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- PDB-7vzu: The structure of GdmN Y82F mutant -

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Basic information

Entry
Database: PDB / ID: 7vzu
TitleThe structure of GdmN Y82F mutant
ComponentsGdmN
KeywordsTRANSFERASE / Homodimer / Carbamoyltransferase / Ansamycins antibiotics
Function / homology
Function and homology information


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
Biological speciesStreptomyces hygroscopicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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

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Assembly

Deposited unit
A: GdmN
B: GdmN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,00615
Polymers153,0422
Non-polymers96413
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-111 kcal/mol
Surface area46700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.692, 111.692, 231.408
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

#1: Protein GdmN


Mass: 76520.984 Da / Num. of mol.: 2 / Mutation: Y82F
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
#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.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
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: 2.72 Å3/Da / Density % sol: 54.82 %
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: Nov 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 75086 / % possible obs: 100 % / Redundancy: 17.5 % / Biso Wilson estimate: 28.78 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 29.188
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.388 / Num. unique obs: 3675 / Rsym value: 0.388

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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: 2.3→35.83 Å / SU ML: 0.2645 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.1065
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2268 3736 4.99 %
Rwork0.1824 71098 -
obs0.1846 74834 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.04 Å2
Refinement stepCycle: LAST / Resolution: 2.3→35.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10391 0 51 292 10734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007910681
X-RAY DIFFRACTIONf_angle_d0.889614522
X-RAY DIFFRACTIONf_chiral_restr0.05191603
X-RAY DIFFRACTIONf_plane_restr0.0091921
X-RAY DIFFRACTIONf_dihedral_angle_d6.65951497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.26921500.22192523X-RAY DIFFRACTION97.31
2.33-2.360.29991470.22072545X-RAY DIFFRACTION99.08
2.36-2.390.31891550.2182547X-RAY DIFFRACTION99.08
2.39-2.430.28691500.20732628X-RAY DIFFRACTION99.86
2.43-2.460.24511230.21442586X-RAY DIFFRACTION99.85
2.46-2.50.30131340.20642597X-RAY DIFFRACTION99.93
2.5-2.540.24861290.2062651X-RAY DIFFRACTION99.96
2.54-2.590.26381210.2042593X-RAY DIFFRACTION100
2.59-2.630.23271590.2072593X-RAY DIFFRACTION100
2.63-2.680.29211520.21412627X-RAY DIFFRACTION100
2.68-2.740.26971380.21142601X-RAY DIFFRACTION100
2.74-2.80.29041400.2172644X-RAY DIFFRACTION100
2.8-2.860.31351070.21752634X-RAY DIFFRACTION100
2.86-2.930.28861210.22152638X-RAY DIFFRACTION100
2.93-3.010.25371330.21482632X-RAY DIFFRACTION100
3.01-3.10.31381350.21942642X-RAY DIFFRACTION100
3.1-3.20.25221220.22262616X-RAY DIFFRACTION100
3.2-3.320.2651270.2212652X-RAY DIFFRACTION100
3.32-3.450.26351440.19652621X-RAY DIFFRACTION100
3.45-3.610.21241510.18372675X-RAY DIFFRACTION100
3.61-3.80.1991580.16332595X-RAY DIFFRACTION100
3.8-4.030.20031310.15962679X-RAY DIFFRACTION100
4.03-4.340.14031530.13922637X-RAY DIFFRACTION100
4.34-4.780.15231160.12792695X-RAY DIFFRACTION100
4.78-5.470.18161440.14172698X-RAY DIFFRACTION100
5.47-6.880.2181500.16952726X-RAY DIFFRACTION100
6.89-35.830.17331460.14282823X-RAY DIFFRACTION98.67

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