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- PDB-4d4p: Crystal Structure of the Kti11 Kti13 heterodimer Spacegroup P65 -

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Basic information

Entry
Database: PDB / ID: 4d4p
TitleCrystal Structure of the Kti11 Kti13 heterodimer Spacegroup P65
ComponentsPROTEIN ATS1, DIPHTHAMIDE BIOSYNTHESIS PROTEIN 3
KeywordsTRANSLATION / KTI11 / KTI13 / TRNA MODIFICATION / ELONGATOR / DIPHTHAMIDE MODIFICATION
Function / homology
Function and homology information


2-(3-amino-3-carboxypropyl)histidine synthase activity / oxidoreductase activity, acting on iron-sulfur proteins as donors / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / Synthesis of diphthamide-EEF2 / tRNA wobble uridine modification / iron chaperone activity / protein histidyl modification to diphthamide / ferrous iron binding / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process ...2-(3-amino-3-carboxypropyl)histidine synthase activity / oxidoreductase activity, acting on iron-sulfur proteins as donors / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / Synthesis of diphthamide-EEF2 / tRNA wobble uridine modification / iron chaperone activity / protein histidyl modification to diphthamide / ferrous iron binding / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / iron ion binding / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Microbial ribonuclease fold / DPH Zinc finger / DPH-type metal-binding domain / DPH-type metal-binding domain superfamily / CSL zinc finger / DPH-type metal-binding (MB) domain profile. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 ...Microbial ribonuclease fold / DPH Zinc finger / DPH-type metal-binding domain / DPH-type metal-binding domain superfamily / CSL zinc finger / DPH-type metal-binding (MB) domain profile. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Roll / Alpha Beta
Similarity search - Domain/homology
: / Protein KTI13 / Diphthamide biosynthesis protein 3
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.999 Å
AuthorsGlatt, S. / Mueller, C.W.
CitationJournal: Structure / Year: 2015
Title: Structure of the Kti11/Kti13 Heterodimer and its Double Role in Modifications of tRNA and Eukaryotic Elongation Factor 2.
Authors: Glatt, S. / Zabel, R. / Vonkova, I. / Kumar, A. / Netz, D.J. / Pierik, A.J. / Rybin, V. / Lill, R. / Gavin, A. / Balbach, J. / Breunig, K.D. / Muller, C.W.
History
DepositionOct 30, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Source and taxonomy
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / diffrn_source
Item: _diffrn_detector.type / _diffrn_source.pdbx_synchrotron_site
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN ATS1, DIPHTHAMIDE BIOSYNTHESIS PROTEIN 3
B: PROTEIN ATS1, DIPHTHAMIDE BIOSYNTHESIS PROTEIN 3
C: PROTEIN ATS1, DIPHTHAMIDE BIOSYNTHESIS PROTEIN 3
E: PROTEIN ATS1, DIPHTHAMIDE BIOSYNTHESIS PROTEIN 3
G: PROTEIN ATS1, DIPHTHAMIDE BIOSYNTHESIS PROTEIN 3
H: PROTEIN ATS1, DIPHTHAMIDE BIOSYNTHESIS PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,89215
Polymers280,1886
Non-polymers7049
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13610 Å2
ΔGint-97.1 kcal/mol
Surface area65800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.060, 152.060, 203.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
PROTEIN ATS1, DIPHTHAMIDE BIOSYNTHESIS PROTEIN 3 / ALPHA-TUBULIN SUPPRESSOR 1 / KLUYVEROMYCES LACTIS TOXIN-INSENSITIVE PROTEIN 11


Mass: 46698.074 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PSTAR RARE / References: UniProt: P31386, UniProt: Q3E840
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
Sequence detailsFUSION PROTEIN OF KTI13 (UNIPROT ID P31386, RESIDUES A1- A333) AND KTI11 (UNIPROT ID Q3E840, ...FUSION PROTEIN OF KTI13 (UNIPROT ID P31386, RESIDUES A1- A333) AND KTI11 (UNIPROT ID Q3E840, RESIDUES A344-A417) USING A GSGSGSGSGS LINKER (RESIDUES A334-A343), LINKER ORDERED FUSION PROTEIN OF KTI13 (UNIPROT ID P31386, RESIDUES G1- G333) AND KTI11 (UNIPROT ID Q3E840, RESIDUES G344-G417) USING A GSGSGSGSGS LINKER (RESIDUES G334-G343), LINKER ORDERED FUSION PROTEIN OF KTI13 (UNIPROT ID P31386, RESIDUES B1- B333) AND KTI11 (UNIPROT ID Q3E840, RESIDUES H344-H417) USING A GSGSGSGSGS LINKER (RESIDUES B334,B335,H343), LINKER PARTIALLY DISORDERED FUSION PROTEIN OF KTI13 (UNIPROT ID P31386, RESIDUES E1- E333) AND KTI11 (UNIPROT ID Q3E840, RESIDUES C344-C417) USING A GSGSGSGSGS LINKER (RESIDUES E334,C343), LINKER PARTIALLY DISORDERED

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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: 2.43 Å3/Da / Density % sol: 49.34 % / Description: NONE
Crystal growDetails: 100 MM TRIS PH 8.4, 2 M LI2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97626
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 53195 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 11.39 % / Biso Wilson estimate: 95.35 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 17.05
Reflection shellResolution: 3→3.08 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 1.23 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.999→110.614 Å / SU ML: 0.38 / σ(F): 1.38 / Phase error: 24.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2337 2660 5 %
Rwork0.2079 --
obs0.2092 53186 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.999→110.614 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12686 0 29 0 12715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313007
X-RAY DIFFRACTIONf_angle_d0.55917651
X-RAY DIFFRACTIONf_dihedral_angle_d11.1234675
X-RAY DIFFRACTIONf_chiral_restr0.0381854
X-RAY DIFFRACTIONf_plane_restr0.0052351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.999-3.05360.38511300.352475X-RAY DIFFRACTION93
3.0536-3.11230.36511400.32042654X-RAY DIFFRACTION100
3.1123-3.17590.31241410.30462675X-RAY DIFFRACTION100
3.1759-3.24490.32651390.29732655X-RAY DIFFRACTION100
3.2449-3.32040.27791400.26962645X-RAY DIFFRACTION100
3.3204-3.40340.28541400.24912668X-RAY DIFFRACTION100
3.4034-3.49550.25011400.24112659X-RAY DIFFRACTION100
3.4955-3.59830.25091400.22422662X-RAY DIFFRACTION100
3.5983-3.71450.22141410.21022673X-RAY DIFFRACTION100
3.7145-3.84730.2341390.19742655X-RAY DIFFRACTION100
3.8473-4.00130.22911420.19732683X-RAY DIFFRACTION100
4.0013-4.18340.21261400.19612661X-RAY DIFFRACTION100
4.1834-4.4040.23361390.17812649X-RAY DIFFRACTION100
4.404-4.67990.20791410.17252679X-RAY DIFFRACTION100
4.6799-5.04120.19061420.16842688X-RAY DIFFRACTION100
5.0412-5.54850.20761400.18252662X-RAY DIFFRACTION100
5.5485-6.35140.23891410.2012692X-RAY DIFFRACTION100
6.3514-8.00170.24921410.20652681X-RAY DIFFRACTION100
8.0017-110.68960.21121440.21362710X-RAY DIFFRACTION100

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