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- PDB-7qyr: Crystal structure of RimK from Pseudomonas aeruginosa PAO1 -

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Basic information

Entry
Database: PDB / ID: 7qyr
TitleCrystal structure of RimK from Pseudomonas aeruginosa PAO1
Components
  • Probable alpha-L-glutamate ligase
  • poly-glutamate
KeywordsLIGASE / ATP-grasp fold / glutamate ligase / ribosomal modification
Function / homology
Function and homology information


C-terminal protein amino acid modification / ribosomal S6-glutamic acid ligase activity / ligase activity, forming carbon-nitrogen bonds / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / SOS response / translation / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Ribosomal protein S6--L-glutamate ligase RimK / RimK, PreATP-grasp domain / RimK PreATP-grasp domain / Ribosomal S6 modification enzyme RimK/Lysine biosynthesis enzyme LysX / ATP-grasp fold, RimK-type / RimK-like ATP-grasp domain / ATP-grasp fold, subdomain 1 / ATP-grasp fold / ATP-grasp fold profile.
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Probable alpha-L-glutamate ligase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsThompson, C.M.A. / Little, R.H. / Stevenson, C.E.M. / Lawson, D.M. / Malone, J.G.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R018154/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BBS/E/J/000PR9797 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BBS/E/J/000PR9790 United Kingdom
CitationJournal: Proteins / Year: 2023
Title: Structural insights into the mechanism of adaptive ribosomal modification by Pseudomonas RimK.
Authors: Thompson, C.M.A. / Little, R.H. / Stevenson, C.E.M. / Lawson, D.M. / Malone, J.G.
History
DepositionJan 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable alpha-L-glutamate ligase
B: Probable alpha-L-glutamate ligase
C: Probable alpha-L-glutamate ligase
D: Probable alpha-L-glutamate ligase
E: Probable alpha-L-glutamate ligase
F: Probable alpha-L-glutamate ligase
G: Probable alpha-L-glutamate ligase
H: Probable alpha-L-glutamate ligase
K: poly-glutamate
L: poly-glutamate
M: poly-glutamate
N: poly-glutamate
O: poly-glutamate
P: poly-glutamate
Q: poly-glutamate
T: poly-glutamate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,95024
Polymers335,53216
Non-polymers3,4188
Water1,838102
1
A: Probable alpha-L-glutamate ligase
C: Probable alpha-L-glutamate ligase
D: Probable alpha-L-glutamate ligase
F: Probable alpha-L-glutamate ligase
K: poly-glutamate
M: poly-glutamate
N: poly-glutamate
P: poly-glutamate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,47512
Polymers167,7668
Non-polymers1,7094
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12770 Å2
ΔGint-66 kcal/mol
Surface area42890 Å2
MethodPISA
2
B: Probable alpha-L-glutamate ligase
E: Probable alpha-L-glutamate ligase
G: Probable alpha-L-glutamate ligase
H: Probable alpha-L-glutamate ligase
L: poly-glutamate
O: poly-glutamate
Q: poly-glutamate
T: poly-glutamate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,47512
Polymers167,7668
Non-polymers1,7094
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12710 Å2
ΔGint-69 kcal/mol
Surface area42810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.898, 153.586, 138.539
Angle α, β, γ (deg.)90.000, 102.390, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROAA1 - 2921 - 292
21PROPROBB1 - 2921 - 292
12ASNASNAA1 - 2891 - 289
22ASNASNCC1 - 2891 - 289
13GLYGLYAA1 - 2911 - 291
23GLYGLYDD1 - 2911 - 291
14ASNASNAA1 - 2891 - 289
24ASNASNEE1 - 2891 - 289
15GLYGLYAA1 - 2901 - 290
25GLYGLYFF1 - 2901 - 290
16GLYGLYAA1 - 2901 - 290
26GLYGLYGG1 - 2901 - 290
17GLYGLYAA1 - 2901 - 290
27GLYGLYHH1 - 2901 - 290
18LYSLYSBB1 - 2881 - 288
28LYSLYSCC1 - 2881 - 288
19PROPROBB1 - 2921 - 292
29PROPRODD1 - 2921 - 292
110GLYGLYBB1 - 2901 - 290
210GLYGLYEE1 - 2901 - 290
111GLYGLYBB1 - 2901 - 290
211GLYGLYFF1 - 2901 - 290
112GLYGLYBB1 - 2901 - 290
212GLYGLYGG1 - 2901 - 290
113GLYGLYBB1 - 2901 - 290
213GLYGLYHH1 - 2901 - 290
114ASNASNCC1 - 2891 - 289
214ASNASNDD1 - 2891 - 289
115ASNASNCC1 - 2891 - 289
215ASNASNEE1 - 2891 - 289
116ASNASNCC1 - 2891 - 289
216ASNASNFF1 - 2891 - 289
117ASNASNCC1 - 2891 - 289
217ASNASNGG1 - 2891 - 289
118ASNASNCC1 - 2891 - 289
218ASNASNHH1 - 2891 - 289
119ASNASNDD1 - 2891 - 289
219ASNASNEE1 - 2891 - 289
120GLYGLYDD1 - 2901 - 290
220GLYGLYFF1 - 2901 - 290
121GLYGLYDD1 - 2901 - 290
221GLYGLYGG1 - 2901 - 290
122GLYGLYDD1 - 2901 - 290
222GLYGLYHH1 - 2901 - 290
123GLYGLYEE1 - 2901 - 290
223GLYGLYFF1 - 2901 - 290
124GLYGLYEE1 - 2901 - 290
224GLYGLYGG1 - 2901 - 290
125GLYGLYEE1 - 2901 - 290
225GLYGLYHH1 - 2901 - 290
126GLYGLYFF1 - 2901 - 290
226GLYGLYGG1 - 2901 - 290
127GLYGLYFF1 - 2901 - 290
227GLYGLYHH1 - 2901 - 290
128GLYGLYGG1 - 2901 - 290
228GLYGLYHH1 - 2901 - 290

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
Probable alpha-L-glutamate ligase


Mass: 34176.707 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: An affinity tag with sequence KLAAALEHHHHHH was appended to the C-terminus of the wild-type sequence
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: rimK, PA5197
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9HTZ2, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein
poly-glutamate


Mass: 7764.839 Da / Num. of mol.: 8 / Source method: obtained synthetically
Details: Poly-glutamate was not explicitly added to the sample but was presumed to have been synthesized by the enzyme.
Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.45 Å3/Da / Density % sol: 49.82 % / Description: NULL
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: NULL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.4→45.1 Å / Num. obs: 105678 / % possible obs: 99.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 59.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.044 / Rrim(I) all: 0.116 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.4-2.446.82.0493514451710.4380.8452.2190.998.8
13.15-45.15.90.03638576530.9980.0160.0440.796.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IWX
Resolution: 2.4→44.45 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.946 / SU B: 23.973 / SU ML: 0.237 / SU R Cruickshank DPI: 0.4036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.404 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 5200 4.9 %RANDOM
Rwork0.2116 ---
obs0.2126 100447 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 170.12 Å2 / Biso mean: 70.8 Å2 / Biso min: 30.83 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å2-0 Å22.32 Å2
2---0.28 Å2-0 Å2
3----1.91 Å2
Refinement stepCycle: final / Resolution: 2.4→44.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17536 0 152 102 17790
Biso mean--101.06 54.61 -
Num. residues----2345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01317940
X-RAY DIFFRACTIONr_bond_other_d0.0010.01517546
X-RAY DIFFRACTIONr_angle_refined_deg1.3271.63724227
X-RAY DIFFRACTIONr_angle_other_deg1.1611.57540286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.57652322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.79821.141868
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.649153116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.30715154
X-RAY DIFFRACTIONr_chiral_restr0.0520.22414
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0220241
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023863
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A84660.04
12B84660.04
21A82500.07
22C82500.07
31A83840.06
32D83840.06
41A84060.06
42E84060.06
51A81870.05
52F81870.05
61A84240.03
62G84240.03
71A81080.07
72H81080.07
81B81630.07
82C81630.07
91B82360.06
92D82360.06
101B82400.07
102E82400.07
111B81560.06
112F81560.06
121B82540.04
122G82540.04
131B81020.06
132H81020.06
141C82910.06
142D82910.06
151C83870.04
152E83870.04
161C80600.07
162F80600.07
171C81700.05
172G81700.05
181C81580.06
182H81580.06
191D84440.05
192E84440.05
201D80600.06
202F80600.06
211D82690.05
212G82690.05
221D82150.05
222H82150.05
231E80950.06
232F80950.06
241E83270.05
242G83270.05
251E81910.05
252H81910.05
261F81270.03
262G81270.03
271F80170.07
272H80170.07
281G79950.06
282H79950.06
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 384 -
Rwork0.343 7350 -
all-7734 -
obs--98.5 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.6120.1506-1.1770.9351-0.30262.4314-0.09410.07340.0775-0.214-0.01720.09660.0782-0.08760.11130.11310.01-0.00040.0064-0.00680.170147.491112.346449.0373
20.96120.1338-0.06110.8583-0.35643.1808-0.02090.0076-0.1458-0.2474-0.0293-0.26190.08220.12480.05020.24670.03790.05670.04610.05070.246649.085260.095120.4717
30.14320.3921-0.05772.3161.01753.05460.0492-0.052-0.08410.3589-0.0098-0.1476-0.23180.2517-0.03940.2745-0.0269-0.04690.04290.02080.175560.328155.838741.1324
41.8886-0.5987-0.9280.7148-0.27631.9997-0.0106-0.08380.29560.1738-0.1344-0.2946-0.3390.6520.1450.164-0.1284-0.02980.26280.05860.28267.839523.66967.0477
51.17250.8742-1.0861.8332-0.99992.81980.0174-0.06350.08330.11950.01130.1802-0.3026-0.1909-0.02870.32280.02320.06010.042-0.03010.196840.355116.8295107.6033
60.79760.02140.55091.6390.07483.6754-0.01520.0652-0.02750.3136-0.01980.585-0.37-0.85310.0350.29330.07510.13130.2840.02590.468633.46850.002550.4798
72.09560.7595-0.94581.4596-0.25532.9217-0.0896-0.3493-0.02640.26540.0939-0.3731-0.07410.685-0.00440.4517-0.004-0.01730.2445-0.09350.354860.985621.9823128.1365
81.46010.1169-0.09840.574-0.63732.954-0.06770.4845-0.1925-0.28740.11780.17140.4253-0.5534-0.05010.3025-0.0894-0.05560.2681-0.02690.224823.524349.0951127.9513
92.9248-0.5886-0.63072.92555.856911.8557-0.0252-0.3427-0.30010.01920.0097-0.01470.0207-0.04380.01560.42410.0167-0.0260.3495-0.04330.530640.244718.630949.2823
104.5141-4.95353.19676.7413-5.97296.97170.24270.19490.3009-0.2289-0.2808-0.16860.1630.3410.03810.45590.02330.03090.50060.01970.483355.793853.7053123.4867
110.04650.20810.07698.5781.80840.40890.12890.0560.0360.2591-0.25380.47880.13970.02220.12490.4772-0.04670.03480.6209-0.01890.443166.165652.24948.135
1211.11136.8988-14.31564.6661-8.700318.53670.69680.37030.61350.43830.3547-0.1477-0.886-0.4301-1.05150.49030.04410.07090.6569-0.04950.784372.329729.959162.9244
130.2757-1.8399-2.110912.832914.614616.67420.0228-0.0570.0181-0.5670.0798-0.0382-0.60350.1935-0.10260.43060.01160.03360.72180.02130.34831.956818.7252111.1897
142.37672.5655-2.23934.573-2.64942.14410.3330.16630.3911-0.0088-0.00980.1226-0.2345-0.1299-0.32320.46660.0216-0.01770.5827-0.03420.458232.173340.161349.0728
158.9884-3.94857.00957.51682.722111.30390.4607-0.2503-0.2896-0.4075-0.1307-0.02470.0867-0.4353-0.330.423-0.0574-0.00480.4422-0.02110.418663.279631.144126.6505
167.06952.2832-0.81949.3090.3898.14850.3267-0.70250.71750.5296-0.3591-0.0586-0.51450.18680.03240.36260.0047-0.06650.5309-0.00250.533273.393364.8911142.1252
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 300
2X-RAY DIFFRACTION2B1 - 300
3X-RAY DIFFRACTION3C1 - 300
4X-RAY DIFFRACTION4D1 - 300
5X-RAY DIFFRACTION5E1 - 300
6X-RAY DIFFRACTION6F1 - 300
7X-RAY DIFFRACTION7G1 - 300
8X-RAY DIFFRACTION8H1 - 300
9X-RAY DIFFRACTION9K1 - 300
10X-RAY DIFFRACTION10L1 - 300
11X-RAY DIFFRACTION11M1 - 300
12X-RAY DIFFRACTION12N1 - 300
13X-RAY DIFFRACTION13O1 - 300
14X-RAY DIFFRACTION14P1 - 300
15X-RAY DIFFRACTION15Q1 - 300
16X-RAY DIFFRACTION16T1 - 300

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