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 / _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: Elongation factor Tu-A
B: Elongation factor Tu-A
C: Elongation factor Tu-A
D: Elongation factor Tu-A
E: Elongation factor Tu-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,40923
Polymers236,8945
Non-polymers3,51418
Water5,693316
1
A: Elongation factor Tu-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2786
Polymers47,3791
Non-polymers8995
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Elongation factor Tu-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0424
Polymers47,3791
Non-polymers6633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Elongation factor Tu-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9654
Polymers47,3791
Non-polymers5863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Elongation factor Tu-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9654
Polymers47,3791
Non-polymers5863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Elongation factor Tu-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1605
Polymers47,3791
Non-polymers7814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)212.505, 155.624, 99.298
Angle α, β, γ (deg.)90.000, 114.760, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-403-

MES

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Elongation factor Tu-A / EF-Tu-A


Mass: 47378.891 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: KT2440 / Gene: PP_0440, tuf-1, tufA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q88QP8

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Non-polymers , 5 types, 334 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 3.15 Å3/Da / Density % sol: 60.91 % / Mosaicity: 0.49 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M MgOAc, 20% MPD, 0.05M MES pH 5.6, 10mM SrCl2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: Pilatus 6M-F / Detector: PIXEL / Date: Oct 23, 2012
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.294→50 Å / Num. all: 130376 / Num. obs: 129510 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 64.07 Å2 / Rmerge(I) obs: 0.056 / Χ2: 1.144 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.385.60.826122081.082193.9
2.38-2.486.50.698129891.089199.9
2.48-2.596.60.462129771.1191100
2.59-2.736.70.308129811.1681100
2.73-2.96.60.195130181.211100
2.9-3.126.90.118130471.2271100
3.12-3.446.70.076130141.1721100
3.44-3.936.80.057130341.182199.9
3.93-4.956.90.044130881.0661100
4.95-506.70.041131541.112199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.27 Å48.24 Å
Translation4.27 Å48.24 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.2phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
GDAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IW3

4iw3


Resolution: 2.294→48.242 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8132 / SU ML: 0.27 / σ(F): 1.34 / Phase error: 25.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2129 2006 1.55 %Random
Rwork0.1736 ---
obs0.1742 129450 99.95 %-
all-129510 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 184.07 Å2 / Biso mean: 67.1045 Å2 / Biso min: 18.67 Å2
Refinement stepCycle: LAST / Resolution: 2.294→48.242 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14005 0 221 316 14542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114538
X-RAY DIFFRACTIONf_angle_d1.25419836
X-RAY DIFFRACTIONf_chiral_restr0.0662333
X-RAY DIFFRACTIONf_plane_restr0.0052554
X-RAY DIFFRACTIONf_dihedral_angle_d16.3815325
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.2938-2.35110.34011310.292780238154815487
2.3511-2.41470.28531400.259590909230923099
2.4147-2.48580.28041460.2353914492909290100
2.4858-2.5660.26771420.2134917593179317100
2.566-2.65770.26591440.2066914592899289100
2.6577-2.76410.2731450.2054920793529352100
2.7641-2.88990.22761440.202914892929292100
2.8899-3.04220.24561470.1987917193189318100
3.0422-3.23280.26111450.1987921393589358100
3.2328-3.48230.27331390.203918893279327100
3.4823-3.83260.21891490.1893919193409340100
3.8326-4.38690.18381430.1521924193849384100
4.3869-5.52580.1521450.1374921193569356100
5.5258-48.25260.20751460.157792979443944399
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)
12.2213-0.3821-0.24112.4511-0.17081.1991-0.0727-0.394-0.32270.4940.09390.0513-0.04580.0734-0.05010.41930.19720.0030.4480.08120.4145183.2399-55.189729.3018
22.3551-0.1269-0.43561.4559-0.59211.8071-0.0677-0.0257-0.08970.17080.1101-0.0435-0.02760.0949-0.03860.36160.1220.00160.36080.01880.349185.7051-52.626820.0715
31.14550.03871.11630.83880.23061.94560.00110.1791-0.052-0.02940.0664-0.15040.1623-0.0279-0.07270.3201-0.02640.02630.3633-0.10240.3711223.2926-54.606735.1149
43.05810.43490.24482.0820.04582.30380.05880.38530.9049-0.18950.03850.1687-0.77660.1234-0.11120.6115-0.06530.04410.47290.13310.5883209.4757-36.144120.5034
51.6507-0.4548-0.29951.9391-0.06911.46310.1631-0.1656-0.26680.1453-0.31010.39520.2288-0.16620.09290.7043-0.01110.15330.3515-0.07990.521157.1046-5.89177.2835
61.94430.0856-0.32771.98310.30661.40460.22850.1564-0.0656-0.0936-0.2122-0.03950.20010.1801-0.0050.53070.0680.1120.342-0.05320.3844162.443-0.68620.7605
71.50310.77530.39162.2565-0.87382.6033-0.0829-0.1239-0.1781-0.17340.1179-0.27710.16660.1934-0.03430.28140.07090.0170.3814-0.03310.2977177.0042-38.3541-2.2962
81.6871-0.3876-0.25122.7833-0.03692.10120.122-0.51840.59240.213-0.0086-0.8465-0.31190.54-0.08880.3835-0.0708-0.01260.6329-0.14150.6788187.9296-14.42972.2494
92.1152-0.4498-0.09022.0150.45422.21360.13010.28440.0955-0.2706-0.2477-0.1036-0.28280.16370.09510.30790.01640.00610.31820.07670.3608154.1404-35.672624.4903
102.032-0.8107-0.04611.5617-0.3012.94920.11960.03050.10240.0666-0.14880.0893-0.22350.20650.02830.2676-0.0443-0.00150.21590.03930.291151.3373-39.063633.3825
110.98460.18750.62961.8857-0.57821.06080.2251-0.12260.270.35720.03720.7853-0.3653-0.3862-0.09140.8451-0.01450.40990.3449-0.05620.8747133.7901-2.642333.4592
121.61910.0127-0.42822.6391-0.42791.88650.1719-0.5150.2521.314-0.0287-0.0438-0.52590.37-0.07281.2366-0.25670.10360.537-0.12960.4449149.3191-15.943850.4882
132.5176-0.0207-1.2352.9064-0.16933.0747-0.37920.2301-0.3311-0.07330.05750.1450.2832-0.23760.27210.3537-0.07610.0650.2604-0.03780.3696169.4378-55.6258-29.0639
141.5116-0.13380.27640.7281-0.14791.18360.07970.62610.47640.1331-0.0721-0.1291-0.20090.19720.4450.6994-0.2475-0.45911.24760.35590.8477155.992-31.269-55.536
151.3303-1.1552-0.03891.1081-0.03791.5008-0.31780.93910.4761-0.3371-0.0919-0.0009-0.0163-0.27950.31040.7114-0.3168-0.32471.32260.21570.7627157.208-38.6016-57.935
161.1135-0.40250.08181.78150.01741.5874-0.12461.0246-0.3751-0.3198-0.17770.28440.4267-0.41530.27270.8692-0.3214-0.02451.3929-0.21970.6145160.8946-58.0177-58.3688
171.22510.493-0.40751.1284-0.18841.3127-0.57780.24930.28750.2333-0.1419-0.0631-0.1754-0.23080.030.63950.0654-0.62381.1983-0.35350.8556127.4364-31.9228-26.1869
182.49090.02860.15584.6794-0.46111.9682-0.239-0.03060.0312-0.0413-0.00220.1220.0878-0.21230.24910.5002-0.06910.10670.4972-0.14340.5639142.9595-52.82131.1821
191.7019-0.09860.29431.0266-0.6191.0563-0.2206-0.2242-0.3364-0.1572-0.06140.29450.3167-0.65860.26240.5395-0.16620.10740.7629-0.2740.7526130.8672-55.7599-3.3211
201.9630.15890.22621.0661-0.37263.1204-0.50640.0737-0.4503-0.1342-0.02020.13940.0816-0.49770.37280.4155-0.19350.02291.0354-0.34340.8566123.2375-55.0077-7.5348
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 9:43)A9 - 43
2X-RAY DIFFRACTION2(CHAIN A AND RESID 60:206)A60 - 206
3X-RAY DIFFRACTION3(CHAIN A AND RESID 207:300)A207 - 300
4X-RAY DIFFRACTION4(CHAIN A AND RESID 301:397)A301 - 397
5X-RAY DIFFRACTION5(CHAIN B AND RESID 9:60)B9 - 60
6X-RAY DIFFRACTION6(CHAIN B AND RESID 61:206)B61 - 206
7X-RAY DIFFRACTION7(CHAIN B AND RESID 207:297)B207 - 297
8X-RAY DIFFRACTION8(CHAIN B AND RESID 298:397)B298 - 397
9X-RAY DIFFRACTION9(CHAIN C AND RESID 9:60)C9 - 60
10X-RAY DIFFRACTION10(CHAIN C AND RESID 61:206)C61 - 206
11X-RAY DIFFRACTION11(CHAIN C AND RESID 207:296)C207 - 296
12X-RAY DIFFRACTION12(CHAIN C AND RESID 297:397)C297 - 397
13X-RAY DIFFRACTION13(CHAIN D AND RESID 9:206)D9 - 206
14X-RAY DIFFRACTION14(CHAIN D AND RESID 207:245)D207 - 245
15X-RAY DIFFRACTION15(CHAIN D AND RESID 246:322)D246 - 322
16X-RAY DIFFRACTION16(CHAIN D AND RESID 323:397)D323 - 397
17X-RAY DIFFRACTION17(CHAIN E AND RESID 9:206)E9 - 206
18X-RAY DIFFRACTION18(CHAIN E AND RESID 207:241)E207 - 241
19X-RAY DIFFRACTION19(CHAIN E AND RESID 242:362)E242 - 362
20X-RAY DIFFRACTION20(CHAIN E AND RESID 363:397)E363 - 397

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