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

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Basic information

Entry
Database: PDB / ID: 3ver
TitleCrystal structure of the O-carbamoyltransferase TobZ in complex with carbamoyl adenylate intermediate
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
Chem-CA0 / : / nebramycin 5' synthase
Similarity search - Component
Biological speciesStreptoalloteichus tenebrarius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 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)64,3105
Polymers63,4511
Non-polymers8594
Water5,350297
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.262, 99.262, 281.323
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-856-

HOH

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Components

#1: Protein O-carbamoyltransferase TobZ


Mass: 63451.160 Da / Num. of mol.: 1
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CA0 / 5'-O-[(S)-(carbamoyloxy)(hydroxy)phosphoryl]adenosine


Mass: 390.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N6O8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 3.15 Å3/Da / Density % sol: 60.99 %
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: Sep 15, 2011
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: 2.34→32.5 Å / Num. all: 35610 / Num. obs: 35505 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 37.579 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.18
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.34-2.40.6122.531073025601100
2.4-2.470.4893.181056325141100
2.47-2.540.4283.58102432442199.9
2.54-2.620.3664.121001423971100
2.62-2.70.3274.7695152264199.8
2.7-2.80.2645.5994022243199.9
2.8-2.90.2157.0290442152199.8
2.9-3.020.1599.2187402097199.9
3.02-3.160.1311.182561982199.7
3.16-3.310.10513.5980601942199.7
3.31-3.490.07718.2174651806199.8
3.49-3.70.05922.9672071754199.5
3.7-3.960.0482966191630199.6
3.96-4.270.03734.0362461544199.6
4.27-4.680.03139.9657161415199.5
4.68-5.230.0339.7252881317199.4
5.23-6.040.0293745171143199.7
6.04-7.40.02639.9939341018199.9
7.4-10.460.01753.343000808199.6
10.46-32.50.01257.031538477193.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
MAR345data collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VEN

3ven


Resolution: 2.34→32.491 Å / Occupancy max: 1 / Occupancy min: 0.47 / SU ML: 0.59 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 19.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2238 1776 5 %RANDOM
Rwork0.169 ---
obs0.1718 35503 99.76 %-
all-35610 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.081 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso max: 118.57 Å2 / Biso mean: 33.5897 Å2 / Biso min: 8.87 Å2
Baniso -1Baniso -2Baniso -3
1-2.7593 Å20 Å2-0 Å2
2--2.7593 Å20 Å2
3----5.5186 Å2
Refinement stepCycle: LAST / Resolution: 2.34→32.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4378 0 54 297 4729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074563
X-RAY DIFFRACTIONf_angle_d1.0576227
X-RAY DIFFRACTIONf_chiral_restr0.068675
X-RAY DIFFRACTIONf_plane_restr0.004822
X-RAY DIFFRACTIONf_dihedral_angle_d15.7841655
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.34-2.40330.28091340.223325372671100
2.4033-2.4740.26621330.204525362669100
2.474-2.55380.2841350.207925512686100
2.5538-2.6450.27531330.197525382671100
2.645-2.75090.25941340.195325432677100
2.7509-2.8760.26511340.187325512685100
2.876-3.02750.24171360.183425682704100
3.0275-3.21710.25441350.182625752710100
3.2171-3.46520.23921360.174925802716100
3.4652-3.81340.21511370.158726072744100
3.8134-4.36410.17471380.130926192757100
4.3641-5.4940.16891410.13482675281699
5.494-32.49420.21071500.16732847299799
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)
11.37420.12970.23240.6171-0.23731.5909-0.0369-0.14920.0226-0.0731-0.00220.1126-0.0412-0.1991-0.00040.11280.0541-0.00170.101-0.00480.127811.425431.695726.3618
21.3653-0.81850.14361.2057-0.14050.48930.03610.16820.0072-0.2140.00190.15-0.0701-0.1148-0.02510.22570.05-0.05430.17710.02110.123815.640828.48821.2163
31.30270.1911-0.03760.53820.08250.95790.01680.07520.2895-0.04630.0253-0.0259-0.34530.16550.01620.2344-0.01570.03270.11750.04510.210631.744542.296917.7604
41.90650.2496-0.23271.2956-0.25641.3941-0.05420.32670.3397-0.19780.0482-0.0422-0.25520.0917-0.00930.2116-0.07160.03180.20310.05730.220635.748644.425413.1523
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:151)A1 - 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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