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- PDB-7vzz: The structure of GdmN in complex with the natural tetrahedral int... -

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Basic information

Entry
Database: PDB / ID: 7vzz
TitleThe structure of GdmN in complex with the natural tetrahedral intermediate, carbamoyl adenylate, and 20-O-methyl-19-chloroproansamitocin
ComponentsGdmN
KeywordsTRANSFERASE / Homodimer / Carbamoyltransferase / Ansamycins antibiotics
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 / Chem-8CW / Chem-CA0 / : / GdmN
Similarity search - Component
Biological speciesStreptomyces hygroscopicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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)156,42927
Polymers153,0742
Non-polymers3,35625
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9360 Å2
ΔGint-100 kcal/mol
Surface area45210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.860, 111.860, 231.272
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) / References: UniProt: Q84G19

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Non-polymers , 7 types, 41 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#3: 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
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-CA0 / 5'-O-[(S)-(carbamoyloxy)(hydroxy)phosphoryl]adenosine


Mass: 390.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N6O8P / Feature type: SUBJECT OF INVESTIGATION
#7: 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.: 1 / Source method: obtained synthetically / Formula: C26H34ClNO6 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.73 Å3/Da / Density % sol: 54.92 %
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: 2.85→50 Å / Num. obs: 39792 / % possible obs: 100 % / Redundancy: 15.2 % / Biso Wilson estimate: 47.78 Å2 / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 27.6
Reflection shellResolution: 2.85→2.9 Å / Rmerge(I) obs: 0.5 / Num. unique obs: 1921 / Rsym value: 0.5

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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: 2.85→25.7 Å / SU ML: 0.317 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.122
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2252 1976 4.99 %
Rwork0.1753 37659 -
obs0.1778 39635 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.98 Å2
Refinement stepCycle: LAST / Resolution: 2.85→25.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10407 0 209 16 10632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009810843
X-RAY DIFFRACTIONf_angle_d1.098414735
X-RAY DIFFRACTIONf_chiral_restr0.05531618
X-RAY DIFFRACTIONf_plane_restr0.00971934
X-RAY DIFFRACTIONf_dihedral_angle_d16.25223896
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.920.30721380.22062599X-RAY DIFFRACTION98.31
2.92-30.28241670.2052613X-RAY DIFFRACTION99.96
3-3.090.29521170.2272682X-RAY DIFFRACTION100
3.09-3.190.27721190.21662680X-RAY DIFFRACTION100
3.19-3.30.28171260.23142681X-RAY DIFFRACTION100
3.31-3.440.25551360.19762658X-RAY DIFFRACTION99.96
3.44-3.590.25361330.19272697X-RAY DIFFRACTION99.93
3.59-3.780.22531580.17392647X-RAY DIFFRACTION99.96
3.78-4.020.22531640.17182668X-RAY DIFFRACTION99.93
4.02-4.330.20621200.15482712X-RAY DIFFRACTION99.93
4.33-4.760.19911470.14042694X-RAY DIFFRACTION99.89
4.76-5.440.20671600.15552706X-RAY DIFFRACTION99.97
5.44-6.840.20481330.17812774X-RAY DIFFRACTION100
6.84-25.70.17471580.1482848X-RAY DIFFRACTION99.04

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