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- PDB-3ven: Crystal structure of the O-carbamoyltransferase TobZ -

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Basic information

Entry
Database: PDB / ID: 3ven
TitleCrystal structure of the O-carbamoyltransferase TobZ
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
: / : / L(+)-TARTARIC ACID / nebramycin 5' synthase
Similarity search - Component
Biological speciesStreptoalloteichus tenebrarius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.57 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 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_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_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

Downloads & links

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Assembly

Deposited unit
A: O-carbamoyltransferase TobZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8327
Polymers63,4171
Non-polymers4156
Water12,304683
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.023, 99.023, 280.896
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-1338-

HOH

21A-1344-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 689 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 683 / 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: 3.13 Å3/Da / Density % sol: 60.76 % / Description: STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
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: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 5, 2009
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.57→34.085 Å / Num. all: 215321 / Num. obs: 214415 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Biso Wilson estimate: 26.432 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 23.71
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.57-1.610.5652.66675388259198.4
1.61-1.650.4813.23688578106198.7
1.65-1.70.3784.17701617868199
1.7-1.760.3135.14710627632199.3
1.76-1.810.2446.66728457424199.4
1.81-1.880.1898.79746567209199.6
1.88-1.950.14911.4805526968199.9
1.95-2.030.11315.628913467101100
2.03-2.120.09320.279878164241100
2.12-2.220.0824.7111049361821100
2.22-2.340.07129.7912275658871100
2.34-2.480.06535.4713871356001100
2.48-2.650.05941.9715736052641100
2.65-2.870.05446.7715306349141100
2.87-3.140.04753.614605945521100
3.14-3.510.04359.7313602941691100
3.51-4.050.03865.111814637001100
4.05-4.960.03470.7210037431851100
4.96-7.020.03865.467506325311100
7.02-30.840.03166.58345871501198

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHELXphasing
SOLOMONphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
MAR345data collection
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.57→34.085 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.31 / Phase error: 14.92 / Stereochemistry target values: ML / Details: STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
RfactorNum. reflection% reflectionSelection details
Rfree0.176 10692 4.99 %RANDOM
Rwork0.1442 ---
obs0.1458 214288 99.6 %-
all-215321 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.846 Å2 / ksol: 0.378 e/Å3
Displacement parametersBiso max: 72.37 Å2 / Biso mean: 23.6643 Å2 / Biso min: 8.51 Å2
Baniso -1Baniso -2Baniso -3
1-1.4419 Å2-0 Å2-0 Å2
2--1.4419 Å20 Å2
3----2.8838 Å2
Refinement stepCycle: LAST / Resolution: 1.57→34.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4423 0 20 683 5126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0194639
X-RAY DIFFRACTIONf_angle_d1.6176329
X-RAY DIFFRACTIONf_chiral_restr0.125684
X-RAY DIFFRACTIONf_plane_restr0.009848
X-RAY DIFFRACTIONf_dihedral_angle_d12.3531695
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.57-1.58790.27493500.22566705705598
1.5879-1.60650.25573570.21546685704298
1.6065-1.62610.22463530.20096741709499
1.6261-1.64670.24453490.18726754710399
1.6467-1.66840.20733540.17256710706499
1.6684-1.69120.20853520.16576704705699
1.6912-1.71540.20963560.16416790714699
1.7154-1.7410.19763610.15936757711899
1.741-1.76820.19263670.14776807717499
1.7682-1.79720.15883560.14046724708099
1.7972-1.82820.18753640.139367797143100
1.8282-1.86140.17363490.134367947143100
1.8614-1.89720.19053570.134468037160100
1.8972-1.9360.16763590.122468047163100
1.936-1.9780.1613470.111668167163100
1.978-2.02410.16583550.119768137168100
2.0241-2.07470.16133600.114868147174100
2.0747-2.13080.16483550.123968097164100
2.1308-2.19340.16413650.118668297194100
2.1934-2.26420.16143570.119767837140100
2.2642-2.34510.17553630.129868297192100
2.3451-2.4390.18033560.136868097165100
2.439-2.550.16243610.132468167177100
2.55-2.68440.17993590.142168397198100
2.6844-2.85250.17443510.149267877138100
2.8525-3.07260.1893560.1568227178100
3.0726-3.38150.18363560.155468017157100
3.3815-3.87030.16873510.144868247175100
3.8703-4.87380.1433610.132168237184100
4.8738-34.09280.18753550.177568257180100

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