[English] 日本語
Yorodumi
- PDB-1f3w: RECOMBINANT RABBIT MUSCLE PYRUVATE KINASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1f3w
TitleRECOMBINANT RABBIT MUSCLE PYRUVATE KINASE
ComponentsPYRUVATE KINASE
KeywordsTRANSFERASE / pyruvate kinase / recombinant / muscle isozyme
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / positive regulation of cytoplasmic translation / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum / non-specific protein-tyrosine kinase / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / mRNA binding ...pyruvate kinase / pyruvate kinase activity / positive regulation of cytoplasmic translation / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum / non-specific protein-tyrosine kinase / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / mRNA binding / magnesium ion binding / ATP binding / nucleus
Similarity search - Function
PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain ...PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / 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 / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / : / PYRUVIC ACID / Pyruvate kinase PKM
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsWooll, J.O. / Friesen, R.H.E. / White, M.A. / Watowich, S.J. / Fox, R.O. / Lee, J.C. / Czerwinski, E.W.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Structural and functional linkages between subunit interfaces in mammalian pyruvate kinase.
Authors: Wooll, J.O. / Friesen, R.H. / White, M.A. / Watowich, S.J. / Fox, R.O. / Lee, J.C. / Czerwinski, E.W.
History
DepositionJun 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _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_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: PYRUVATE KINASE
B: PYRUVATE KINASE
C: PYRUVATE KINASE
D: PYRUVATE KINASE
E: PYRUVATE KINASE
F: PYRUVATE KINASE
G: PYRUVATE KINASE
H: PYRUVATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)465,31932
Polymers463,8638
Non-polymers1,45724
Water00
1
A: PYRUVATE KINASE
B: PYRUVATE KINASE
C: PYRUVATE KINASE
D: PYRUVATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,66016
Polymers231,9314
Non-polymers72812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18900 Å2
ΔGint-124 kcal/mol
Surface area69290 Å2
MethodPISA
2
E: PYRUVATE KINASE
F: PYRUVATE KINASE
G: PYRUVATE KINASE
H: PYRUVATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,66016
Polymers231,9314
Non-polymers72812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19090 Å2
ΔGint-124 kcal/mol
Surface area69110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.0, 105.4, 143.5
Angle α, β, γ (deg.)95.9, 92.8, 111.9
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.815384, 0.257957, -0.518274), (0.375937, -0.444871, -0.812872), (-0.440251, -0.857641, 0.265765)12.1489, 1.0177, 5.6776
2given(-0.374687, -0.870548, -0.318993), (-0.859858, 0.197591, 0.470747), (-0.346778, 0.450671, -0.822582)9.3938, 3.4514, 8.369
3given(0.242431, 0.515617, 0.821807), (0.513428, -0.786921, 0.342269), (0.823176, 0.338962, -0.455506)1.2097, -3.8539, 0.553
4given(0.999885, 0.003586, 0.014713), (0.003624, -0.99999, -0.002571), (0.014704, 0.002624, -0.999888)39.0167, 16.4532, 72.8169
5given(-0.825447, 0.25336, -0.504426), (-0.359776, 0.452452, 0.815995), (0.434969, 0.855042, -0.282322)51.0006, 15.3482, 67.4061
6given(-0.38773, -0.858534, -0.335536), (0.857075, -0.201813, -0.474018), (0.339245, -0.471371, 0.814078)48.5517, 13.0709, 64.7632
7given(0.259154, 0.526749, 0.809552), (-0.527534, 0.779313, -0.338199), (-0.809041, -0.339421, 0.479841)40.108, 20.3208, 72.3321
DetailsThe biological assembly is a tetramer of homomonomers

-
Components

#1: Protein
PYRUVATE KINASE


Mass: 57982.820 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Tissue: MUSCLE / Plasmid: PRMPK / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P11974, pyruvate kinase
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H4O3

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 8000, manganese chloride, potassium chloride, sodium pyruvate, succinate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.9 mMsodium pyruvate1drop
21.2 mM1dropMnCl2
30.45 M1dropKCl
430 mMsuccinate adjusted1drop
59-11 %(w/v)PEG80001drop
61.5 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: MAC Science DIP-2000H / Detector: IMAGE PLATE / Date: Aug 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→52 Å / Num. all: 82732 / Num. obs: 82732 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 64.7 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 9.1
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.258 / Num. unique all: 9404 / % possible all: 93.2
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 82.9 % / Mean I/σ(I) obs: 3.1

-
Processing

Software
NameVersionClassification
X-PLORmodel building
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 3→52 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3699007.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Strict non-crystallographic symmetry followed by eight-fold density averaging
RfactorNum. reflection% reflectionSelection details
Rfree0.257 8315 10.1 %RANDOM
Rwork0.238 ---
all0.238 82732 --
obs0.238 82732 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.96 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 52.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å24.73 Å21.14 Å2
2---0.94 Å22.48 Å2
3---0.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 3→52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3958 0 8 0 3966
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.272
X-RAY DIFFRACTIONc_scbond_it2.762
X-RAY DIFFRACTIONc_scangle_it4.092.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3→3.11 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.362 776 9.7 %
Rwork0.366 7204 -
obs--93.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION_PARAM.LINK
X-RAY DIFFRACTION4PYR_PAR.LINK
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 52 Å / σ(F): 0 / % reflection Rfree: 10.1 % / Rfactor obs: 0.239 / Rfactor Rfree: 0.247
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 52.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.362 / % reflection Rfree: 9.7 % / Rfactor Rwork: 0.366

+
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