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

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Basic information

Entry
Database: PDB / ID: 3vet
TitleCrystal structure of the O-carbamoyltransferase TobZ in complex with Tobramycin, carbamoyl phosphate and ADP
ComponentsO-carbamoyltransferase TobZ
KeywordsTRANSFERASE/ANTIBIOTIC / antibiotic biosynthesis / substrate assisted catalysis / substrate channeling / adenylation / structural enzymology / enzyme evolution / TRANSFERASE-ANTIBIOTIC complex
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 / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / : / : / : / TOBRAMYCIN / nebramycin 5' synthase
Similarity search - Component
Biological speciesStreptoalloteichus tenebrarius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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.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_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

Downloads & links

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Assembly

Deposited unit
A: O-carbamoyltransferase TobZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0929
Polymers63,4171
Non-polymers1,6758
Water5,188288
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.818, 98.818, 280.908
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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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 , 8 types, 296 molecules

#2: 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
#3: Chemical ChemComp-CP / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER


Mass: 141.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4NO5P
#4: Chemical ChemComp-TOY / TOBRAMYCIN / 4-AMINO-2-[4,6-DIAMINO-3-(3-AMINO-6-AMINOMETHYL-5-HYDROXY-TETRAHYDRO-PYRAN-2-YLOXY)-2-HYDROXY-CYCLOHEXYLOXY]-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,5-DIOL


Mass: 467.514 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37N5O9 / Comment: antibiotic*YM
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 3.12 Å3/Da / Density % sol: 60.6 %
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: 14.1 / Wavelength: 0.9184 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 25, 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: 2.2→34.041 Å / Num. all: 42176 / Num. obs: 42176 / % possible obs: 99.961 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Biso Wilson estimate: 37.968 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 22.23
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.2-2.260.732.42357725782199.9
2.26-2.320.5923.013599255891100
2.32-2.390.5443.43675154481100
2.39-2.460.4374.333785953331100
2.46-2.540.3655.373845951501100
2.54-2.630.3146.453901049401100
2.63-2.730.267.964022848161100
2.73-2.840.20810.284087146251100
2.84-2.970.15414.124134044131100
2.97-3.110.12418.684292142491100
3.11-3.280.09924.514470140291100
3.28-3.480.07332.94321137811100
3.48-3.720.05841.014229235891100
3.72-4.020.04749.334034133221100
4.02-4.40.0455.253840030711100
4.4-4.920.03761.063606327871100
4.92-5.680.03959.513353524271100
5.68-6.960.03763.583195020651100
6.96-9.840.03286.923286616081100
9.84-34.040.02996.818160847197.7

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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 3VEO

3veo


Resolution: 2.2→34.041 Å / Occupancy max: 1 / Occupancy min: 0.38 / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.56 / Phase error: 19.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2042 2108 5.03 %RANDOM
Rwork0.1654 ---
obs0.1674 42176 99.98 %-
all-42176 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.48 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso max: 124.23 Å2 / Biso mean: 35.7308 Å2 / Biso min: 4.57 Å2
Baniso -1Baniso -2Baniso -3
1-4.125 Å2-0 Å2-0 Å2
2--4.125 Å20 Å2
3----8.2499 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.041 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4385 0 101 288 4774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074625
X-RAY DIFFRACTIONf_angle_d1.1316320
X-RAY DIFFRACTIONf_chiral_restr0.07693
X-RAY DIFFRACTIONf_plane_restr0.005824
X-RAY DIFFRACTIONf_dihedral_angle_d16.8121696
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.22680.25521430.230926212764
2.2268-2.2550.29051410.222226772818
2.255-2.28470.25851410.219426102751
2.2847-2.3160.28131410.214926372778
2.316-2.3490.28791400.209126542794
2.349-2.38410.23421370.211726182755
2.3841-2.42130.24071410.191226672808
2.4213-2.4610.21861360.18826472783
2.461-2.50350.22281420.171326052747
2.5035-2.5490.21831400.182226732813
2.549-2.5980.24851390.183126382777
2.598-2.6510.23821390.172826332772
2.651-2.70860.21211340.172226222756
2.7086-2.77160.20821380.172426392777
2.7716-2.84090.23391400.171726762816
2.8409-2.91760.24651410.176426272768
2.9176-3.00340.22841460.175326502796
3.0034-3.10030.22231410.175826472788
3.1003-3.2110.21741340.171226292763
3.211-3.33950.21161430.169926352778
3.3395-3.49130.19271330.157726622795
3.4913-3.67520.19941360.153726392775
3.6752-3.90520.16131360.136726452781
3.9052-4.20620.14311440.133526282772
4.2062-4.62850.17111430.130826532796
4.6285-5.29610.17851400.133426242764
5.2961-6.66440.20521370.163426552792
6.6644-34.04470.1731470.174826442791
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)
10.0673-0.0302-0.0110.06450.02220.0248-0.0136-0.03160.0327-0.0645-0.07540.0618-0.0374-0.0911-0.06860.03450.11250.00570.016-0.04560.044411.883732.334426.3868
20.1124-0.01840.02720.1701-0.0060.10450.03460.1039-0.0154-0.1435-0.04350.0367-0.0348-0.0919-0.00990.2620.0704-0.050.1783-0.00460.167216.593328.62751.163
30.60520.2277-0.20240.23320.14050.4028-0.0175-0.13860.0598-0.11920.0046-0.011-0.21510.1302-0.01360.1825-0.00040.0220.16890.0250.157532.483242.533817.7783
40.71670.3716-0.34540.6064-0.12420.3349-0.0390.00830.1204-0.15530.07970.0152-0.07010.1913-0.00850.2103-0.01340.01860.2380.0370.184836.476344.650413.1337
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 0:151)A0 - 151
2X-RAY DIFFRACTION2chain 'A' and (resseq 152:322)A152 - 322
3X-RAY DIFFRACTION3chain 'A' and (resseq 323:463)A323 - 463
4X-RAY DIFFRACTION4chain 'A' and (resseq 464:566)A464 - 566

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