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- PDB-7vyp: The structure of GdmN complex with the natural tetrahedral interm... -

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Basic information

Entry
Database: PDB / ID: 7vyp
TitleThe structure of GdmN complex with the natural tetrahedral intermediate, carbamoylated derivative, and AMP
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 / Carbamoyltransferase, C-terminal / Carbamoyltransferase, C-terminal domain superfamily / Carbamoyltransferase N-terminus / Carbamoyltransferase C-terminus / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Chem-82Z / Chem-8CW / ADENOSINE MONOPHOSPHATE / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / : / GdmN
Similarity search - Component
Biological speciesStreptomyces hygroscopicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 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 15, 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)152,13826
Polymers148,7312
Non-polymers3,40624
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9990 Å2
ΔGint-147 kcal/mol
Surface area44940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.029, 111.029, 231.276
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, 94 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CP / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER


Mass: 141.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4NO5P
#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-82Z / [(5S,6E,8S,9S,12R,13E,15E)-21-chloranyl-12,20-dimethoxy-6,8,16-trimethyl-5-oxidanyl-3,11-bis(oxidanylidene)-2-azabicyclo[16.3.1]docosa-1(21),6,13,15,18(22),19-hexaen-9-yl] carbamate


Mass: 535.029 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35ClN2O7 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#8: Chemical ChemComp-8CW / [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl [(~{S})-azanyl-[[(5~{S},6~{E},8~{S},9~{S},12~{R},13~{E},15~{E})-21-chloranyl-12,20-dimethoxy-6,8,16-trimethyl-5-oxidanyl-3,11-bis(oxidanylidene)-2-azabicyclo[16.3.1]docosa-1(21),6,13,15,18(22),19-hexaen-9-yl]oxy]-oxidanyl-methyl] hydrogen phosphate


Mass: 882.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H49ClN7O14P / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.79 Å3/Da / Density % sol: 55.94 %
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 Å
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: 2.88→50 Å / Num. obs: 38176 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 49.6 Å2 / CC1/2: 0.989 / CC star: 0.997 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.043 / Rrim(I) all: 0.136 / Rsym value: 0.129 / Χ2: 0.907 / Net I/σ(I): 21.167
Reflection shellResolution: 2.88→2.93 Å / Num. unique obs: 1880 / CC1/2: 0.973

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000v716.1data reduction
HKL-3000v716.1data scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VEN

3ven


Resolution: 2.88→27.76 Å / SU ML: 0.2955 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.1538
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2156 1845 4.85 %
Rwork0.166 36186 -
obs0.1685 38031 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.76 Å2
Refinement stepCycle: LAST / Resolution: 2.88→27.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10322 0 210 70 10602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008610778
X-RAY DIFFRACTIONf_angle_d1.058114669
X-RAY DIFFRACTIONf_chiral_restr0.05651618
X-RAY DIFFRACTIONf_plane_restr0.00871924
X-RAY DIFFRACTIONf_dihedral_angle_d9.83041521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.88-2.960.26911140.19472755X-RAY DIFFRACTION99.55
2.96-3.050.26281520.18832725X-RAY DIFFRACTION99.9
3.05-3.140.32621460.20842742X-RAY DIFFRACTION100
3.14-3.260.27231250.21062796X-RAY DIFFRACTION99.97
3.26-3.390.29991220.20612741X-RAY DIFFRACTION99.97
3.39-3.540.28191310.17852761X-RAY DIFFRACTION100
3.54-3.730.23161620.17222764X-RAY DIFFRACTION100
3.73-3.960.21321480.16322757X-RAY DIFFRACTION100
3.96-4.260.20491380.15382790X-RAY DIFFRACTION99.93
4.26-4.690.1861550.13622753X-RAY DIFFRACTION100
4.69-5.370.1921480.14862824X-RAY DIFFRACTION99.97
5.37-6.740.20841360.17222839X-RAY DIFFRACTION100
6.74-27.760.14861680.1432939X-RAY DIFFRACTION98.92

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