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- PDB-7vyj: The structure of GdmN in complex with carbamoyl adenylate intermediate -

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Basic information

Entry
Database: PDB / ID: 7vyj
TitleThe structure of GdmN in complex with carbamoyl adenylate intermediate
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-CA0 / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / : / DI(HYDROXYETHYL)ETHER / GdmN
Similarity search - Component
Biological speciesStreptomyces hygroscopicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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 14, 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)151,46630
Polymers148,7312
Non-polymers2,73528
Water11,944663
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10050 Å2
ΔGint-76 kcal/mol
Surface area46230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.531, 110.531, 231.460
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, 691 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-CA0 / 5'-O-[(S)-(carbamoyloxy)(hydroxy)phosphoryl]adenosine


Mass: 390.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N6O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CP / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER


Mass: 141.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4NO5P
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 663 / 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: 2.74 Å3/Da / Density % sol: 55.18 %
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: Dec 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 114099 / % possible obs: 100 % / Redundancy: 9.7 % / Biso Wilson estimate: 25.58 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.029 / Rrim(I) all: 0.09 / Rsym value: 0.087 / Net I/σ(I): 27.737
Reflection shellResolution: 1.98→2.01 Å / Num. unique obs: 5676 / Rsym value: 1.046

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Processing

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

3ven


Resolution: 1.98→36.88 Å / SU ML: 0.1961 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.1693
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2071 5629 5.04 %
Rwork0.1772 106078 -
obs0.1787 111707 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.43 Å2
Refinement stepCycle: LAST / Resolution: 1.98→36.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10423 0 166 663 11252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810851
X-RAY DIFFRACTIONf_angle_d0.948614739
X-RAY DIFFRACTIONf_chiral_restr0.05771620
X-RAY DIFFRACTIONf_plane_restr0.00971937
X-RAY DIFFRACTIONf_dihedral_angle_d29.48671533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-20.29791220.23292340X-RAY DIFFRACTION64.86
2-2.030.26711370.24122856X-RAY DIFFRACTION80.57
2.03-2.050.28831930.23283366X-RAY DIFFRACTION93.51
2.05-2.080.29431830.2193484X-RAY DIFFRACTION98.02
2.08-2.110.25251860.2243567X-RAY DIFFRACTION99.58
2.11-2.140.25781810.21663563X-RAY DIFFRACTION99.68
2.14-2.170.27111820.20993586X-RAY DIFFRACTION99.87
2.17-2.20.24561950.20573577X-RAY DIFFRACTION99.95
2.2-2.230.24261630.20773557X-RAY DIFFRACTION100
2.23-2.270.23692250.20053557X-RAY DIFFRACTION100
2.27-2.310.2511770.20513588X-RAY DIFFRACTION100
2.31-2.350.23192000.20383601X-RAY DIFFRACTION100
2.35-2.40.27061690.20163610X-RAY DIFFRACTION100
2.4-2.440.22011630.18933598X-RAY DIFFRACTION100
2.44-2.50.20471900.1993582X-RAY DIFFRACTION100
2.5-2.560.23221880.18913612X-RAY DIFFRACTION99.97
2.56-2.620.23082020.19233574X-RAY DIFFRACTION100
2.62-2.690.23472180.19183574X-RAY DIFFRACTION99.97
2.69-2.770.23532080.19423583X-RAY DIFFRACTION100
2.77-2.860.20931930.19313602X-RAY DIFFRACTION100
2.86-2.960.23532070.1823581X-RAY DIFFRACTION100
2.96-3.080.2182140.18643618X-RAY DIFFRACTION99.97
3.08-3.220.22642120.18253591X-RAY DIFFRACTION100
3.22-3.390.20471920.18263609X-RAY DIFFRACTION99.95
3.39-3.60.18831920.16113642X-RAY DIFFRACTION100
3.6-3.880.16561880.15323649X-RAY DIFFRACTION100
3.88-4.270.16341690.14413696X-RAY DIFFRACTION99.97
4.27-4.890.14241960.13273676X-RAY DIFFRACTION99.95
4.89-6.150.17311810.16353766X-RAY DIFFRACTION100
6.15-36.880.17772030.15293873X-RAY DIFFRACTION99.63

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