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- PDB-7vzn: The structure of GdmN in complex with carbamoyl adenylate interme... -

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Basic information

Entry
Database: PDB / ID: 7vzn
TitleThe structure of GdmN in complex with carbamoyl adenylate intermediate and 20-O-methyl-19-chloroproansamitocin
ComponentsGdmN
KeywordsTRANSFERASE / Homodimer / Carbamoyltransferase / Ansamycins antibiotics
Function / homology
Function and homology information


biosynthetic process / catalytic activity / ATP binding / metal ion binding
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
Chem-83Z / Chem-CA0 / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / : / DI(HYDROXYETHYL)ETHER / GdmN
Similarity search - Component
Biological speciesStreptomyces hygroscopicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWei, J. / Zheng, J. / Zhou, J. / Kang, Q. / Bai, L.
Funding support7items
OrganizationGrant numberCountry
Other government2019YFA0905400
Other government2021YFC2100600
Other government31830104
Other government31800023
Other government31801036
Other governmentU1703236
Other government17JC1403600
CitationJournal: Nat Commun / Year: 2022
Title: Endowing homodimeric carbamoyltransferase GdmN with iterative functions through structural characterization and mechanistic studies.
Authors: Wei, J. / Zhang, X. / Zhou, Y. / Cheng, X. / Lin, Z. / Tang, M. / Zheng, J. / Wang, B. / Kang, Q. / Bai, L.
History
DepositionNov 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GdmN
B: GdmN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,07227
Polymers148,7312
Non-polymers3,34125
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8620 Å2
ΔGint-38 kcal/mol
Surface area46150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.394, 111.394, 230.892
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein GdmN


Mass: 74365.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces hygroscopicus (bacteria) / Gene: gdmN / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q84G19

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Non-polymers , 9 types, 380 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-83Z / (5~{S},6~{E},8~{S},9~{S},12~{R},15~{E})-21-chloranyl-12,20-dimethoxy-6,8,16-trimethyl-5,9-bis(oxidanyl)-2-azabicyclo[16.3.1]docosa-1(21),6,15,18(22),19-pentaene-3,11-dione


Mass: 492.004 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H34ClNO6 / Feature type: SUBJECT OF INVESTIGATION
#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 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-CP / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER


Mass: 141.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4NO5P
#9: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.78 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: Lithium sulfate monohydrate, Polyethylene glycol 3,350, Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 A
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 97290 / % possible obs: 100 % / Redundancy: 19.9 % / Biso Wilson estimate: 24.72 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 34.636
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.798 / Num. unique obs: 4801

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VEN

3ven


Resolution: 2.1→28.62 Å / SU ML: 0.2092 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8093
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2145 4940 5.09 %
Rwork0.1828 92198 -
obs0.1845 97138 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.46 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10399 0 212 355 10966
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710848
X-RAY DIFFRACTIONf_angle_d0.903214739
X-RAY DIFFRACTIONf_chiral_restr0.05171620
X-RAY DIFFRACTIONf_plane_restr0.0091939
X-RAY DIFFRACTIONf_dihedral_angle_d10.10871547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.25671640.21752939X-RAY DIFFRACTION97.76
2.12-2.150.24891340.20783079X-RAY DIFFRACTION99.97
2.15-2.180.25241470.20323047X-RAY DIFFRACTION100
2.18-2.20.2371550.20462999X-RAY DIFFRACTION100
2.2-2.230.26691520.20853100X-RAY DIFFRACTION100
2.23-2.260.27221840.20323004X-RAY DIFFRACTION100
2.26-2.30.25151480.20143082X-RAY DIFFRACTION100
2.3-2.330.2421340.19833060X-RAY DIFFRACTION100
2.33-2.370.25161910.20143016X-RAY DIFFRACTION100
2.37-2.40.26471320.20383086X-RAY DIFFRACTION99.97
2.4-2.450.21521590.19713043X-RAY DIFFRACTION100
2.45-2.490.27141590.20063063X-RAY DIFFRACTION100
2.49-2.540.25941750.19683065X-RAY DIFFRACTION100
2.54-2.590.27031670.19773053X-RAY DIFFRACTION100
2.59-2.650.24541600.20063040X-RAY DIFFRACTION100
2.65-2.710.26381800.19513040X-RAY DIFFRACTION100
2.71-2.780.25331900.20153049X-RAY DIFFRACTION100
2.78-2.850.24841610.19893076X-RAY DIFFRACTION100
2.85-2.930.20471790.20293028X-RAY DIFFRACTION100
2.93-3.030.25491560.20623082X-RAY DIFFRACTION100
3.03-3.140.22621370.21513093X-RAY DIFFRACTION100
3.14-3.260.25911820.20523085X-RAY DIFFRACTION100
3.26-3.410.27461370.19553103X-RAY DIFFRACTION100
3.41-3.590.20141690.18543099X-RAY DIFFRACTION100
3.59-3.810.18971490.16863101X-RAY DIFFRACTION100
3.82-4.110.18241860.15753113X-RAY DIFFRACTION100
4.11-4.520.14961570.13993120X-RAY DIFFRACTION100
4.52-5.170.17861690.14083138X-RAY DIFFRACTION100
5.17-6.50.17542020.17643158X-RAY DIFFRACTION100
6.5-28.620.14952250.14973237X-RAY DIFFRACTION98.86

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