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- PDB-4iw3: Crystal structure of a Pseudomonas putida prolyl-4-hydroxylase (P... -

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Basic information

Entry
Database: PDB / ID: 4iw3
TitleCrystal structure of a Pseudomonas putida prolyl-4-hydroxylase (P4H) in complex with elongation factor Tu (EF-Tu)
Components
  • Elongation factor Tu-A
  • Putative uncharacterized protein
KeywordsMETAL BINDING PROTEIN/TRANSLATION / 2-oxoglutarate oxygenase / oxygen sensing / protein synthesis regulation / double-stranded beta helix / jellyroll fold / prolyl-4-hydroxylase / translation / METAL BINDING PROTEIN-TRANSLATION complex
Function / homology
Function and homology information


L-ascorbic acid binding / guanosine tetraphosphate binding / dioxygenase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / translation elongation factor activity / iron ion binding / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / q2cbj1_9rhob like domain / 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 ...Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / q2cbj1_9rhob like domain / 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 / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / 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 / Jelly Rolls / Beta Barrel / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / : / N-OXALYLGLYCINE / Fe2OG dioxygenase domain-containing protein / Elongation factor Tu-A
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.697 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 23, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Other
Revision 1.2Sep 17, 2014Group: Database references
Revision 1.3Oct 1, 2014Group: Database references
Revision 1.4Nov 20, 2019Group: Data collection / Database references / Category: reflns / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.5Nov 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_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_asym_id / _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.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.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_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: Putative uncharacterized protein
B: Elongation factor Tu-A
K: Elongation factor Tu-A
J: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,37812
Polymers146,0394
Non-polymers1,3398
Water2,990166
1
A: Putative uncharacterized protein
B: Elongation factor Tu-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6896
Polymers73,0202
Non-polymers6704
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-32 kcal/mol
Surface area24150 Å2
MethodPISA
2
K: Elongation factor Tu-A
J: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6896
Polymers73,0202
Non-polymers6704
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-33 kcal/mol
Surface area24690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.704, 200.704, 74.833
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 2 types, 4 molecules AJBK

#1: Protein Putative uncharacterized protein / Prolyl-4-hydroxylase


Mass: 25640.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: KT2440 / Gene: PP_5159 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q88CM1
#2: Protein Elongation factor Tu-A / EF-Tu-A


Mass: 47378.891 Da / Num. of mol.: 2
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, 174 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-OGA / N-OXALYLGLYCINE / N-Oxalylglycine


Mass: 147.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.98 Å3/Da / Density % sol: 58.71 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.8mM MnCl2, 0.9mM OGA, 1mM GDP, 0.1M MgCl2, 22% polyacrylate 5100, 0.1M Hepes pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 23, 2012
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.697→29.558 Å / Num. obs: 47788 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 74.727 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 13.37
Reflection shell

Rmerge(I) obs: 0.013 / Diffraction-ID: 1

Resolution (Å)Rmerge F obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.7-2.860.4461.76305214961148421.43799.2
2.86-3.050.7512.466690413992139900.723100
3.05-3.30.9334.786300013106131060.359100
3.3-3.610.9839.985746711966119660.17100
3.61-4.020.99316.55193810903109030.098100
4.02-4.630.99725.1245481969896950.061100
4.63-5.640.99728.5236912813481250.05599.9
5.64-7.830.99831.6830835637863770.046100
7.83-29.5580.99939.9817726380537290.03198

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.7 Å29.56 Å
Translation2.7 Å29.56 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
GDAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DG1, 4J25

1dg1

4j25


Resolution: 2.697→29.558 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8207 / SU ML: 0.36 / σ(F): 1.34 / Phase error: 24.85 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflectionSelection details
Rfree0.2181 2419 5.06 %Random
Rwork0.1679 ---
obs0.1705 47788 99.95 %-
all-47794 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.08 Å2 / Biso mean: 60.1937 Å2 / Biso min: 14.27 Å2
Refinement stepCycle: LAST / Resolution: 2.697→29.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8724 0 80 166 8970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118993
X-RAY DIFFRACTIONf_angle_d1.21512257
X-RAY DIFFRACTIONf_chiral_restr0.0611390
X-RAY DIFFRACTIONf_plane_restr0.0061616
X-RAY DIFFRACTIONf_dihedral_angle_d15.0883231
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.6972-2.75230.35291440.293726202764276499
2.7523-2.81210.32991570.2814264127982798100
2.8121-2.87740.32431260.2575265427802780100
2.8774-2.94930.29831400.2407265127912791100
2.9493-3.0290.32291450.2276263327782778100
3.029-3.1180.27581510.2132268228332833100
3.118-3.21850.28361190.1988263527542754100
3.2185-3.33340.25471230.1976268128042804100
3.3334-3.46670.25731250.1879267728022802100
3.4667-3.62420.22531370.1774267828152815100
3.6242-3.81490.23171520.1717263427862786100
3.8149-4.05340.24191490.1574266828172817100
4.0534-4.36540.19151560.1384267228282828100
4.3654-4.8030.14151490.1193266328122812100
4.803-5.49420.18971540.1334268428382838100
5.4942-6.90750.19271520.1641271028622862100
6.9075-29.55980.20291400.1625278629262926100
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)
12.4895-0.5902-0.22844.5345-2.18323.2985-0.5241-0.3181-0.52771.1150.72060.60910.2639-0.674-0.27110.55080.08590.10550.23630.00670.3479-67.921619.82911.3872
24.00571.15290.53585.5635-1.19854.4159-0.41160.2881-0.406-0.17080.0029-1.08480.58761.11790.15390.30260.18950.01030.6174-0.11050.5056-48.353422.3468-2.0694
39.0797-4.82926.28889.5135-6.0155.98010.35340.151-1.0163-0.09290.56720.50760.9127-0.2078-0.72090.4567-0.11080.12260.2837-0.07220.3599-68.35114.4518-7.9424
42.0793-0.11661.1063.74811.254.1729-0.22870.0039-0.06390.23880.3926-0.1527-0.11560.3072-0.06280.21960.01660.05590.21730.0430.1925-61.470629.2678-1.6894
52.53-0.05750.42274.88261.47434.7312-0.23490.1664-0.22480.14750.5023-0.40380.82421.3237-0.30870.15030.04160.07260.2612-0.03310.3393-57.848823.6865-5.1731
62.19540.6824-1.36160.50840.36773.0030.10580.29140.5493-0.35590.2783-0.701-0.1410.0519-0.22890.4285-0.08930.24260.47930.02050.9404-37.757131.8386-26.5654
74.80281.3422-0.77171.45820.38871.58560.00410.9003-0.2747-0.76940.2703-0.9667-0.10080.57040.03230.6568-0.11160.43280.7352-0.08990.9451-33.951229.8463-39.7957
82.90870.1464-1.23574.04610.47213.46470.01910.434-1.2184-0.4045-0.09020.08930.4216-0.08730.06050.4885-0.1186-0.00680.198-0.16090.616-59.281213.6967-31.3935
91.72472.60911.59573.41192.30242.55380.26510.4407-0.0082-0.07680.1646-0.6299-0.24020.2395-0.47640.5347-0.03890.16690.56350.14770.6945-56.210275.161525.0366
107.58023.36-1.32833.7454-1.81475.16390.1482-0.7711.7580.3091-0.0566-0.3708-0.64180.2249-0.09940.7283-0.11220.12230.39650.16270.9893-51.817590.519233.9138
113.04912.5584-2.0864.8726-1.37912.02650.44850.31760.03720.3097-0.1412-0.97-0.67760.5502-0.22330.547-0.08870.07430.74180.10020.8081-46.578576.484730.5234
123.4978-1.26740.10986.4375-0.71491.769-0.0129-0.13810.46980.62360.1082-0.2288-0.13010.1597-0.07750.45250.00350.06220.23620.00160.2455-73.18665.362544.2104
139.7491.05212.62393.57681.02023.53190.40390.3123-0.96660.7567-0.41290.02360.5543-0.3354-0.03710.42610.0620.06780.26950.03170.2659-76.597638.732424.2018
145.77781.0757-0.19343.17622.05081.4849-0.08821.15480.2976-0.933-0.29930.9642-0.6753-0.8688-0.15460.54940.3464-0.13660.78540.05750.4608-90.813251.415910.6579
154.85133.7641.97813.41331.49631.7141-0.8857-0.32870.9580.14350.22391.0421-1.3229-0.53050.56231.29580.1833-0.14930.45420.14240.5701-79.098963.985610.9691
164.84092.7506-1.92892.8717-0.95924.42790.2323-0.07810.9926-0.496-0.32870.7155-1.3672-0.3419-0.49630.92040.23650.05250.2510.13030.4041-78.761161.29413.6736
177.6941-1.51471.88113.9840.69982.036-0.154-0.56790.27750.3343-0.38380.30990.0267-0.84180.2590.32890.09020.15530.4097-0.1270.3427-82.532648.385628.8384
182.9-2.46023.83862.8916-3.80435.40970.1533-0.117-0.06090.16590.37180.3803-1.5456-0.4464-0.20210.54980.10510.07640.3140.07610.3552-77.639954.414322.5033
194.30981.37522.5162.89471.43726.8981-0.13960.2109-0.169-0.47270.1701-0.0885-0.84590.04250.03110.36750.09980.11830.22330.06960.2511-72.424550.897712.4443
207.41560.4594-2.75782.5620.8142.67480.00710.1699-0.1190.25350.1097-0.1132-0.0390.3729-0.0990.34770.09650.01420.39130.0250.1687-68.463641.731812.2085
211.5732-0.859-0.59413.0906-0.31381.57940.26180.18690.683-0.1470.2801-0.1377-1.23190.43280.080.49520.10940.08990.23850.14610.1554-72.57952.728418.4723
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 7:47 )A0
2X-RAY DIFFRACTION2CHAIN A AND (RESID 48:80 )A0
3X-RAY DIFFRACTION3CHAIN A AND (RESID 81:101 )A0
4X-RAY DIFFRACTION4CHAIN A AND (RESID 102:185 )A0
5X-RAY DIFFRACTION5CHAIN A AND (RESID 186:207 )A0
6X-RAY DIFFRACTION6CHAIN B AND (RESID 10:94 )B0
7X-RAY DIFFRACTION7CHAIN B AND (RESID 95:219 )B0
8X-RAY DIFFRACTION8CHAIN B AND (RESID 220:397 )B0
9X-RAY DIFFRACTION9CHAIN K AND (RESID 10:100 )K0
10X-RAY DIFFRACTION10CHAIN K AND (RESID 101:169 )K0
11X-RAY DIFFRACTION11CHAIN K AND (RESID 170:219 )K0
12X-RAY DIFFRACTION12CHAIN K AND (RESID 220:397 )K0
13X-RAY DIFFRACTION13CHAIN J AND (RESID 7:30 )J0
14X-RAY DIFFRACTION14CHAIN J AND (RESID 31:46 )J0
15X-RAY DIFFRACTION15CHAIN J AND (RESID 47:57 )J0
16X-RAY DIFFRACTION16CHAIN J AND (RESID 58:82 )J0
17X-RAY DIFFRACTION17CHAIN J AND (RESID 83:101 )J0
18X-RAY DIFFRACTION18CHAIN J AND (RESID 102:115 )J0
19X-RAY DIFFRACTION19CHAIN J AND (RESID 116:153 )J0
20X-RAY DIFFRACTION20CHAIN J AND (RESID 154:172 )J0
21X-RAY DIFFRACTION21CHAIN J AND (RESID 173:207 )J0

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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