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- PDB-3vf2: Crystal structure of the O-carbamoyltransferase TobZ M473I varian... -

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Basic information

Entry
Database: PDB / ID: 3vf2
TitleCrystal structure of the O-carbamoyltransferase TobZ M473I variant in complex with carbamoyl phosphate and 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 / Nucleotidyltransferase; domain 5 ...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 / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / : / : / nebramycin 5' synthase
Similarity search - Component
Biological speciesStreptoalloteichus tenebrarius (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 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 1.3Sep 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_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_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)64,0965
Polymers63,4331
Non-polymers6634
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.160, 99.160, 280.919
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: 63433.121 Da / Num. of mol.: 1 / Mutation: M473I
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-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CP / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / Carbamoyl phosphate


Mass: 141.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4NO5P
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 3.14 Å3/Da / Density % sol: 60.86 %
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: Aug 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→29.34 Å / Num. all: 19007 / Num. obs: 18717 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 16.45 Å2 / Rmerge(I) obs: 0.148 / Net I/σ(I): 10.21
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.9-30.4213.8272931763198.6
3-3.10.3564.464371557198.7
3.1-3.20.3175.0556791367198.8
3.2-3.30.2695.8549171194199.1
3.3-3.580.1868.01112032720199.3
3.58-3.860.12711.2881481985199.4
3.86-4.140.10512.9161441523199.7
4.14-4.420.0914.8746711142199.7
4.42-4.70.07816.513666903198.5
4.7-100.09114.61162224071197.8
10-200.04218.531278439191.8
20-300.0524.7210053189.8
20-300.0524.72189.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VEN

3ven


Resolution: 2.9→29.336 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.8 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2572 934 4.99 %INHERITED FROM 3VEN
Rwork0.195 ---
obs0.1981 18708 98.58 %-
all-19007 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 6.452 Å2 / ksol: 0.374 e/Å3
Displacement parametersBiso max: 92.58 Å2 / Biso mean: 17.541 Å2 / Biso min: 3.41 Å2
Baniso -1Baniso -2Baniso -3
1-2.5183 Å20 Å2-0 Å2
2--2.5183 Å20 Å2
3----5.0366 Å2
Refinement stepCycle: LAST / Resolution: 2.9→29.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4378 0 37 0 4415
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094524
X-RAY DIFFRACTIONf_angle_d1.2696171
X-RAY DIFFRACTIONf_chiral_restr0.076670
X-RAY DIFFRACTIONf_plane_restr0.006815
X-RAY DIFFRACTIONf_dihedral_angle_d14.9341635
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-3.05280.33171290.26452472260199
3.0528-3.24380.32261290.24172478260799
3.2438-3.49390.31851320.20892493262599
3.4939-3.84480.26581330.19092530266399
3.8448-4.39960.19361340.148125492683100
4.3996-5.53690.20261350.15062566270198
5.5369-29.3370.24821420.21622686282897

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