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- PDB-3zeu: Structure of a Salmonella typhimurium YgjD-YeaZ heterodimer bound... -

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Basic information

Entry
Database: PDB / ID: 3zeu
TitleStructure of a Salmonella typhimurium YgjD-YeaZ heterodimer bound to ATPgammaS
Components
  • PROBABLE TRNA THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN GCP
  • PUTATIVE M22 PEPTIDASE YEAZ
KeywordsHYDROLASE / NUCLEOTIDE BINDING
Function / homology
Function and homology information


N6-L-threonylcarbamoyladenine synthase / tRNA N(6)-L-threonylcarbamoyladenine synthase activity / tRNA threonylcarbamoyladenosine modification / iron ion binding / nucleotide binding / cytoplasm / cytosol
Similarity search - Function
tRNA N6-adenosine threonylcarbamoyltransferase, TsaD / tRNA threonylcarbamoyl adenosine modification protein TsaB / 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 ...tRNA N6-adenosine threonylcarbamoyltransferase, TsaD / tRNA threonylcarbamoyl adenosine modification protein TsaB / 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-5'-DIPHOSPHATE / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / tRNA threonylcarbamoyladenosine biosynthesis protein TsaB / tRNA N6-adenosine threonylcarbamoyltransferase / tRNA N6-adenosine threonylcarbamoyltransferase
Similarity search - Component
Biological speciesSALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.653 Å
AuthorsNichols, C.E. / Lamb, H.K. / Thompson, P. / El Omari, K. / Lockyer, M. / Charles, I. / Hawkins, A.R. / Stammers, D.K.
CitationJournal: Protein Sci. / Year: 2013
Title: Crystal Structure of the Dimer of Two Essential Salmonella Typhimurium Proteins, Ygjd & Yeaz and Calorimetric Evidence for the Formation of a Ternary Ygjd-Yeaz-Yjee Complex.
Authors: Nichols, C.E. / Lamb, H.K. / Thompson, P. / Omari, K.E. / Lockyer, M. / Charles, I. / Hawkins, A.R. / Stammers, D.K.
History
DepositionDec 7, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2Mar 29, 2017Group: Atomic model / Database references / Structure summary
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: PUTATIVE M22 PEPTIDASE YEAZ
B: PROBABLE TRNA THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN GCP
D: PUTATIVE M22 PEPTIDASE YEAZ
E: PROBABLE TRNA THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN GCP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,23518
Polymers121,9644
Non-polymers2,27114
Water15,529862
1
D: PUTATIVE M22 PEPTIDASE YEAZ
E: PROBABLE TRNA THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN GCP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0828
Polymers60,9822
Non-polymers1,1006
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-104.3 kcal/mol
Surface area21770 Å2
MethodPISA
2
A: PUTATIVE M22 PEPTIDASE YEAZ
B: PROBABLE TRNA THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN GCP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,15310
Polymers60,9822
Non-polymers1,1718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-123 kcal/mol
Surface area21800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.214, 68.084, 87.624
Angle α, β, γ (deg.)107.66, 92.63, 116.45
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 4 molecules ADBE

#1: Protein PUTATIVE M22 PEPTIDASE YEAZ / YEAZ


Mass: 25000.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
Strain: STRAIN 4/74 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: E8X8J1
#2: Protein PROBABLE TRNA THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN GCP / T(6)A37 THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN / YGJD


Mass: 35981.348 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: TITLE STRUCTURE OF A SALMONELLA TYPHIMURIUM YGJD-YEAZ HETERODIMER BOUND TO ATPGAMMAS
Source: (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: E8XBD7, UniProt: P40731*PLUS

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Non-polymers , 6 types, 876 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#7: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 862 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 51.2 % / Description: NONE
Crystal growpH: 8
Details: 16% PEG3350, 0.1M TRIS PH8.0, 0.2M AMMONIUM SULPHATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9755
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9755 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 135840 / % possible obs: 96.4 % / Observed criterion σ(I): 2.5 / Redundancy: 6 % / Biso Wilson estimate: 14.65 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 31.2
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.5 / % possible all: 87.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8_1069)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.653→29.085 Å / SU ML: 0.15 / σ(F): 1.97 / Phase error: 18.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1863 6812 5 %
Rwork0.159 --
obs0.1604 135337 95.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.653→29.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8459 0 126 862 9447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079123
X-RAY DIFFRACTIONf_angle_d1.14712477
X-RAY DIFFRACTIONf_dihedral_angle_d12.8753319
X-RAY DIFFRACTIONf_chiral_restr0.0741401
X-RAY DIFFRACTIONf_plane_restr0.0051621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6528-1.67160.26871520.253112X-RAY DIFFRACTION70
1.6716-1.69120.23542040.24353854X-RAY DIFFRACTION86
1.6912-1.71190.25892260.23264203X-RAY DIFFRACTION94
1.7119-1.73350.26411940.2284243X-RAY DIFFRACTION95
1.7335-1.75630.25692490.21254245X-RAY DIFFRACTION95
1.7563-1.78040.24132210.20984266X-RAY DIFFRACTION96
1.7804-1.80580.23992130.2034275X-RAY DIFFRACTION95
1.8058-1.83280.22182170.18874282X-RAY DIFFRACTION96
1.8328-1.86140.22512500.18354248X-RAY DIFFRACTION96
1.8614-1.89190.20042520.17444323X-RAY DIFFRACTION96
1.8919-1.92450.19422220.16334240X-RAY DIFFRACTION96
1.9245-1.95950.21582480.16364312X-RAY DIFFRACTION97
1.9595-1.99720.18532290.1554334X-RAY DIFFRACTION97
1.9972-2.0380.17132470.14784324X-RAY DIFFRACTION97
2.038-2.08230.17662350.14994323X-RAY DIFFRACTION97
2.0823-2.13070.19532240.1534393X-RAY DIFFRACTION97
2.1307-2.1840.18772600.15114304X-RAY DIFFRACTION97
2.184-2.2430.19942360.15414308X-RAY DIFFRACTION98
2.243-2.3090.20072120.15514394X-RAY DIFFRACTION98
2.309-2.38350.20072090.15164428X-RAY DIFFRACTION98
2.3835-2.46860.18642180.15114356X-RAY DIFFRACTION98
2.4686-2.56740.1822310.15264385X-RAY DIFFRACTION98
2.5674-2.68420.19662260.15724426X-RAY DIFFRACTION98
2.6842-2.82560.18092400.16044400X-RAY DIFFRACTION98
2.8256-3.00240.19172390.16214373X-RAY DIFFRACTION98
3.0024-3.2340.18472350.1624437X-RAY DIFFRACTION99
3.234-3.55890.16852210.15174417X-RAY DIFFRACTION99
3.5589-4.07270.16672280.13644447X-RAY DIFFRACTION99
4.0727-5.12660.14052400.13074431X-RAY DIFFRACTION99
5.1266-29.090.1512340.15264442X-RAY DIFFRACTION99

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