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

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Basic information

Entry
Database: PDB / ID: 3veo
TitleCrystal structure of the O-carbamoyltransferase TobZ in complex with carbamoyl phosphate
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
PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / : / : / nebramycin 5' synthase
Similarity search - Component
Biological speciesStreptoalloteichus tenebrarius (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.187 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

Downloads & links

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Assembly

Deposited unit
A: O-carbamoyltransferase TobZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7546
Polymers63,4171
Non-polymers3375
Water7,566420
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.200, 98.200, 279.200
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-979-

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, 425 molecules

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


Mass: 141.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4NO5P
#3: Chemical ChemComp-FE2 / FE (II) ION


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


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 420 / 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: 3.06 Å3/Da / Density % sol: 59.86 %
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: Oct 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.187→29.2 Å / Num. all: 42167 / Num. obs: 41968 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.2 % / Biso Wilson estimate: 28.525 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 46.97
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.187-2.290.15115.4946011499796.7
2.29-2.390.12321.71507124357100
2.39-2.490.09427.28427353665100
2.49-2.590.08130.54368453158100
2.59-2.990.05640.691031668814100
2.99-3.390.03757.73602515185100
3.39-3.790.02872.48371763259100
3.79-4.190.02482.33239792132100
4.19-4.590.02288.1165071480100
4.59-100.02482.56480544398100
10-200.02577.414453467100
20-300.02758.9437756100
30

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Processing

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

3ven


Resolution: 2.187→29.196 Å / Occupancy max: 1 / Occupancy min: 0.41 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 17.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2111 2100 5 %RANDOM
Rwork0.1641 ---
obs0.1665 41966 99.61 %-
all-42167 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.199 Å2 / ksol: 0.385 e/Å3
Displacement parametersBiso max: 124.44 Å2 / Biso mean: 24.5828 Å2 / Biso min: 3.02 Å2
Baniso -1Baniso -2Baniso -3
1-2.7655 Å20 Å2-0 Å2
2--2.7655 Å2-0 Å2
3----5.5309 Å2
Refinement stepCycle: LAST / Resolution: 2.187→29.196 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4423 0 15 420 4858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074599
X-RAY DIFFRACTIONf_angle_d1.0726273
X-RAY DIFFRACTIONf_chiral_restr0.07679
X-RAY DIFFRACTIONf_plane_restr0.005837
X-RAY DIFFRACTIONf_dihedral_angle_d13.6971685
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.187-2.2380.24321310.1842456258794
2.238-2.2940.23871360.17325892725100
2.294-2.3560.23521380.154126232761100
2.356-2.42520.22341370.166626012738100
2.4252-2.50350.22261380.153826242762100
2.5035-2.59290.20851380.162626282766100
2.5929-2.69670.2371370.1726072744100
2.6967-2.81930.23951410.170926652806100
2.8193-2.96780.22681380.176526352773100
2.9678-3.15350.2541410.181426642805100
3.1535-3.39670.21081400.185426702810100
3.3967-3.73790.22581410.16426692810100
3.7379-4.27730.16031430.137427302873100
4.2773-5.38340.19181450.133127522897100
5.3834-29.1990.18081560.184529533109100
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)
10.0111-0.0017-0.010.00660.01340.0189-0.0065-0.01980.0047-0.014-0.02460.0104-0.0144-0.0397-0.00720.0490.04020.01120.0224-0.02830.025711.36731.610426.4567
20.0173-0.0188-0.0020.01060.00980.02080.00110.05230.0069-0.055-0.00110.006-0.0572-0.04630.00190.12690.0466-0.02310.10050.00220.087115.671829.55331.8879
30.09260.0257-0.01980.05750.02640.08430.01920.03460.0815-0.01710.0088-0.0124-0.12280.0178-0.01150.0859-0.04660.02360.05110.01910.088932.496442.955616.7822
40.01280.0023-0.00430.0026-0.00230.01080.01960.02340.0225-0.00690.0144-0.0096-0.01530.0172-0.00560.1146-0.03920.02960.08650.01240.109539.054442.201515.3402
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 152:337)A152 - 337
3X-RAY DIFFRACTION3chain 'A' and (resseq 338:483)A338 - 483
4X-RAY DIFFRACTION4chain 'A' and (resseq 484:570)A484 - 570

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