[English] 日本語
Yorodumi
- PDB-4edh: The crystal structure of thymidylate kinase from Pseudomonas aeru... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4edh
TitleThe crystal structure of thymidylate kinase from Pseudomonas aeruginosa PAO1 in complex with ADP,TMP and Mg.
ComponentsThymidylate kinase
KeywordsTRANSFERASE / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics (MCSG) / structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)
Function / homology
Function and homology information


dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / phosphorylation / ATP binding / cytosol / cytoplasm
Similarity search - Function
Thymidylate kinase / Thymidylate kinase-like domain / Thymidylate kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / THYMIDINE-5'-PHOSPHATE / Thymidylate kinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsTan, K. / Joachimiak, G. / Jedrzejczak, R. / Sacchettini, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)
CitationJournal: To be Published
Title: The crystal structure of thymidylate kinase from Pseudomonas aeruginosa PAO1 in complex with ADP,TMP and Mg.
Authors: Tan, K. / Joachimiak, G. / Jedrzejczak, R. / Sacchettini, J. / Joachimiak, A.
History
DepositionMar 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_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_label_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thymidylate kinase
B: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,64511
Polymers46,8172
Non-polymers1,8289
Water8,161453
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-58 kcal/mol
Surface area17440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.597, 46.807, 53.101
Angle α, β, γ (deg.)94.98, 112.33, 105.83
Int Tables number1
Space group name H-MP1
DetailsExperimentally unknown.

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Thymidylate kinase / / dTMP kinase


Mass: 23408.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: PA2962, tmk / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q9HZN8, dTMP kinase

-
Non-polymers , 7 types, 462 molecules

#2: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N2O8P
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 453 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Ammonium Sulfate, 0.1M Tris:HCl, 20% (w/v) PEG3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 16, 2012 / Details: mirrow
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.32→25.6 Å / Num. all: 84807 / Num. obs: 84807 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 26.3
Reflection shellResolution: 1.32→1.34 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 1.7 / Num. unique all: 4148 / % possible all: 91.8

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4E5U

4e5u


Resolution: 1.32→25.588 Å / SU ML: 0.34 / σ(F): 1.96 / Phase error: 18.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1887 4257 5.02 %Random
Rwork0.1681 ---
all0.1692 84789 --
obs0.1692 84789 94.47 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.159 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.7523 Å2-3.6054 Å2-0.2536 Å2
2--0.2929 Å20.7886 Å2
3----2.0452 Å2
Refinement stepCycle: LAST / Resolution: 1.32→25.588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3236 0 115 453 3804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063548
X-RAY DIFFRACTIONf_angle_d1.2064849
X-RAY DIFFRACTIONf_dihedral_angle_d15.2961397
X-RAY DIFFRACTIONf_chiral_restr0.073541
X-RAY DIFFRACTIONf_plane_restr0.005642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3199-1.33490.33821140.31592501X-RAY DIFFRACTION86
1.3349-1.35060.33121490.30392567X-RAY DIFFRACTION92
1.3506-1.36710.30031460.29312629X-RAY DIFFRACTION92
1.3671-1.38440.31311310.26972677X-RAY DIFFRACTION93
1.3844-1.40260.27711240.2562639X-RAY DIFFRACTION93
1.4026-1.42180.24251550.24872652X-RAY DIFFRACTION93
1.4218-1.44210.23241150.21682667X-RAY DIFFRACTION93
1.4421-1.46370.23031410.21122694X-RAY DIFFRACTION94
1.4637-1.48650.23711500.19392633X-RAY DIFFRACTION94
1.4865-1.51090.2141660.19042705X-RAY DIFFRACTION94
1.5109-1.5370.18791250.1772666X-RAY DIFFRACTION94
1.537-1.56490.19571360.16642675X-RAY DIFFRACTION95
1.5649-1.5950.2071460.16422683X-RAY DIFFRACTION95
1.595-1.62750.18741370.16542709X-RAY DIFFRACTION95
1.6275-1.66290.16231240.15942712X-RAY DIFFRACTION95
1.6629-1.70160.20231350.16312685X-RAY DIFFRACTION95
1.7016-1.74420.17841540.15952732X-RAY DIFFRACTION95
1.7442-1.79130.16751680.15412681X-RAY DIFFRACTION96
1.7913-1.8440.16091360.15472755X-RAY DIFFRACTION96
1.844-1.90350.15781550.15942684X-RAY DIFFRACTION96
1.9035-1.97150.1961450.15772751X-RAY DIFFRACTION96
1.9715-2.05040.20681570.16412711X-RAY DIFFRACTION96
2.0504-2.14370.18381320.15852740X-RAY DIFFRACTION97
2.1437-2.25660.17421290.15482759X-RAY DIFFRACTION96
2.2566-2.39790.19431570.15832739X-RAY DIFFRACTION96
2.3979-2.58290.21410.16752732X-RAY DIFFRACTION97
2.5829-2.84250.20431460.16882749X-RAY DIFFRACTION97
2.8425-3.25310.17861470.16722777X-RAY DIFFRACTION98
3.2531-4.09590.16251600.13892726X-RAY DIFFRACTION96
4.0959-25.59240.17191360.17342502X-RAY DIFFRACTION88
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)
12.1991.16210.52562.3658-0.25842.25070.0788-0.15570.08720.1108-0.11890.0142-0.02860.12590.020.1138-0.00290.00820.117-0.00460.13797.6655-2.24868.4081
21.6631-0.75570.96651.1055-0.510.80790.0161-0.08530.03350.0452-0.0187-0.07960.0050.00320.00480.1517-0.00750.00390.1299-0.00680.11550.71249.176-2.0593
31.2112-0.8514-0.00271.339-0.49741.48650.17120.1063-0.049-0.2985-0.09630.0728-0.00480.0412-0.07960.17760.01-0.02220.0994-0.01850.1098-3.8764-1.7399-7.2305
41.1747-0.46420.53870.3692-0.88482.3981-0.1215-0.1457-0.040.30050.32630.0648-0.783-0.0839-0.20160.21290.00010.06540.20490.01120.1797-13.98824.17029.9729
55.0217-1.6468-0.52223.7972-0.50051.3933-0.00980.15-0.2067-0.22080.120.3845-0.0496-0.2254-0.07020.1483-0.0169-0.05030.14990.02130.1693-11.7676-7.5045-0.3548
63.09010.3801-3.07521.7133-0.33947.9058-0.2173-0.0316-0.4316-0.2434-0.1784-0.11260.29190.36140.3250.15590.01070.01860.13540.00080.16630.3382-12.37713.8757
76.7130.1767-2.63824.76870.12916.95460.2345-0.2696-0.7032-0.609-0.1403-0.56530.28780.7887-0.07320.2480.025-0.00560.26160.02890.287910.4749-11.49378.1386
82.64380.2094-0.69451.49180.05161.6986-0.1077-0.1212-0.21230.0683-0.0040.1660.0961-0.19250.09260.0870.00860.0140.12780.01340.1259-18.696225.2972-24.3728
97.020.6221.56750.9434-0.27271.9048-0.0105-0.13170.30350.1580.00510.2177-0.0417-0.24260.02570.14630.02640.01440.1251-0.01150.1801-20.316736.1264-23.6124
102.7004-0.73180.83181.2451-0.7550.8772-0.05890.02490.04260.13010.02630.0341-0.1209-0.01120.06810.13250.00910.01320.1076-0.0140.108-10.666925.3503-12.5076
110.83720.070.39540.9677-0.47661.09350.0048-0.0040.01-0.0227-0.00130.07210.051-0.0139-0.01130.11380.01840.00950.1027-0.0130.1148-10.367419.1295-19.1133
124.95350.1853-1.1032.5752-0.82292.2597-0.0071-0.0612-0.3693-0.2336-0.0354-0.08770.46010.18280.02260.23330.03570.00750.1476-0.01120.1477-6.743310.2172-22.8707
131.11870.04120.05831.0929-1.1461.25050.1022-0.03910.11770.196-0.1603-0.0474-0.06780.19410.08480.1475-0.01940.01550.1506-0.02390.1325-3.834929.4609-23.4686
144.69910.7252.06632.38830.06424.12280.03630.2839-0.2141-0.0634-0.0057-0.22990.14480.3925-0.04510.11640.03570.01940.17220.00430.13330.528224.8575-30.8147
152.01093.19490.47287.91860.82680.6881-0.1280.27790.0824-0.0970.23310.32240.0192-0.0175-0.09330.1432-0.0147-0.00380.1588-0.0020.1442-11.123328.6221-34.6924
165.00373.488-0.0577.39410.28432.4546-0.24040.44470.1103-0.74310.23990.67620.5001-0.2695-0.00690.2459-0.0268-0.07270.20240.03260.2135-21.262733.2171-33.6412
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:30)
2X-RAY DIFFRACTION2chain 'A' and (resseq 31:97)
3X-RAY DIFFRACTION3chain 'A' and (resseq 98:138)
4X-RAY DIFFRACTION4chain 'A' and (resseq 139:159)
5X-RAY DIFFRACTION5chain 'A' and (resseq 160:176)
6X-RAY DIFFRACTION6chain 'A' and (resseq 177:189)
7X-RAY DIFFRACTION7chain 'A' and (resseq 190:209)
8X-RAY DIFFRACTION8chain 'B' and (resseq -2:15)
9X-RAY DIFFRACTION9chain 'B' and (resseq 16:29)
10X-RAY DIFFRACTION10chain 'B' and (resseq 30:62)
11X-RAY DIFFRACTION11chain 'B' and (resseq 63:112)
12X-RAY DIFFRACTION12chain 'B' and (resseq 113:124)
13X-RAY DIFFRACTION13chain 'B' and (resseq 125:159)
14X-RAY DIFFRACTION14chain 'B' and (resseq 160:176)
15X-RAY DIFFRACTION15chain 'B' and (resseq 177:189)
16X-RAY DIFFRACTION16chain 'B' and (resseq 190:210)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • 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

-
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

Read more