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- PDB-7vx0: The structure of GdmN complex with ATP -

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Basic information

Entry
Database: PDB / ID: 7vx0
TitleThe structure of GdmN complex with ATP
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
ADENOSINE-5'-TRIPHOSPHATE / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / : / PHOSPHATE ION / GdmN
Similarity search - Component
Biological speciesStreptomyces hygroscopicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 12, 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)156,41335
Polymers153,0742
Non-polymers3,33933
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13610 Å2
ΔGint-138 kcal/mol
Surface area45380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.717, 111.717, 230.717
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, 478 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#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-SO4 / SULFATE ION


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


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.81 Å3/Da / Density % sol: 56.25 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium sulfate monohydrate, 25% w/v Polyethylene glycol 3,350 and 0.1 M Tris, pH 8.5

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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 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 113024 / % possible obs: 100 % / Redundancy: 18.7 % / Biso Wilson estimate: 24.58 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 36.368
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 1.025 / Num. unique obs: 5618 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VEN

3ven


Resolution: 2→25.64 Å / SU ML: 0.1953 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.4677
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2115 5598 4.99 %
Rwork0.1822 106582 -
obs0.1837 112180 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.16 Å2
Refinement stepCycle: LAST / Resolution: 2→25.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10429 0 195 445 11069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710858
X-RAY DIFFRACTIONf_angle_d0.898414750
X-RAY DIFFRACTIONf_chiral_restr0.05211615
X-RAY DIFFRACTIONf_plane_restr0.00871931
X-RAY DIFFRACTIONf_dihedral_angle_d8.9251527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.26781940.2293154X-RAY DIFFRACTION89.64
2.02-2.050.27911450.22583388X-RAY DIFFRACTION95.46
2.05-2.070.26361740.22433480X-RAY DIFFRACTION97.6
2.07-2.10.29121880.21583499X-RAY DIFFRACTION98.87
2.1-2.130.27221660.21483512X-RAY DIFFRACTION99.43
2.13-2.150.23882190.2163534X-RAY DIFFRACTION99.65
2.15-2.190.25311880.20913495X-RAY DIFFRACTION99.81
2.19-2.220.25972130.21123513X-RAY DIFFRACTION99.95
2.22-2.250.25691800.20333566X-RAY DIFFRACTION100
2.25-2.290.24051970.20233536X-RAY DIFFRACTION100
2.29-2.330.2521810.20153587X-RAY DIFFRACTION100
2.33-2.370.2441950.20223514X-RAY DIFFRACTION100
2.37-2.420.23731870.19393554X-RAY DIFFRACTION100
2.42-2.470.26311280.19553605X-RAY DIFFRACTION100
2.47-2.520.2541610.19823554X-RAY DIFFRACTION100
2.52-2.580.22482120.19753558X-RAY DIFFRACTION100
2.58-2.640.23532170.20013525X-RAY DIFFRACTION100
2.64-2.710.20781980.1993574X-RAY DIFFRACTION100
2.71-2.790.21351770.2013586X-RAY DIFFRACTION100
2.79-2.880.251870.20033559X-RAY DIFFRACTION99.97
2.88-2.990.2511860.19563568X-RAY DIFFRACTION100
2.99-3.110.21321790.2043602X-RAY DIFFRACTION100
3.11-3.250.22471930.20043576X-RAY DIFFRACTION99.97
3.25-3.420.21251960.18673589X-RAY DIFFRACTION100
3.42-3.630.22091820.1743587X-RAY DIFFRACTION99.97
3.63-3.910.16471650.15783649X-RAY DIFFRACTION99.97
3.91-4.30.17032040.14373630X-RAY DIFFRACTION100
4.3-4.920.16031790.13483666X-RAY DIFFRACTION99.97
4.92-6.190.17471870.16583689X-RAY DIFFRACTION99.9
6.19-25.640.15292200.15193733X-RAY DIFFRACTION97.7

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