[English] 日本語
Yorodumi
- PDB-5wsc: Crystal of pyruvate kinase (PYK) from Mycobacterium tuberculosis ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wsc
TitleCrystal of pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate, soaked with allosteric activators AMP and Glucose 6-Phosphate
ComponentsPyruvate kinase
KeywordsTRANSFERASE / pyruvate kinase / glycolysis / tetramer / allostery / synergism / phospho transferase
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / potassium ion binding / glycolytic process / kinase activity / magnesium ion binding / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily ...Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / 6-O-phosphono-alpha-D-glucopyranose / : / OXALATE ION / PHOSPHATE ION / Pyruvate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsZhong, W. / Cai, Q. / El Sahili, A. / Lescar, J. / Dedon, P.C.
Funding support Singapore, 2items
OrganizationGrant numberCountry
National Research FoundationS916137 Singapore
Singapore-MIT Alliance for Research and Technology (SMART) FellowshipS900184 Singapore
CitationJournal: Nat Commun / Year: 2017
Title: Allosteric pyruvate kinase-based "logic gate" synergistically senses energy and sugar levels in Mycobacterium tuberculosis.
Authors: Zhong, W. / Cui, L. / Goh, B.C. / Cai, Q. / Ho, P. / Chionh, Y.H. / Yuan, M. / Sahili, A.E. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D. / Lescar, J. / Dedon, P.C.
History
DepositionDec 6, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pyruvate kinase
B: Pyruvate kinase
C: Pyruvate kinase
D: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,16523
Polymers204,0574
Non-polymers3,10819
Water6,035335
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17040 Å2
ΔGint-124 kcal/mol
Surface area66030 Å2
Unit cell
Length a, b, c (Å)124.370, 124.370, 144.192
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 2 - 472 / Label seq-ID: 5 - 475

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
2
1
3
4
5
6

-
Components

-
Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Pyruvate kinase / PK


Mass: 51014.336 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: pyk, pykA, Rv1617, MTCY01B2.09 / Plasmid: pYUB28b-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WKE5, pyruvate kinase
#3: Sugar
ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 6 types, 350 molecules

#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2O4
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 3.16 Å3/Da / Density % sol: 61.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 12% PEG 8000, 20% glycerol, 50 mM triethanolamine-HCl (TEA) buffer pH 7.2, 100 mM KCl, 50 mM MgCl2, 5 mM oxalate, 5 mM ATP, 5 mM AMP, 5 mM D-glucose 6-phosphate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.245
11-K, -H, -L20.248
11-h,-k,l30.254
11K, H, -L40.253
ReflectionResolution: 2.4→53.85 Å / Num. obs: 97539 / % possible obs: 100 % / Redundancy: 5.5 % / Net I/σ(I): 8.3
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 1.6 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WRP

5wrp


Resolution: 2.4→53.85 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.792 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.047 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22696 4790 4.9 %RANDOM
Rwork0.1793 ---
obs0.18162 92706 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.566 Å2
Baniso -1Baniso -2Baniso -3
1-10.11 Å20 Å20 Å2
2--10.11 Å20 Å2
3----20.23 Å2
Refinement stepCycle: 1 / Resolution: 2.4→53.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14172 0 195 335 14702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01914564
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214068
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.98819804
X-RAY DIFFRACTIONr_angle_other_deg0.714332420
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.65951880
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.66623.243592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.274152448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.43215148
X-RAY DIFFRACTIONr_chiral_restr0.0990.22380
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02116168
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022808
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_it1.5791.9767532
X-RAY DIFFRACTIONr_mcbond_other1.5791.9767531
X-RAY DIFFRACTIONr_mcangle_it2.1152.9629408
X-RAY DIFFRACTIONr_mcangle_other2.1142.9629409
X-RAY DIFFRACTIONr_scbond_it1.5892.0227032
X-RAY DIFFRACTIONr_scbond_other1.5832.027004
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0883.01110361
X-RAY DIFFRACTIONr_long_range_B_refined2.77338.06361662
X-RAY DIFFRACTIONr_long_range_B_other2.77138.05761509
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)
11A295240.08
12B295240.08
21A291900.08
22C291900.08
31A291660.08
32D291660.08
41B292160.09
42C292160.09
51B291060.09
52D291060.09
61C293980.07
62D293980.07
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.464 313 -
Rwork0.425 6814 -
obs--99.65 %
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)
10.4484-0.14310.48030.1862-0.27111.16270.07560.0609-0.0379-0.0237-0.1058-0.11820.06610.12090.03010.08780.0335-0.02310.07880.05840.1342-13.8879-52.594430.9786
21.06560.1478-0.2441.1113-0.68521.75260.06440.12780.0521-0.1213-0.03550.06190.0783-0.0332-0.02880.07160.0096-0.01240.0415-0.00530.0734-28.4073-72.30478.6781
30.870.1021-0.0340.7335-0.12460.83910.04180.0086-0.0009-0.0262-0.0330.0331-0.0003-0.0383-0.00890.0820.0455-0.01980.028-0.01150.0058-24.2505-48.880119.8666
40.6733-0.58890.10191.7102-0.44221.4595-0.0136-0.11650.04710.08170.0082-0.0996-0.05640.03670.00540.09190.03320.00160.0438-0.00060.0339-23.6821-27.895135.0214
50.17690.27210.08340.95320.41211.0358-0.02820.0174-0.15560.08250.0341-0.06680.1521-0.0093-0.00590.10290.04930.04220.0474-0.02520.1974-9.6341-50.1469-17.4578
61.1447-0.432-0.48280.84810.12431.5769-0.0073-0.10070.05980.1392-0.01860.03-0.030.09210.02590.06690.0129-0.00250.0697-0.00640.055314.7354-47.39144.6598
71.00270.056-0.1250.6515-0.01580.9897-0.02610.00060.02670.04980.021-0.0453-0.03020.00680.00510.08190.0502-0.01020.032-0.0050.0046-7.7238-39.333-6.4861
80.7552-0.6632-0.28781.33940.33661.34560.01150.0977-0.0404-0.10140.00590.0822-0.0288-0.0731-0.01740.0730.0441-0.0010.07150.00850.0374-26.1571-29.2684-21.6698
91.40020.1934-0.6330.30740.43071.31520.0578-0.04510.22580.0215-0.09130.1045-0.0963-0.14140.03350.14520.03450.02120.0622-0.01380.0626-46.868916.008431.0264
100.41440.21130.60550.43740.05851.1120.0310.0514-0.06970.13430.032-0.014-0.04290.1264-0.0630.11230.01310.02160.11740.03250.1296-35.40935.50138.2508
110.4607-0.28890.24290.38190.06571.07160.0033-0.0110.04450.0147-0.0024-0.068-0.04670.0864-0.00090.09250.02420.0350.02990.02210.0554-36.897212.193919.6231
120.5236-0.55750.18231.7237-0.06521.03570.033-0.0835-0.00750.14990.00670.07120.0196-0.0225-0.03970.11890.02390.01270.0408-0.00350.0234-36.984-8.580635.1322
130.50.45140.2510.9169-0.5981.4781-0.05840.00030.16280.04220.00460.1598-0.162-0.03080.05380.10320.05110.00360.07680.01160.0658-52.677212.6752-17.5493
140.52210.24420.13120.66660.65641.43450.06390.1627-0.0267-0.06570.0102-0.0610.1028-0.1383-0.07410.12740.0170.02890.09830.01720.0941-75.329112.36725.1331
150.56520.06650.32840.85390.02830.9986-0.00610.0028-0.03220.0049-0.00170.08210.0487-0.08820.00790.06640.04170.03150.04890.01190.0388-54.31562.1462-6.1934
161.179-0.7082-0.00391.3331-0.08351.15220.04560.15470.0625-0.1242-0.0336-0.0605-0.02880.0389-0.01210.08980.04950.00450.06090.00280.0197-36.3014-8.2793-21.7471
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 70
2X-RAY DIFFRACTION2A71 - 167
3X-RAY DIFFRACTION3A168 - 344
4X-RAY DIFFRACTION4A345 - 467
5X-RAY DIFFRACTION5B2 - 70
6X-RAY DIFFRACTION6B71 - 167
7X-RAY DIFFRACTION7B168 - 344
8X-RAY DIFFRACTION8B345 - 467
9X-RAY DIFFRACTION9C2 - 70
10X-RAY DIFFRACTION10C71 - 167
11X-RAY DIFFRACTION11C168 - 344
12X-RAY DIFFRACTION12C345 - 467
13X-RAY DIFFRACTION13D2 - 70
14X-RAY DIFFRACTION14D71 - 167
15X-RAY DIFFRACTION15D168 - 344
16X-RAY DIFFRACTION16D345 - 467

+
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