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

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Basic information

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


N6-L-threonylcarbamoyladenine synthase / N(6)-L-threonylcarbamoyladenine synthase activity / tRNA threonylcarbamoyladenosine modification / iron ion binding / nucleotide binding / cytosol / cytoplasm
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 MONOPHOSPHATE / : / tRNA threonylcarbamoyladenosine biosynthesis protein TsaB / tRNA N6-adenosine threonylcarbamoyltransferase
Similarity search - Component
Biological speciesSALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM STR. ST4/74 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 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 1.2Nov 13, 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_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.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_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: PUTATIVE M22 PEPTIDASE YEAZ
B: PROBABLE TRNA THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN GCP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1125
Polymers60,4892
Non-polymers6233
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-37.7 kcal/mol
Surface area23150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.152, 61.663, 83.835
Angle α, β, γ (deg.)90.00, 101.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein PUTATIVE M22 PEPTIDASE YEAZ / YEAZ


Mass: 24507.877 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM STR. ST4/74 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: E8X8J1
#2: Protein PROBABLE TRNA THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN GCP / YGJD / T(6)A37 THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN


Mass: 35981.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: TITLE STRUCTURE OF A SALMONELLA TYPHIMURIUM YGJD-YEAZ HETERODIMER.
Source: (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM STR. ST4/74 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: E8XBD7

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Non-polymers , 4 types, 210 molecules

#3: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 8
Details: 20 GLYCEROL, 16 POLYETHYLENE GLYCOL 8000, 0.080 M SODIUM CACODYLATE PH 6.5, 0.160 M MAGNESIUM ACETATE, 20 MM CADMIUM CHLORIDE DIHYDRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9801
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 26090 / % possible obs: 96.7 % / Observed criterion σ(I): 5.2 / Redundancy: 4 % / Biso Wilson estimate: 32.5 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 25.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 5.2 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→34.38 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.9018 / SU R Cruickshank DPI: 0.307 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.309 / SU Rfree Blow DPI: 0.224 / SU Rfree Cruickshank DPI: 0.227
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CD. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=4460. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CD. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=4460. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=1.
RfactorNum. reflection% reflectionSelection details
Rfree0.2347 1316 5.07 %RANDOM
Rwork0.1781 ---
obs0.1811 25974 96.74 %-
Displacement parametersBiso mean: 29.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.971 Å20 Å2-3.5039 Å2
2---1.9195 Å20 Å2
3---2.8905 Å2
Refine analyzeLuzzati coordinate error obs: 0.268 Å
Refinement stepCycle: LAST / Resolution: 2.31→34.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4219 0 35 207 4461
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014338HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.035890HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1981SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes93HARMONIC2
X-RAY DIFFRACTIONt_gen_planes655HARMONIC5
X-RAY DIFFRACTIONt_it4338HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.12
X-RAY DIFFRACTIONt_other_torsion2.84
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion567SEMIHARMONIC5
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_contact5114SEMIHARMONIC4
LS refinement shellResolution: 2.31→2.4 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2843 152 5.02 %
Rwork0.2126 2874 -
all0.2162 3026 -
obs--96.74 %
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)
11.09020.32940.02190.81150.16651.53680.05430.05670.02460.03340.03320.02160.0167-0.0731-0.0874-0.03770.0184-0.0101-0.05470.0227-0.021423.9168-2.367816.0014
20.88940.1806-0.36130.44190.15451.52990.0846-0.105-0.11770.0584-0.0266-0.03470.04080.1565-0.058-0.0394-0.0252-0.0208-0.07110.0095-0.009630.19711.066954.7504
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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