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- PDB-7vzy: The structure of GdmN complex with AMP and 20-O-methyl-19-chlorop... -

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Basic information

Entry
Database: PDB / ID: 7vzy
TitleThe structure of GdmN complex with AMP and 20-O-methyl-19-chloroproansamitocin
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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-83Z / ADENOSINE MONOPHOSPHATE / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / : / DI(HYDROXYETHYL)ETHER / GdmN
Similarity search - Component
Biological speciesStreptomyces hygroscopicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 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 17, 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

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Assembly

Deposited unit
A: GdmN
B: GdmN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,24824
Polymers153,0742
Non-polymers3,17422
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10730 Å2
ΔGint-154 kcal/mol
Surface area45230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.483, 111.483, 231.355
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: 76536.984 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, 22 molecules

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


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3

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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: 55.92 %
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: Apr 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 41601 / % possible obs: 100 % / Redundancy: 15.8 % / Biso Wilson estimate: 46.05 Å2 / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 27
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 0.625 / Num. unique obs: 2071 / Rsym value: 0.625 / % possible all: 100

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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: 2.81→31.88 Å / SU ML: 0.3443 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3765
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2202 2016 4.86 %
Rwork0.1707 39462 -
obs0.1731 41478 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.42 Å2
Refinement stepCycle: LAST / Resolution: 2.81→31.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10411 0 196 0 10607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009210867
X-RAY DIFFRACTIONf_angle_d1.092214779
X-RAY DIFFRACTIONf_chiral_restr0.05471622
X-RAY DIFFRACTIONf_plane_restr0.01071942
X-RAY DIFFRACTIONf_dihedral_angle_d15.95433935
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.880.35841290.2532777X-RAY DIFFRACTION99.38
2.88-2.950.3341490.22352785X-RAY DIFFRACTION100
2.95-3.040.29461480.20942761X-RAY DIFFRACTION100
3.04-3.140.26461390.20742782X-RAY DIFFRACTION99.97
3.14-3.250.30541280.20712795X-RAY DIFFRACTION99.97
3.25-3.380.2411470.20752822X-RAY DIFFRACTION100
3.38-3.530.26491220.20092764X-RAY DIFFRACTION99.93
3.53-3.720.23761440.162851X-RAY DIFFRACTION99.97
3.72-3.950.2371320.15562801X-RAY DIFFRACTION99.97
3.95-4.260.17831420.1482816X-RAY DIFFRACTION99.93
4.26-4.680.17041440.13432842X-RAY DIFFRACTION100
4.68-5.360.1691490.14522846X-RAY DIFFRACTION99.97
5.36-6.740.19141500.17552867X-RAY DIFFRACTION100
6.75-31.880.19211930.14952953X-RAY DIFFRACTION98.99

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