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- PDB-7vyo: The structure of GdmN -

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Basic information

Entry
Database: PDB / ID: 7vyo
TitleThe structure of GdmN
ComponentsGdmN
KeywordsTRANSFERASE / Carbamoylation / Ansamycins antibiotics / Homodimer
Function / homology
Function and homology information


biosynthetic process / catalytic activity / ATP binding / metal ion 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 / : / DI(HYDROXYETHYL)ETHER / GdmN
Similarity search - Component
Biological speciesStreptomyces hygroscopicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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
Citation
Journal: 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.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Liebschner, D. / Afonine, P.V. / Baker, M.L. / Chen, V.B. / Croll, T.I. / Hintze, B. / Hung, L.W. / Jain, S. / McCoy, A.J. / Moriarty, N.W. / Oeffner, R.D. / Poon, B.K. / Prisant, M.G. / ...Authors: Liebschner, D. / Afonine, P.V. / Baker, M.L. / Chen, V.B. / Croll, T.I. / Hintze, B. / Hung, L.W. / Jain, S. / McCoy, A.J. / Moriarty, N.W. / Oeffner, R.D. / Poon, B.K. / Prisant, M.G. / Read, R.J. / Richardson, J.S. / Richardson, D.C. / Sammito, M.D. / Sobolev, O.V. / Stockwell, D.H. / Terwilliger, T.C. / Urzhumtsev, A.G. / Videau, L.L. / Williams, C.J. / Adams, P.D.
History
DepositionNov 14, 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)150,90529
Polymers148,7312
Non-polymers2,17427
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10530 Å2
ΔGint-191 kcal/mol
Surface area45570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.955, 110.955, 231.544
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 , 8 types, 316 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-CP / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER


Mass: 141.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4NO5P
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.77 Å3/Da / Density % sol: 55.54 %
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: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.25→40 Å / Num. obs: 78953 / % possible obs: 100 % / Redundancy: 9.4 % / Biso Wilson estimate: 29.62 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.024 / Rrim(I) all: 0.076 / Rsym value: 0.072 / Net I/σ(I): 32.533
Reflection shellResolution: 2.25→2.33 Å / Num. unique obs: 7778 / CC1/2: 0.96

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VEN

3ven


Resolution: 2.25→36.97 Å / SU ML: 0.2126 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.7206
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2089 4052 5.14 %
Rwork0.1761 74759 -
obs0.1778 78811 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.15 Å2
Refinement stepCycle: LAST / Resolution: 2.25→36.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10386 0 121 289 10796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007410760
X-RAY DIFFRACTIONf_angle_d0.874914618
X-RAY DIFFRACTIONf_chiral_restr0.05071606
X-RAY DIFFRACTIONf_plane_restr0.011923
X-RAY DIFFRACTIONf_dihedral_angle_d30.42661521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.280.25891480.21392496X-RAY DIFFRACTION98.62
2.28-2.310.22571310.19842534X-RAY DIFFRACTION99.4
2.31-2.330.25711150.20332554X-RAY DIFFRACTION99.66
2.33-2.370.2481320.20162562X-RAY DIFFRACTION99.67
2.37-2.40.25061440.20162539X-RAY DIFFRACTION100
2.4-2.430.27861390.19282519X-RAY DIFFRACTION99.92
2.43-2.470.23251410.18542612X-RAY DIFFRACTION100
2.47-2.510.26221140.19412534X-RAY DIFFRACTION99.92
2.51-2.550.2141390.17982543X-RAY DIFFRACTION100
2.55-2.590.20591360.1772562X-RAY DIFFRACTION99.93
2.59-2.640.2411320.18582567X-RAY DIFFRACTION100
2.64-2.690.23341600.18022532X-RAY DIFFRACTION100
2.69-2.740.22811270.18682557X-RAY DIFFRACTION100
2.75-2.80.22181380.19162551X-RAY DIFFRACTION100
2.8-2.870.24331400.19772581X-RAY DIFFRACTION100
2.87-2.940.22991330.18942576X-RAY DIFFRACTION100
2.94-3.020.23561500.19182563X-RAY DIFFRACTION100
3.02-3.110.21161520.19772549X-RAY DIFFRACTION100
3.11-3.210.23421360.18192584X-RAY DIFFRACTION99.96
3.21-3.320.21191330.18992578X-RAY DIFFRACTION100
3.33-3.460.26591170.18482628X-RAY DIFFRACTION100
3.46-3.620.21261900.17272517X-RAY DIFFRACTION100
3.62-3.810.21011170.16382623X-RAY DIFFRACTION100
3.81-4.040.19731390.15632578X-RAY DIFFRACTION100
4.04-4.360.1641510.15222624X-RAY DIFFRACTION100
4.36-4.790.16121580.14252595X-RAY DIFFRACTION100
4.79-5.480.19511490.16222637X-RAY DIFFRACTION100
5.49-6.90.20321320.19482685X-RAY DIFFRACTION99.89
6.9-36.970.16121590.15912779X-RAY DIFFRACTION99.69

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