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- PDB-3wuh: Qri7 and AMP complex -

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Basic information

Entry
Database: PDB / ID: 3wuh
TitleQri7 and AMP complex
ComponentstRNA N6-adenosine threonylcarbamoyltransferase, mitochondrial
KeywordsMETAL BINDING PROTEIN / t6A synthesis
Function / homology
Function and homology information


mitochondrial tRNA threonylcarbamoyladenosine modification / N6-L-threonylcarbamoyladenine synthase / tRNA N(6)-L-threonylcarbamoyladenine synthase activity / nucleotidase activity / tRNA threonylcarbamoyladenosine modification / tRNA binding / mitochondrial matrix / mitochondrion / metal ion binding
Similarity search - Function
tRNA N6-adenosine threonylcarbamoyltransferase, TsaD / Peptidase M22, conserved site / Glycoprotease family signature. / Kae1/TsaD family / Gcp-like domain / tRNA N6-adenosine threonylcarbamoyltransferase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / tRNA N6-adenosine threonylcarbamoyltransferase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.937 Å
AuthorsTominaga, T. / Kobayashi, K. / Ishii, R. / Ishitani, R. / Nureki, O.
CitationJournal: ACTA CRYSTALLOGR.,SECT.F / Year: 2014
Title: Structure of Saccharomyces cerevisiae mitochondrial Qri7 in complex with AMP
Authors: Tominaga, T. / Kobayashi, K. / Ishii, R. / Ishitani, R. / Nureki, O.
History
DepositionApr 24, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_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_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_label_asym_id / _struct_ref_seq_dif.details / _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: tRNA N6-adenosine threonylcarbamoyltransferase, mitochondrial
B: tRNA N6-adenosine threonylcarbamoyltransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9976
Polymers85,1722
Non-polymers8254
Water362
1
A: tRNA N6-adenosine threonylcarbamoyltransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9993
Polymers42,5861
Non-polymers4132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: tRNA N6-adenosine threonylcarbamoyltransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9993
Polymers42,5861
Non-polymers4132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: tRNA N6-adenosine threonylcarbamoyltransferase, mitochondrial
hetero molecules

B: tRNA N6-adenosine threonylcarbamoyltransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9976
Polymers85,1722
Non-polymers8254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation21_546z+1/4,y-1/4,-x+7/41
Buried area3510 Å2
ΔGint-24 kcal/mol
Surface area28230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.315, 180.315, 180.315
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein tRNA N6-adenosine threonylcarbamoyltransferase, mitochondrial / t(6)A37 threonylcarbamoyladenosine biosynthesis protein QRI7 / tRNA threonylcarbamoyladenosine ...t(6)A37 threonylcarbamoyladenosine biosynthesis protein QRI7 / tRNA threonylcarbamoyladenosine biosynthesis protein QRI7


Mass: 42585.898 Da / Num. of mol.: 2 / Fragment: UNP residues 30-407
Source method: isolated from a genetically manipulated source
Details: bearing the Turbo3C protease recognition site
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: QRI7, YDL104C, D2366 / Plasmid: modified pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: P43122, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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: 2.87 Å3/Da / Density % sol: 57.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG 400, 3% w/v dextran sulfate sodium salt (Mr 5000), 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.937→50.1 Å / Num. all: 22014 / Num. obs: 22014 / Biso Wilson estimate: 89.19 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.3_1479)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4K25

4k25


Resolution: 2.937→50.01 Å / SU ML: 0.37 / σ(F): 1.35 / Phase error: 29.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2734 1121 5.14 %
Rwork0.2229 --
obs0.2255 21792 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.937→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5229 0 48 2 5279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025377
X-RAY DIFFRACTIONf_angle_d0.6677300
X-RAY DIFFRACTIONf_dihedral_angle_d13.7811918
X-RAY DIFFRACTIONf_chiral_restr0.023855
X-RAY DIFFRACTIONf_plane_restr0.003926
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9371-3.07080.34531300.28542555100
3.0708-3.23260.31121530.26012513100
3.2326-3.43510.27121420.2453252899
3.4351-3.70030.33541340.2305254799
3.7003-4.07250.26591310.2243254999
4.0725-4.66140.23551550.1904254199
4.6614-5.87140.25751580.2108260899
5.8714-50.01760.28141180.2283283099
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)
12.6212-1.4046-0.97176.62660.3611.92460.08830.19210.3098-0.5211-0.0732-0.0921-0.25540.2312-0.00490.4483-0.0381-0.02740.5327-0.04720.6154193.693738.9528168.1962
26.75073.5788-5.92524.6687-1.69667.5043-0.4094-0.36580.4079-0.92140.45710.14550.73871.2472-0.09820.64320.04190.01730.8770.17351.0028189.808455.0921148.5246
31.10710.2419-4.96742.2823-4.10498.47040.4956-0.03350.778-0.0979-0.00180.4548-0.76150.1184-0.37290.6089-0.0418-0.02140.73640.07070.9911188.069861.0284147.6137
43.7732-0.96541.70088.473-1.38653.217-0.14770.30060.0756-0.14020.1859-0.0326-0.15240.4536-0.04150.496-0.0246-0.07050.631-0.10520.6169184.168143.3942168.0204
51.7667-1.11371.04998.3263-0.90823.65220.05110.08-0.0682-0.40930.10350.02670.1652-0.2914-0.15910.482-0.01-0.05330.54040.03860.4641147.06155.3873148.7657
65-0.5365-3.63910.86510.54552.62780.35471.4360.1991-0.65430.10570.0787-0.4789-1.2638-0.27720.93750.0689-0.31581.04870.23980.9296162.714940.3819137.2308
74.0506-0.4905-3.27763.99740.35074.6393-0.1660.749-0.2725-0.39320.1802-0.67710.8062-0.4327-0.08830.7689-0.0665-0.03250.8746-0.02341.0287167.60734.2211138.4325
83.56520.7192-0.03756.64771.84482.30530.164-0.4553-0.29270.2582-0.1386-0.6428-0.19460.1093-0.0260.4360.0013-0.08680.64770.15730.6431153.29253.7023155.8835
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 31:171)
2X-RAY DIFFRACTION2chain 'A' and (resseq 172:254)
3X-RAY DIFFRACTION3chain 'A' and (resseq 255:338)
4X-RAY DIFFRACTION4chain 'A' and (resseq 339:406)
5X-RAY DIFFRACTION5chain 'B' and (resseq 31:171)
6X-RAY DIFFRACTION6chain 'B' and (resseq 172:234)
7X-RAY DIFFRACTION7chain 'B' and (resseq 235:352)
8X-RAY DIFFRACTION8chain 'B' and (resseq 353:406)

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