[English] 日本語
Yorodumi
- PDB-3ori: Mycobacterium tuberculosis PknB kinase domain L33D mutant (crysta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ori
TitleMycobacterium tuberculosis PknB kinase domain L33D mutant (crystal form 1)
ComponentsSerine/threonine protein kinase
KeywordsTRANSFERASE / Structural Genomics / TB Structural Genomics Consortium / TBSGC / Kinase / Signal transduction
Function / homology
Function and homology information


negative regulation of growth rate / regulation of primary metabolic process / acetyltransferase activator activity / negative regulation of catalytic activity / negative regulation of fatty acid biosynthetic process / response to host immune response / positive regulation of catalytic activity / positive regulation of DNA binding / peptidoglycan biosynthetic process / peptidoglycan-based cell wall ...negative regulation of growth rate / regulation of primary metabolic process / acetyltransferase activator activity / negative regulation of catalytic activity / negative regulation of fatty acid biosynthetic process / response to host immune response / positive regulation of catalytic activity / positive regulation of DNA binding / peptidoglycan biosynthetic process / peptidoglycan-based cell wall / negative regulation of protein binding / manganese ion binding / regulation of cell shape / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / : / Serine/threonine-protein kinase PknB / Serine/threonine-protein kinase PknB
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLombana, T.N. / Echols, N. / Good, M.C. / Thomsen, N.D. / Ng, H.-L. / Alber, T. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Structure / Year: 2010
Title: Allosteric activation mechanism of the Mycobacterium tuberculosis receptor Ser/Thr protein kinase, PknB.
Authors: Lombana, T.N. / Echols, N. / Good, M.C. / Thomsen, N.D. / Ng, H.L. / Greenstein, A.E. / Falick, A.M. / King, D.S. / Alber, T.
History
DepositionSep 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 18, 2017Group: Database references
Revision 1.3Sep 6, 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_ncs_dom_lim / 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_auth_seq_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_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 / _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: Serine/threonine protein kinase
B: Serine/threonine protein kinase
C: Serine/threonine protein kinase
D: Serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,61516
Polymers134,0824
Non-polymers2,53212
Water16,340907
1
A: Serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1544
Polymers33,5211
Non-polymers6333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1544
Polymers33,5211
Non-polymers6333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1544
Polymers33,5211
Non-polymers6333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1544
Polymers33,5211
Non-polymers6333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.931, 51.544, 141.409
Angle α, β, γ (deg.)90.00, 106.62, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 4 / Auth seq-ID: 10 - 289 / Label seq-ID: 13 - 292

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

-
Components

#1: Protein
Serine/threonine protein kinase


Mass: 33520.605 Da / Num. of mol.: 4 / Fragment: Kinase domain (UNP residues 1 to 308) / Mutation: L33D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MRA_0016, pknB, PknB (Rv0014c) / Production host: Escherichia coli (E. coli) / References: UniProt: A5TY84, UniProt: P9WI81*PLUS
#2: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 907 / 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: 2.11 Å3/Da / Density % sol: 41.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.5
Details: 25% PEG 3350, 100mM Tris pH 8.5, 200mM (NH4)2SO4, VAPOR DIFFUSION, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 1, 2004
RadiationMonochromator: Y / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11591
21.1161
ReflectionResolution: 2→20 Å / Num. all: 75618 / Num. obs: 75618 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 11.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0 / Mean I/σ(I) obs: 2.25 / % possible all: 97.1

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1mru

1mru


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.326 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25794 3895 5.2 %RANDOM
Rwork0.2009 ---
obs0.20396 71720 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20.29 Å2
2---0.32 Å20 Å2
3---0.81 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8085 0 132 907 9124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228385
X-RAY DIFFRACTIONr_bond_other_d0.0010.027623
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.98611460
X-RAY DIFFRACTIONr_angle_other_deg0.844317621
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.83751060
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.59523.441372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.915151258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0311572
X-RAY DIFFRACTIONr_chiral_restr0.0860.21299
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029400
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021624
X-RAY DIFFRACTIONr_nbd_refined0.2180.21776
X-RAY DIFFRACTIONr_nbd_other0.1860.27774
X-RAY DIFFRACTIONr_nbtor_refined0.1770.24113
X-RAY DIFFRACTIONr_nbtor_other0.0860.24960
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.2754
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1390.21
X-RAY DIFFRACTIONr_metal_ion_refined0.2350.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1230.234
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.2134
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8071.55511
X-RAY DIFFRACTIONr_mcbond_other0.1991.52136
X-RAY DIFFRACTIONr_mcangle_it1.15828580
X-RAY DIFFRACTIONr_scbond_it1.8633242
X-RAY DIFFRACTIONr_scangle_it2.874.52880
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3877 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.390.5
2Bmedium positional0.410.5
3Cmedium positional0.390.5
4Dmedium positional0.410.5
1Amedium thermal0.472
2Bmedium thermal0.482
3Cmedium thermal0.52
4Dmedium thermal0.462
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.243 5384 -
Rfree-0 -
obs--100 %
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)
12.08230.45680.08173.07620.93361.2845-0.08840.12840.104-0.43690.0210.1384-0.1417-0.11590.06740.0304-0.0078-0.0106-0.0654-0.0067-0.0873-23.46934.229111.476
21.7324-0.06520.24051.3791-0.05620.65060.0122-0.0582-0.06-0.05270.01970.00030.0439-0.0344-0.0319-0.0488-0.04880.0073-0.03190.0012-0.0485-9.99716.726124.788
32.083-0.59540.11843.13071.07811.271-0.1132-0.1709-0.06740.34160.05960.08010.1405-0.13370.05360.00060.00440.0088-0.07570.002-0.0901-2.26315.44590.753
41.75910.0067-0.13151.4431-0.22660.9876-0.01210.07580.07690.02940.04590.0225-0.0627-0.0079-0.0337-0.0640.03640.0045-0.0565-0.0006-0.049310.38532.90378.538
52.07440.175-0.44242.05011.25562.2636-0.04030.0168-0.03380.3069-0.01360.07210.1227-0.35390.05380.07110.0142-0.0114-0.04760.0096-0.0988-43.35414.60491.571
61.32320.3343-0.23291.4582-0.08380.65920.02240.08650.07070.04560.0246-0.0197-0.0768-0.1121-0.047-0.0560.0457-0.0046-0.0539-0.0082-0.0563-30.46632.08278.426
72.1078-0.45220.73772.31421.89272.1555-0.02130.07360.064-0.3416-0.01420.1439-0.2003-0.26490.03540.0554-0.0325-0.0118-0.02070.0301-0.1047-63.78835.041111.336
81.2703-0.28120.28881.4159-0.14740.62490.0077-0.0746-0.0499-0.0430.03610.0180.088-0.1161-0.0438-0.0561-0.0528-0.0035-0.0396-0.0078-0.0525-50.74317.481124.807
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 96
2X-RAY DIFFRACTION2A97 - 285
3X-RAY DIFFRACTION3B11 - 96
4X-RAY DIFFRACTION4B97 - 285
5X-RAY DIFFRACTION5C11 - 96
6X-RAY DIFFRACTION6C97 - 285
7X-RAY DIFFRACTION7D11 - 96
8X-RAY DIFFRACTION8D97 - 285

+
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