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- PDB-3vew: Crystal structure of the O-carbamoyltransferase TobZ in complex w... -

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Basic information

Entry
Database: PDB / ID: 3vew
TitleCrystal structure of the O-carbamoyltransferase TobZ in complex with ADP
ComponentsO-carbamoyltransferase TobZ
KeywordsTRANSFERASE / antibiotic biosynthesis / substrate assisted catalysis / substrate channeling / adenylation / structural enzymology / enzyme evolution
Function / homology
Function and homology information


nebramycin 5' synthase / tobramycin biosynthetic process / kanamycin biosynthetic process / carboxyl- or carbamoyltransferase activity / ligase activity / hydrolase activity / iron ion binding / ATP binding
Similarity search - Function
Carbamoyltransferase, C-terminal domain / Carbamoyltransferase / Carbamoyltransferase, C-terminal / Carbamoyltransferase, C-terminal domain superfamily / : / Carbamoyltransferase N-terminus / Carbamoyltransferase C-terminus / DHBP synthase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain ...Carbamoyltransferase, C-terminal domain / Carbamoyltransferase / Carbamoyltransferase, C-terminal / Carbamoyltransferase, C-terminal domain superfamily / : / Carbamoyltransferase N-terminus / Carbamoyltransferase C-terminus / DHBP synthase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / nebramycin 5' synthase
Similarity search - Component
Biological speciesStreptoalloteichus tenebrarius (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.352 Å
AuthorsParthier, C. / Stubbs, M.T. / Goerlich, S. / Jaenecke, F.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2012
Title: The O-Carbamoyltransferase TobZ Catalyzes an Ancient Enzymatic Reaction.
Authors: Parthier, C. / Gorlich, S. / Jaenecke, F. / Breithaupt, C. / Brauer, U. / Fandrich, U. / Clausnitzer, D. / Wehmeier, U.F. / Bottcher, C. / Scheel, D. / Stubbs, M.T.
History
DepositionJan 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2012Group: Database references
Revision 1.2May 2, 2012Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 13, 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_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_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

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Assembly

Deposited unit
A: O-carbamoyltransferase TobZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9964
Polymers63,4171
Non-polymers5793
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.022, 98.022, 280.697
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein O-carbamoyltransferase TobZ


Mass: 63417.145 Da / Num. of mol.: 1 / Mutation: F35L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptoalloteichus tenebrarius (bacteria)
Strain: DSM40770T / Gene: tacA, tobZ / Plasmid: pUWL201PW / Production host: Streptomyces lividans (bacteria) / Strain (production host): TK24
References: UniProt: Q70IY1, Transferases; Transferring one-carbon groups; Carboxy- and carbamoyltransferases
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 3.07 Å3/Da / Density % sol: 59.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6 M sodium potassium tartrate, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. all: 34253 / Num. obs: 33813 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 46.047 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 20.08
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.35-2.450.5362.23144643770195.6
2.45-2.550.4363.29165323299199.8
2.55-2.650.3464.16144062872199.5
2.65-2.750.2865.07123062442199.8
2.75-3.120.1688.55333006608199.5
3.12-3.490.08117.38209454149199.6
3.49-3.860.04430.12136662723199.3
3.86-4.230.0342.1992901864199.8
4.23-4.60.02549.7965561323199.4
4.6-100.02155.54209014281198
10-200.01288.781947436193.4
20-300.01580.715346182.1
20-300.01580.7182.1

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
MAR345data collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VEN

3ven


Resolution: 2.352→29.275 Å / Occupancy max: 1 / Occupancy min: 0.37 / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2487 1690 5 %INHERITED FROM 3VEN
Rwork0.2059 ---
obs0.208 33801 99.07 %-
all-34253 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.558 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso max: 106.03 Å2 / Biso mean: 42.7007 Å2 / Biso min: 21.84 Å2
Baniso -1Baniso -2Baniso -3
1-6.5983 Å2-0 Å2-0 Å2
2--6.5983 Å20 Å2
3----13.1965 Å2
Refinement stepCycle: LAST / Resolution: 2.352→29.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4385 0 33 182 4600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084566
X-RAY DIFFRACTIONf_angle_d1.1026234
X-RAY DIFFRACTIONf_chiral_restr0.069677
X-RAY DIFFRACTIONf_plane_restr0.004824
X-RAY DIFFRACTIONf_dihedral_angle_d15.5361665
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.352-2.42160.38131360.31742564270098
2.4216-2.49970.32131420.282526312773100
2.4997-2.5890.32561300.270826422772100
2.589-2.69260.30911440.26426242768100
2.6926-2.8150.32451340.25592639277399
2.815-2.96330.30161460.23362646279299
2.9633-3.14870.28271380.2262673281199
3.1487-3.39150.26051420.221726662808100
3.3915-3.73220.25431400.19626912831100
3.7322-4.27090.19641440.16012715285999
4.2709-5.37540.1951430.160927652908100
5.3754-29.27750.20611510.1912855300696

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