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- PDB-5uai: Crystal structure of Methionyl-tRNA formyltransferase from Pseudo... -

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Basic information

Entry
Database: PDB / ID: 5uai
TitleCrystal structure of Methionyl-tRNA formyltransferase from Pseudomonas aeruginosa
ComponentsMethionyl-tRNA formyltransferase
KeywordsTRANSFERASE / SSGCID / fmt / Methionyl-tRNA formyltransferase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


methionyl-tRNA formyltransferase / conversion of methionyl-tRNA to N-formyl-methionyl-tRNA / methionyl-tRNA formyltransferase activity / cytosol
Similarity search - Function
Methionyl-tRNA formyltransferase / Methionyl-tRNA formyltransferase, N-terminal domain / Methionyl-tRNA formyltransferase, C-terminal domain / Formyl transferase, C-terminal domain / Methionyl-tRNA Fmet Formyltransferase; Chain A, domain 2 / Formyl transferase, C-terminal domain superfamily / Formyl transferase, C-terminal / Formyl transferase, C-terminal domain / Formyl transferase-like, C-terminal domain superfamily / Formyl transferase, N-terminal domain ...Methionyl-tRNA formyltransferase / Methionyl-tRNA formyltransferase, N-terminal domain / Methionyl-tRNA formyltransferase, C-terminal domain / Formyl transferase, C-terminal domain / Methionyl-tRNA Fmet Formyltransferase; Chain A, domain 2 / Formyl transferase, C-terminal domain superfamily / Formyl transferase, C-terminal / Formyl transferase, C-terminal domain / Formyl transferase-like, C-terminal domain superfamily / Formyl transferase, N-terminal domain / Phosphoribosylglycinamide formyltransferase, active site / Phosphoribosylglycinamide formyltransferase active site. / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Methionyl-tRNA formyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of Methionyl-tRNA formyltransferase from Pseudomonas aeruginosa
Authors: Conrady, D.G. / Lorimer, D.D. / Edwards, T.E.
History
DepositionDec 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Methionyl-tRNA formyltransferase
B: Methionyl-tRNA formyltransferase
C: Methionyl-tRNA formyltransferase
D: Methionyl-tRNA formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,4475
Polymers136,3854
Non-polymers621
Water3,873215
1
A: Methionyl-tRNA formyltransferase


Theoretical massNumber of molelcules
Total (without water)34,0961
Polymers34,0961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methionyl-tRNA formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1582
Polymers34,0961
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Methionyl-tRNA formyltransferase


Theoretical massNumber of molelcules
Total (without water)34,0961
Polymers34,0961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Methionyl-tRNA formyltransferase


Theoretical massNumber of molelcules
Total (without water)34,0961
Polymers34,0961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.920, 109.060, 109.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 28 or (resid 29...
21(chain B and (resid 4 through 57 or (resid 58...
31(chain C and (resid 4 through 177 or (resid 178...
41(chain D and (resid 4 through 57 or (resid 58...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 4 through 28 or (resid 29...A4 - 28
121(chain A and (resid 4 through 28 or (resid 29...A29
131(chain A and (resid 4 through 28 or (resid 29...A4 - 313
141(chain A and (resid 4 through 28 or (resid 29...A4 - 313
151(chain A and (resid 4 through 28 or (resid 29...A4 - 313
161(chain A and (resid 4 through 28 or (resid 29...A4 - 313
211(chain B and (resid 4 through 57 or (resid 58...B4 - 57
221(chain B and (resid 4 through 57 or (resid 58...B58
231(chain B and (resid 4 through 57 or (resid 58...B3 - 393
241(chain B and (resid 4 through 57 or (resid 58...B3 - 393
251(chain B and (resid 4 through 57 or (resid 58...B3 - 393
261(chain B and (resid 4 through 57 or (resid 58...B3 - 393
311(chain C and (resid 4 through 177 or (resid 178...C4 - 177
321(chain C and (resid 4 through 177 or (resid 178...C178 - 179
331(chain C and (resid 4 through 177 or (resid 178...C3 - 313
341(chain C and (resid 4 through 177 or (resid 178...C3 - 313
351(chain C and (resid 4 through 177 or (resid 178...C3 - 313
361(chain C and (resid 4 through 177 or (resid 178...C3 - 313
411(chain D and (resid 4 through 57 or (resid 58...D4 - 57
421(chain D and (resid 4 through 57 or (resid 58...D58
431(chain D and (resid 4 through 57 or (resid 58...D3 - 313
441(chain D and (resid 4 through 57 or (resid 58...D3 - 313
451(chain D and (resid 4 through 57 or (resid 58...D3 - 313
461(chain D and (resid 4 through 57 or (resid 58...D3 - 313

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Components

#1: Protein
Methionyl-tRNA formyltransferase


Mass: 34096.164 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: fmt, PA0018 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O85732, methionyl-tRNA formyltransferase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 20.7 mg/mL PsaeA.17389.a.B1.PW37587 crystallized in sitting drop vapor diffusion with Rigaku MCSG1 B5: 0.2 M MgCl2; 0.1 M Tris pH 8.5; 25% PEG3350, cryo: 20% EG. tray 259534b5, puck rzw4-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.75→49.084 Å / Num. obs: 36266 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.402 % / Biso Wilson estimate: 36.84 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Net I/σ(I): 18.88
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.75-2.827.5460.5314.360.9341100
2.82-2.97.5380.4115.570.9571100
2.9-2.987.5280.3576.370.9671100
2.98-3.077.5510.3147.180.9731100
3.07-3.187.5090.2468.980.9831100
3.18-3.297.520.19111.180.9911100
3.29-3.417.4980.1513.70.9931100
3.41-3.557.4780.12516.240.9951100
3.55-3.717.4750.10319.440.9961100
3.71-3.897.4460.08422.830.9971100
3.89-4.17.4270.06727.350.9981100
4.1-4.357.4350.05830.650.9991100
4.35-4.657.3660.05233.280.999199.9
4.65-5.027.3310.05232.340.9991100
5.02-5.57.3130.05930.120.9981100
5.5-6.157.2670.05929.310.998199.9
6.15-7.17.1750.05232.530.999199.8
7.1-8.77.0080.03641.080.9991100
8.7-12.36.650.02748.451199.8
12.3-49.0845.4320.02836.430.999196

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FMT

1fmt


Resolution: 2.75→49.084 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.16
RfactorNum. reflection% reflection
Rfree0.2344 2192 6.3 %
Rwork0.1666 --
obs0.1709 34774 95.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.63 Å2 / Biso mean: 36.0318 Å2 / Biso min: 0.39 Å2
Refinement stepCycle: final / Resolution: 2.75→49.084 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8955 0 4 215 9174
Biso mean--36.49 24.56 -
Num. residues----1243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089139
X-RAY DIFFRACTIONf_angle_d1.05712479
X-RAY DIFFRACTIONf_chiral_restr0.0551476
X-RAY DIFFRACTIONf_plane_restr0.0081651
X-RAY DIFFRACTIONf_dihedral_angle_d12.6415522
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5441X-RAY DIFFRACTION8.327TORSIONAL
12B5441X-RAY DIFFRACTION8.327TORSIONAL
13C5441X-RAY DIFFRACTION8.327TORSIONAL
14D5441X-RAY DIFFRACTION8.327TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.75-2.80970.35961180.27061901201991
2.8097-2.87510.32931210.23361894201590
2.8751-2.9470.3031270.21431917204492
2.947-3.02670.30871570.22321933209093
3.0267-3.11570.32141370.22131937207493
3.1157-3.21630.32821150.22212022213795
3.2163-3.33120.27191230.20492037216096
3.3312-3.46450.27161550.1912014216997
3.4645-3.62220.27041470.18062048219597
3.6222-3.81310.22871380.15892065220398
3.8131-4.05190.20951450.13512093223898
4.0519-4.36450.18391260.12482134226099
4.3645-4.80340.15321540.11362099225399
4.8034-5.49770.19361340.13522142227699
5.4977-6.92340.19691510.15152133228499
6.9234-49.09140.19891440.14822213235797
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)
13.1175-0.0119-0.15992.6736-0.17631.69-0.0742-0.17690.32670.056-0.0071-0.1229-0.40380.02180.11520.2937-0.0163-0.05530.1336-0.01420.1937-22.022319.8068-45.1393
21.05140.4373-0.28693.001-0.85652.7286-0.08510.0171-0.02060.0766-0.1006-0.3942-0.0180.29070.11810.09690.0212-0.00540.19090.01810.1748-14.95183.1928-43.5443
34.42390.6931-0.11675.41321.79394.2249-0.1466-0.0662-0.00330.1686-0.12920.6866-0.1667-0.32560.21260.2493-0.01420.02590.2625-0.04980.2516-40.7358-14.0559-40.1034
42.4363-0.4047-0.2551.83062.03812.25320.08250.04850.20940.8993-0.311.31580.0901-1.07860.65270.04120.01770.59910.5121-0.34841.0375-52.7009-15.8994-36.4451
52.0575-0.01720.31952.3273-0.1974.1080.23120.0659-0.0924-0.0461-0.08410.38150.5663-0.2832-0.08520.2031-0.0565-0.04960.2002-0.00520.2725-41.31217.7063-61.2997
61.0826-0.19580.11024.49670.46341.89350.08180.0807-0.1377-0.43480.0075-0.11710.08770.0308-0.08390.1490.0104-0.0040.2088-0.00320.1754-37.56420.3071-68.9816
72.58840.6541-0.4312.24520.95564.79150.4242-0.43690.12990.6047-0.34590.2580.2945-0.0432-0.11590.3091-0.07310.05950.3215-0.02450.2036-45.075840.5514-41.3826
80.0152-0.0493-0.4011.65540.38373.54260.4422-0.01470.311-0.0827-0.0188-0.1638-1.69260.1601-0.22510.6316-0.1160.10520.2684-0.03890.3789-37.1898-8.12578.8328
90.58720.29310.04893.3251.46163.2844-0.05550.05910.1736-0.11910.18790.1068-0.1092-0.0324-0.11210.1671-0.00710.01670.24340.03240.1999-42.5107-31.9524.2716
103.9864-2.22583.38175.8578-2.65035.53220.09540.3064-0.5426-0.00720.05240.2172-0.10320.1828-0.08120.3219-0.06790.06010.15890.04920.2319-18.0973-20.0649-15.3705
113.0708-0.591-3.14512.03560.56953.17170.13810.1837-0.1697-0.1798-0.21210.1204-0.0165-0.01130.05360.3689-0.06630.02230.30070.02550.3232-27.4494-22.5698-8.3861
126.8267-0.65080.73912.326-1.46313.9813-0.4551-1.439-0.78691.21580.14570.33910.2633-0.1551-0.03830.72410.06060.03120.44910.16830.2883-17.8104-24.5084-0.2071
133.70432.29431.80754.9127-1.50432.9805-0.3063-0.56190.00310.45790.4924-0.7947-0.09730.2565-0.06270.28690.1010.00320.3251-0.02220.2637-13.9366-18.0702-5.576
142.9133-0.37220.40893.7672-0.19681.2627-0.0866-0.0725-0.1261-0.0140.0383-0.12340.15540.10290.05790.18480.0113-0.00880.2020.00860.1224-14.2734-4.7553-13.1084
154.991-0.90191.41313.72221.75272.7145-0.21540.10660.11590.12240.15410.9681-0.1043-0.2880.0670.22760.01640.02710.37140.10220.3552-39.684811.5352-15.8921
160.3156-0.4859-0.96442.82830.50143.29150.18020.18770.143-0.7220.24971.96130.0199-1.5192-0.15190.39230.0237-0.25020.63170.14881.1107-51.201411.4796-20.3633
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 81 )A4 - 81
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 211 )A82 - 211
3X-RAY DIFFRACTION3chain 'A' and (resid 212 through 294 )A212 - 294
4X-RAY DIFFRACTION4chain 'A' and (resid 295 through 313 )A295 - 313
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 59 )B3 - 59
6X-RAY DIFFRACTION6chain 'B' and (resid 60 through 211 )B60 - 211
7X-RAY DIFFRACTION7chain 'B' and (resid 212 through 313 )B212 - 313
8X-RAY DIFFRACTION8chain 'C' and (resid 3 through 81 )C3 - 81
9X-RAY DIFFRACTION9chain 'C' and (resid 82 through 313 )C82 - 313
10X-RAY DIFFRACTION10chain 'D' and (resid 3 through 25 )D3 - 25
11X-RAY DIFFRACTION11chain 'D' and (resid 26 through 58 )D26 - 58
12X-RAY DIFFRACTION12chain 'D' and (resid 59 through 81 )D59 - 81
13X-RAY DIFFRACTION13chain 'D' and (resid 82 through 96 )D82 - 96
14X-RAY DIFFRACTION14chain 'D' and (resid 97 through 211 )D97 - 211
15X-RAY DIFFRACTION15chain 'D' and (resid 212 through 291 )D212 - 291
16X-RAY DIFFRACTION16chain 'D' and (resid 292 through 313 )D292 - 313

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