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- PDB-9s2t: Carbamoyl transferase NovN involved in Novobiocin biosynthesis -

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Basic information

Entry
Database: PDB / ID: 9s2t
TitleCarbamoyl transferase NovN involved in Novobiocin biosynthesis
ComponentsDecarbamoylnovobiocin carbamoyltransferase
KeywordsTRANSFERASE / carbamoylation / homodimer / novobiocin
Function / homology
Function and homology information


decarbamoylnovobiocin carbamoyltransferase / novobiocin biosynthetic process / carboxyl- or carbamoyltransferase activity
Similarity search - Function
Carbamoyltransferase / Carbamoyltransferase, C-terminal / Carbamoyltransferase, C-terminal domain superfamily / : / Carbamoyltransferase N-terminus / Carbamoyltransferase C-terminus / ATPase, nucleotide binding domain
Similarity search - Domain/homology
: / PHOSPHATE ION / Decarbamoylnovobiocin carbamoyltransferase
Similarity search - Component
Biological speciesStreptomyces niveus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.24 Å
AuthorsGomez Garcia, I. / Lawson, D.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)B19400 United Kingdom
Citation
Journal: To Be Published
Title: Carbamoyl transferase NovN involved in Novobiocin biosynthesis
Authors: Gomez Garcia, I. / Lawson, D.M.
#1: Journal: Acta Crystallogr Sect F Struct Biol Cryst Commun / Year: 2008
Title: Crystallization and preliminary X-ray analysis of the O-carbamoyltransferase NovN from the novobiocin-biosynthetic cluster of Streptomyces spheroides.
Authors: Gomez Garcia, I. / Freel Meyers, C.L. / Walsh, C.T. / Lawson, D.M.
History
DepositionJul 22, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Decarbamoylnovobiocin carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3998
Polymers75,7731
Non-polymers6267
Water7,819434
1
A: Decarbamoylnovobiocin carbamoyltransferase
hetero molecules

A: Decarbamoylnovobiocin carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,79816
Polymers151,5472
Non-polymers1,25114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7540 Å2
ΔGint-104 kcal/mol
Surface area47100 Å2
Unit cell
Length a, b, c (Å)108.5, 113.26, 166.71
Angle α, β, γ (deg.)90, 90, 90
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Decarbamoylnovobiocin carbamoyltransferase / Novobiocin biosynthesis protein N


Mass: 75773.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces niveus (bacteria) / Gene: novN / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9L9F4, decarbamoylnovobiocin carbamoyltransferase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.31 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: NULL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9507 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9507 Å / Relative weight: 1
ReflectionResolution: 2.24→46.95 Å / Num. obs: 46701 / % possible obs: 94.1 % / Redundancy: 5.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.039 / Rrim(I) all: 0.071 / Χ2: 0.88 / Net I/σ(I): 17.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
8.96-46.9560.03333.38360.9980.0210.040.5697
2.24-2.313.30.2234.231240.9090.1650.2790.8569.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.105)refinement
Aimless0.8.2data scaling
MOSFLMdata reduction
gemmi0.7.1data extraction
SHELXDEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.24→39.173 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 8.489 / SU ML: 0.11 / Cross valid method: FREE R-VALUE / ESU R: 0.193 / ESU R Free: 0.168 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2 2364 5.062 %
Rwork0.1599 44335 -
all0.162 --
obs-46699 94.032 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.102 Å2
Baniso -1Baniso -2Baniso -3
1--1.583 Å2-0 Å2-0 Å2
2--2.055 Å2-0 Å2
3----0.472 Å2
Refinement stepCycle: LAST / Resolution: 2.24→39.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5194 0 31 434 5659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125434
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.837417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7575690
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.331560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.04410848
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.65210259
X-RAY DIFFRACTIONr_chiral_restr0.1080.2830
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024202
X-RAY DIFFRACTIONr_nbd_refined0.1990.22458
X-RAY DIFFRACTIONr_nbtor_refined0.3050.23662
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2409
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1510.287
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1150.220
X-RAY DIFFRACTIONr_mcbond_it1.852.482697
X-RAY DIFFRACTIONr_mcangle_it3.0084.4553375
X-RAY DIFFRACTIONr_scbond_it2.6052.7132737
X-RAY DIFFRACTIONr_scangle_it4.074.8794031
X-RAY DIFFRACTIONr_lrange_it6.75826.518310
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.24-2.2980.271320.26323210.26336140.9520.9667.87490.238
2.298-2.3610.2491830.224920.20335340.9640.97575.69330.173
2.361-2.4290.2171400.17827460.1834470.9730.9883.7250.155
2.429-2.5030.2471580.18728870.1933000.960.97892.27270.162
2.503-2.5850.2471740.1830610.18432560.9620.9899.3550.157
2.585-2.6750.2171520.16729730.1731300.9690.98299.84030.147
2.675-2.7760.2311680.17828760.1830490.9710.98199.8360.159
2.776-2.8890.2241560.17727440.1829040.9650.9899.86230.16
2.889-3.0160.2411620.1726590.17428230.9660.98199.92920.157
3.016-3.1630.1961250.17425450.17526710.9760.98199.96260.161
3.163-3.3330.2161080.17824560.1825640.9710.981000.171
3.333-3.5330.2281060.16323140.16524210.970.98499.95870.159
3.533-3.7750.1871010.1521730.15122770.9760.98799.86820.15
3.775-4.0740.1561000.13220490.13321490.9880.991000.137
4.074-4.4580.164910.12718820.12919730.9840.9911000.134
4.458-4.9760.141860.11217090.11318050.9890.99399.4460.123
4.976-5.7310.167790.13215070.13315940.9840.9999.49810.141
5.731-6.9820.193530.16412980.16513610.9780.98699.26530.174
6.982-9.720.163480.14910300.1510990.9810.98798.08920.168
9.72-39.1730.175420.1826120.1816770.980.97896.60270.208
Refinement TLS params.Method: refined / Origin x: 5.2537 Å / Origin y: 23.478 Å / Origin z: 33.5549 Å
111213212223313233
T0.048 Å20.0045 Å2-0.013 Å2-0.0288 Å2-0.0022 Å2--0.0131 Å2
L0.6177 °20.1171 °2-0.067 °2-0.5216 °2-0.0251 °2--0.8138 °2
S0.0035 Å °-0.1117 Å °-0.0354 Å °0.1425 Å °-0.0233 Å °-0.0358 Å °0.0548 Å °0.0157 Å °0.0198 Å °
Refinement TLS groupSelection: ALL

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