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- PDB-7naa: Crystal structure of Mycobacterium tuberculosis H37Rv PknF kinase... -

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Basic information

Entry
Database: PDB / ID: 7naa
TitleCrystal structure of Mycobacterium tuberculosis H37Rv PknF kinase domain
ComponentsNon-specific serine/threonine protein kinase
KeywordsTRANSFERASE / pknF / Mtb / Structural Genomics / PSI-Biology / Protein Structure Initiative / Structural Genomics Consortium / SGC / ANTIMICROBIAL PROTEIN
Function / homology
Function and homology information


protein serine/threonine kinase activity => GO:0004674 / membrane => GO:0016020 / non-specific serine/threonine protein kinase / protein serine kinase activity / ATP binding
Similarity search - Function
Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-V17 / Non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsOliveira, A.A. / Cabarca, S. / dos Reis, C.V. / Takarada, J.E. / Counago, R.M. / Balan, A. / Structural Genomics Consortium (SGC)
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2016/20182-9 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)401505/2016-2 Brazil
CitationJournal: Curr Res Struct Biol / Year: 2021
Title: Structure of the Mycobacterium tuberculosis c PknF and conformational changes induced in forkhead-associated regulatory domains.
Authors: Cabarca, S. / Frazao de Souza, M. / Albert de Oliveira, A. / Vignoli Muniz, G.S. / Lamy, M.T. / Vinicius Dos Reis, C. / Takarada, J. / Effer, B. / Souza, L.S. / Iriarte de la Torre, L. / ...Authors: Cabarca, S. / Frazao de Souza, M. / Albert de Oliveira, A. / Vignoli Muniz, G.S. / Lamy, M.T. / Vinicius Dos Reis, C. / Takarada, J. / Effer, B. / Souza, L.S. / Iriarte de la Torre, L. / Counago, R. / Pinto Oliveira, C.L. / Balan, A.
History
DepositionJun 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: 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: Non-specific serine/threonine protein kinase
B: Non-specific serine/threonine protein kinase
C: Non-specific serine/threonine protein kinase
D: Non-specific serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,4208
Polymers121,4854
Non-polymers1,9354
Water2,108117
1
A: Non-specific serine/threonine protein kinase
B: Non-specific serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7104
Polymers60,7432
Non-polymers9672
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Non-specific serine/threonine protein kinase
D: Non-specific serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7104
Polymers60,7432
Non-polymers9672
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.127, 239.330, 53.982
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEULEULEUAA3 - 2783 - 278
21LEULEULEULEUBB3 - 2783 - 278
12GLYGLYARGARGAA24 - 27724 - 277
22GLYGLYARGARGCC24 - 27724 - 277
13ALAALAARGARGAA4 - 2774 - 277
23ALAALAARGARGDD4 - 2774 - 277
14GLYGLYARGARGBB24 - 27724 - 277
24GLYGLYARGARGCC24 - 27724 - 277
15ALAALAARGARGBB4 - 2774 - 277
25ALAALAARGARGDD4 - 2774 - 277
16GLYGLYHISHISCC24 - 27624 - 276
26LEULEUHISHISDD18 - 27618 - 276

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Non-specific serine/threonine protein kinase


Mass: 30371.281 Da / Num. of mol.: 4 / Fragment: Protein kinase domain, residues 1-278
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: pknF_1, pknF, pknF_2, C0094_09540, DSI38_08510, E5M05_19500, E5M52_18375, E5M78_18220, ERS007741_01296, ERS013471_03424, ERS027661_00065, ERS094182_03016, F6W99_00312, FRD82_04005, GCL30_17545, SAMEA2683035_01332
Plasmid: pOP5GT / Details (production host): gst tag / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A045H1A5, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-V17 / (4-{[4-(1-benzothiophen-2-yl)pyrimidin-2-yl]amino}phenyl)[4-(pyrrolidin-1-yl)piperidin-1-yl]methanone


Mass: 483.628 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H29N5OS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.51 Å3/Da / Density % sol: 51.03 % / Description: Orthorhombic
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PEG 4000, Citrate buffer, Ammonium acetate pH 5.5, 10 mM Ikk16
Temp details: 18

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: Liquid Nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.75→39.9 Å / Num. obs: 34601 / % possible obs: 99.41 % / Redundancy: 5.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.065 / Rrim(I) all: 0.159 / Net I/σ(I): 11.14
Reflection shellResolution: 2.75→2.84 Å / Rmerge(I) obs: 1.57 / Mean I/σ(I) obs: 1.38 / Num. unique obs: 3428 / CC1/2: 0.6 / Rpim(I) all: 0.76 / Rrim(I) all: 1.76 / % possible all: 98.93

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5m06
Resolution: 2.75→39.9 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.891 / SU B: 36.199 / SU ML: 0.33 / Cross valid method: FREE R-VALUE / ESU R: 0.827 / ESU R Free: 0.362 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.27887 1688 4.9 %RANDOM
Rwork0.2369 ---
obs0.23888 32914 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å2-0 Å2-0 Å2
2---2.11 Å20 Å2
3---1.24 Å2
Refinement stepCycle: 1 / Resolution: 2.75→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6831 0 140 117 7088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0137158
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176510
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.6439813
X-RAY DIFFRACTIONr_angle_other_deg1.171.60414857
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9485921
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.23821.231333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05715903
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1361548
X-RAY DIFFRACTIONr_chiral_restr0.0540.2967
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028775
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021581
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.333.7463732
X-RAY DIFFRACTIONr_mcbond_other1.333.7493733
X-RAY DIFFRACTIONr_mcangle_it2.2955.6174641
X-RAY DIFFRACTIONr_mcangle_other2.2965.6144641
X-RAY DIFFRACTIONr_scbond_it1.2654.0073426
X-RAY DIFFRACTIONr_scbond_other1.2654.013427
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1815.9565173
X-RAY DIFFRACTIONr_long_range_B_refined5.1344.3377216
X-RAY DIFFRACTIONr_long_range_B_other5.11144.2887206
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A69530.08
12B69530.08
21A62220.07
22C62220.07
31A64400.07
32D64400.07
41B61750.09
42C61750.09
51B64050.08
52D64050.08
61C60140.07
62D60140.07
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 118 -
Rwork0.354 2371 -
obs--98.73 %
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)
14.74330.737-2.41981.5843-0.54335.1005-0.0302-0.3481-0.09220.19360.0982-0.1770.70870.1303-0.06810.42910.0317-0.10270.10620.0630.38526.79230.182925.7343
224.16965.21370.636310.80115.12292.5864-0.40860.61361.07231.08830.8158-0.62940.59750.356-0.40720.49480.0839-0.16490.43450.00930.326931.424810.646211.9198
31.1968-0.0683-0.43690.21660.30410.6679-0.03410.0932-0.08630.04480.0864-0.0263-0.0138-0.0179-0.05230.33160.0094-0.00920.12620.0740.617321.54021.08549.5846
45.06072.0612-1.0041.8949-0.49651.62320.0524-0.07120.1740.2204-0.01670.25260.13660.0511-0.03570.37510.037-0.020.13060.08320.520619.53660.21148.6015
51.8462-0.7920.01861.15790.15120.2602-0.130.0073-0.0160.04560.0528-0.02660.2222-0.03960.07720.3898-0.0374-0.01630.12980.00840.519828.6225-10.3819-3.8073
65.08052.7649-0.80657.01010.92030.46550.3620.58280.4358-0.1482-0.2540.1351-0.1416-0.2171-0.1080.33890.0079-0.07820.30510.04730.331624.00660.3391-9.9806
717.20561.9077-10.5621.91-1.21966.4861-0.3803-0.18991.06260.15761.05850.28670.22460.0905-0.67830.6267-0.088-0.00870.81520.01620.50230.191831.071327.4292
83.59831.35490.39560.6137-0.05262.36580.38820.05260.2760.2711-0.00930.0898-0.06420.1717-0.37890.3565-0.02720.10670.0889-0.04840.542523.294921.414422.2463
91.8697-0.12110.67130.032-0.03650.2644-0.0201-0.07170.4792-0.0048-0.0414-0.09390.0354-0.02820.06150.366-0.00620.03260.06670.02560.72811.91323.376714.7237
103.4992-2.733-3.09246.16646.87677.79460.0601-0.51450.2115-0.15770.0024-0.1671-0.27820.1508-0.06250.358-0.03120.01760.27950.08690.654412.467722.879513.1219
110.259-0.1478-0.47252.24330.48391.7015-0.0502-0.00660.2735-0.0899-0.08640.2065-0.04660.01350.13660.3068-0.0015-0.08050.0042-0.01630.8161-5.396129.746614.721
123.56291.50480.834710.1453-7.68787.0484-0.4681-0.4280.3506-0.89120.1866-0.17320.541-0.54610.28150.3536-0.0886-0.02630.46190.03570.3874-4.314721.56142.7622
137.73110.00860.72490.0036-0.00670.0845-0.0273-0.4605-0.50440.0247-0.0124-0.0378-0.0346-0.02690.03970.5794-0.1786-0.04010.32520.13170.531959.574739.007925.3304
140.53311.26360.31283.06270.87070.43680.1998-0.1318-0.22790.2277-0.1882-0.5234-0.24270.1051-0.01160.5472-0.3073-0.05810.17580.02540.971358.023744.043214.7675
155.56650.7238-3.38350.1815-0.41782.06330.3232-0.93350.00720.1119-0.3117-0.0744-0.17710.5225-0.01150.3232-0.1753-0.05260.52760.1480.740350.51733.898118.5112
160.7966-0.3152-1.37581.8235-0.50493.14130.1598-0.00590.10140.1014-0.1913-0.0577-0.24050.10690.03150.3103-0.05130.05320.036-0.00620.737945.415536.02867.227
171.3944-1.0061-1.3721.29870.58381.6546-0.00990.0390.0750.03440.021-0.03460.0021-0.0399-0.01110.3361-0.00260.03580.07480.06560.667650.688224.87481.1463
181.7511-0.50230.23211.07380.95481.36520.00660.21670.2289-0.22140.00570.1089-0.06830.0196-0.01220.3237-0.0278-0.04130.13120.13640.722940.364228.0975-5.9281
194.5181-1.33610.83683.4662-0.67811.1333-0.2875-0.01980.19460.6188-0.0721-0.9739-0.25850.12290.35960.3912-0.2553-0.18020.22050.08830.744965.068158.345216.966
207.11741.83821.47993.51260.85980.4019-0.0749-0.0737-0.26670.24250.1034-0.2676-0.06750.0268-0.02860.5167-0.1275-0.14640.12050.00270.518256.354854.873721.0761
214.2938-1.48852.91354.7052-1.88093.84910.1397-0.40910.1765-0.8781-0.1109-0.239-0.0923-0.3395-0.02880.5968-0.05080.07620.09720.01090.523750.000165.83335.4608
220.3062-1.06650.44414.1636-1.63542.4920.06140.00620.0538-0.0201-0.19970.2423-0.0267-0.06430.13830.4315-0.1188-0.02850.083-0.1440.591243.161659.919412.2064
230.420.4534-0.71343.44731.47662.9684-0.07260.01950.029-0.1196-0.2810.30710.0784-0.29870.35360.3543-0.0468-0.00940.0676-0.1750.782840.333973.212818.7355
241.00650.9355-1.64533.02341.03586.0192-0.05170.09420.2835-0.1653-0.25860.90040.004-0.74750.31030.1431-0.0273-0.10930.2037-0.18650.79829.371570.383414.1306
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 60
2X-RAY DIFFRACTION2A61 - 67
3X-RAY DIFFRACTION3A68 - 132
4X-RAY DIFFRACTION4A133 - 159
5X-RAY DIFFRACTION5A160 - 258
6X-RAY DIFFRACTION6A259 - 278
7X-RAY DIFFRACTION7B3 - 9
8X-RAY DIFFRACTION8B10 - 71
9X-RAY DIFFRACTION9B72 - 149
10X-RAY DIFFRACTION10B150 - 181
11X-RAY DIFFRACTION11B182 - 269
12X-RAY DIFFRACTION12B270 - 278
13X-RAY DIFFRACTION13C24 - 33
14X-RAY DIFFRACTION14C34 - 81
15X-RAY DIFFRACTION15C82 - 104
16X-RAY DIFFRACTION16C105 - 153
17X-RAY DIFFRACTION17C154 - 233
18X-RAY DIFFRACTION18C234 - 278
19X-RAY DIFFRACTION19D4 - 65
20X-RAY DIFFRACTION20D66 - 87
21X-RAY DIFFRACTION21D88 - 109
22X-RAY DIFFRACTION22D110 - 155
23X-RAY DIFFRACTION23D156 - 230
24X-RAY DIFFRACTION24D231 - 277

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