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- PDB-3vex: Crystal structure of the O-carbamoyltransferase TobZ H14N variant... -

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Basic information

Entry
Database: PDB / ID: 3vex
TitleCrystal structure of the O-carbamoyltransferase TobZ H14N variant 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: 1.9 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 1.3Nov 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.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)64,2528
Polymers63,4271
Non-polymers8247
Water12,737707
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.648, 98.648, 280.229
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-1333-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein O-carbamoyltransferase TobZ


Mass: 63427.121 Da / Num. of mol.: 1 / Mutation: H14N
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, 714 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CA0 / 5'-O-[(S)-(carbamoyloxy)(hydroxy)phosphoryl]adenosine


Mass: 390.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N6O8P
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 707 / 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: 3.1 Å3/Da / Density % sol: 60.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 100 mM HEPES, pH 7.4, 2 M ammonium sulfate, 2% PEG400, 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: Aug 23, 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: 1.9→19.63 Å / Num. all: 64463 / Num. obs: 64352 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 24.876 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 15.56
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.9-20.5753.746384789821100
2-2.10.3935.415340474071100
2.1-2.20.3046.934450161131100
2.2-2.30.2398.623733651201100
2.3-2.750.1612.26109102149551100
2.75-3.20.08919.815618877691100
3.2-3.650.05728.463160744711100
3.65-4.10.04335.61189402733199.9
4.1-4.550.03838.58121011768199.9
4.55-100.03441.24307184563199.8
10-200.02449.262721471199.4

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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: 1.9→19.626 Å / Occupancy max: 1 / Occupancy min: 0.28 / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 3212 4.99 %INHERITED FROM 3VEN
Rwork0.1669 ---
obs0.1687 64350 99.96 %-
all-64463 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.664 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso max: 80.78 Å2 / Biso mean: 21.1786 Å2 / Biso min: 5.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.4802 Å2-0 Å2-0 Å2
2--1.4802 Å20 Å2
3----2.9604 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4376 0 49 707 5132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074592
X-RAY DIFFRACTIONf_angle_d1.0246265
X-RAY DIFFRACTIONf_chiral_restr0.069677
X-RAY DIFFRACTIONf_plane_restr0.005831
X-RAY DIFFRACTIONf_dihedral_angle_d13.7311677
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-1.92830.2581280.237826142742
1.9283-1.95840.27391370.224325742711
1.9584-1.99050.24411380.198626302768
1.9905-2.02480.24431460.195425852731
2.0248-2.06160.24981390.192126242763
2.0616-2.10120.23531250.182126222747
2.1012-2.1440.24481430.171626242767
2.144-2.19060.20761440.171726142758
2.1906-2.24150.17961340.163426282762
2.2415-2.29750.20541350.163226032738
2.2975-2.35950.22981390.166926292768
2.3595-2.42880.1921360.157426182754
2.4288-2.5070.20781400.154626462786
2.507-2.59640.21881410.157626652806
2.5964-2.70010.21741370.163326282765
2.7001-2.82270.20461390.164626592798
2.8227-2.9710.23071420.168626582800
2.971-3.15650.20871410.166126712812
3.1565-3.3990.211410.167126992840
3.399-3.73890.16591430.157326952838
3.7389-4.27510.16731430.137427362879
4.2751-5.36790.16351450.146527592904
5.3679-19.62710.20041560.189229573113
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)
10.1150.0286-0.03650.01190.01920.1707-0.0116-0.0270.023-0.0326-0.03920.0176-0.0344-0.0713-0.02680.08490.02470.00720.0814-0.00570.079110.838631.246426.1535
20.1134-0.01520.04220.0507-0.00920.18910.00070.0632-0.0074-0.0511-0.01580.018-0.0414-0.0316-0.01390.09430.0404-0.02080.08180.00990.072615.275228.06641.1866
30.20460.10010.02160.08770.04350.1150.02960.00790.0699-0.02050.003-0.0079-0.14510.02970.01490.1032-0.01630.00930.06140.02560.09330.306143.27316.2617
40.13270.017-0.00490.0551-0.00880.03570.01840.01080.0876-0.02590.0239-0.0045-0.03420.04610.01470.1217-0.0250.00740.09980.01780.120637.605842.777615.208
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 323:483)A323 - 483
4X-RAY DIFFRACTION4chain 'A' and (resseq 484:566)A484 - 566

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