[English] 日本語
Yorodumi
- PDB-3tlx: Crystal Structure of PF10_0086, adenylate kinase from plasmodium ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tlx
TitleCrystal Structure of PF10_0086, adenylate kinase from plasmodium falciparum
ComponentsAdenylate kinase 2
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC / Rossmann fold / ATP binding / phosphorylation
Function / homology
Function and homology information


Factors involved in megakaryocyte development and platelet production / Interconversion of nucleotide di- and triphosphates / adenylate kinase / AMP kinase activity / generation of precursor metabolites and energy / mitochondrion / ATP binding / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2370 / Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / Adenylate kinase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2370 / Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / Adenylate kinase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE MONOPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Adenylate kinase 1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsWernimont, A.K. / Loppnau, P. / Crombet, L. / Weadge, J. / Perieteanu, A. / Edwards, A.M. / Arrowsmith, C.H. / Park, H. / Bountra, C. / Hui, R. ...Wernimont, A.K. / Loppnau, P. / Crombet, L. / Weadge, J. / Perieteanu, A. / Edwards, A.M. / Arrowsmith, C.H. / Park, H. / Bountra, C. / Hui, R. / Amani, M. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of PF10_0086, adenylate kinase from plasmodium falciparum
Authors: Wernimont, A.K. / Loppnau, P. / Crombet, L. / Weadge, J. / Perieteanu, A. / Edwards, A.M. / Arrowsmith, C.H. / Park, H. / Bountra, C. / Hui, R. / Amani, M.
History
DepositionAug 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Structure summary
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Adenylate kinase 2
B: Adenylate kinase 2
C: Adenylate kinase 2
D: Adenylate kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,03211
Polymers110,8474
Non-polymers2,1857
Water00
1
A: Adenylate kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5355
Polymers27,7121
Non-polymers8234
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adenylate kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5663
Polymers27,7121
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Adenylate kinase 2


Theoretical massNumber of molelcules
Total (without water)27,7121
Polymers27,7121
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Adenylate kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2192
Polymers27,7121
Non-polymers5071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.395, 76.663, 93.768
Angle α, β, γ (deg.)90.00, 100.78, 90.00
Int Tables number4
Space group name H-MP1211
DetailsRuns as a higher species, on gel filtration. The crystal packing shows a tetramer linked at the N-terminus.

-
Components

#1: Protein
Adenylate kinase 2


Mass: 27711.834 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: Q7Z0H0, adenylate kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 3350, 0.2 M Ammonium Acetate, 0.1 M Hepes, 5 mM ADP, 5 mM MgCl2, 0.3 mM glyglyglycine, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.75→35 Å / Num. all: 29714 / Num. obs: 29685 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 75.59 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.75-2.84.20.6352.1751100
2.8-2.854.20.5892.2751100
2.85-2.94.20.5332.61100
2.9-2.964.20.4251100
2.96-3.034.20.361100
3.03-3.14.20.3171100
3.1-3.174.20.2251100
3.17-3.264.20.1781100
3.26-3.364.20.1461100
3.36-3.464.20.1231100
3.46-3.594.20.1121100
3.59-3.734.20.0961100
3.73-3.94.20.081100
3.9-4.114.20.071100
4.11-4.364.20.0661100
4.36-4.74.10.0641100
4.7-5.174.10.063199.9
5.17-5.9240.059199.9
5.92-7.4440.0481100
7.44-353.90.039198.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→34.56 Å / Cor.coef. Fo:Fc: 0.9204 / Cor.coef. Fo:Fc free: 0.8894 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: MOLECULAR REPLACEMENT WAS SUCCESSFUL IN FINDING TWO OF FOUR MOLECULES IN THE ASYMMETRIC UNIT, WHICH REFINE WELL AND HAD INTERPRETABLE ELECTRON DENSITY THAT MATCHED THE QUALITY AND RESOLUTION ...Details: MOLECULAR REPLACEMENT WAS SUCCESSFUL IN FINDING TWO OF FOUR MOLECULES IN THE ASYMMETRIC UNIT, WHICH REFINE WELL AND HAD INTERPRETABLE ELECTRON DENSITY THAT MATCHED THE QUALITY AND RESOLUTION OF THE DATA. TWO ADDITIONAL MOLECULES WERE FOUND BY HAND BUILDING INTO SEVERAL AREAS OF ADDITIONAL POSITIVE DENSITY AND TRANSFORMING PARTS OF MOLECULE A ONTO THE BUILT PARTIAL MODEL. NCS AND STRICT GEOMETRIC RESTRAINTS WERE USED THROUGHOUT REFINEMENT AFTER THIS. THE AUTHORS BELIEVE THAT THE POOR DENSITY FOR C AND D ARE DUE TO MARGINAL CRYSTAL PACKING.
RfactorNum. reflection% reflectionSelection details
Rfree0.2596 1503 5.07 %RANDOM
Rwork0.2255 ---
obs0.2272 29652 --
all-29681 --
Displacement parametersBiso mean: 100.31 Å2
Baniso -1Baniso -2Baniso -3
1-15.8282 Å20 Å2-2.4215 Å2
2--7.021 Å20 Å2
3----22.8492 Å2
Refine analyzeLuzzati coordinate error obs: 0.521 Å
Refinement stepCycle: LAST / Resolution: 2.75→34.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5630 0 137 0 5767
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015916HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.188099HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1778SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes123HARMONIC2
X-RAY DIFFRACTIONt_gen_planes897HARMONIC5
X-RAY DIFFRACTIONt_it5742HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.47
X-RAY DIFFRACTIONt_other_torsion22.38
X-RAY DIFFRACTIONt_improper_torsion24HARMONIC0
X-RAY DIFFRACTIONt_chiral_improper_torsion826SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6540SEMIHARMONIC4
LS refinement shellResolution: 2.75→2.85 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2788 150 5.22 %
Rwork0.2345 2725 -
all0.2367 2875 -
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)
16.61440.7404-0.30793.4554-0.63142.12490.06720.4276-0.4602-0.2978-0.11860.17840.105-0.15820.0513-0.32620.00710.0501-0.26750.00910.09270.362-13.7617-2.5329
23.71-2.0605-0.22236.22531.07521.66460.1794-0.06830.16840.0584-0.058-0.70170.0449-0.0864-0.1213-0.1902-0.01130.0117-0.31640.05390.152437.7743-2.43122.6111
33.5882-0.8499-1.706501.423310.0322-0.2335-0.29010.4316-0.2055-0.28910.01010.0163-0.19360.52260.08080.15150.1094-0.27180.0907-0.18371.27148.341452.0197
41.77430.0037-1.78370-0.81813.16270.0085-0.4136-0.036-0.33410.310.30450.40031.0293-0.31850.26550.1854-0.06120.1025-0.0573-0.415522.5952-14.061256.4835
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A8 - 242
2X-RAY DIFFRACTION2{ B|* }B3 - 242
3X-RAY DIFFRACTION3{ C|* }C3 - 241
4X-RAY DIFFRACTION4{ D|* }D6 - 242

+
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