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- PDB-7qrh: Crystal structure of the 5-(aminomethyl)furan-3-yl methyl phospha... -

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Basic information

Entry
Database: PDB / ID: 7qrh
TitleCrystal structure of the 5-(aminomethyl)furan-3-yl methyl phosphate kinase MfnE from Methanococcus vannielii.
ComponentsAspartate/glutamate/uridylate kinase
KeywordsTRANSFERASE / Phosphate Kinase
Function / homologyMfnE family / : / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family / kinase activity / Aspartate/glutamate/uridylate kinase
Function and homology information
Biological speciesMethanococcus vannielii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsMaddock, R.M.A. / Race, P.R. / Burton, N.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI) United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of the 5-(aminomethyl)furan-3-yl methyl phosphate kinase MfnE from Methanococcus vannielii.
Authors: Maddock, R.M.A. / Race, P.R.
History
DepositionJan 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: 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
AAA: Aspartate/glutamate/uridylate kinase
BBB: Aspartate/glutamate/uridylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6384
Polymers50,4462
Non-polymers1922
Water32418
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Other members of this family present as trimers. PISA analysis indicates this protein exists as either a dimer or quatramer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.147, 86.147, 234.105
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Aspartate/glutamate/uridylate kinase


Mass: 25223.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus vannielii (archaea) / Strain: ATCC 35089 / DSM 1224 / JCM 13029 / OCM 148 / SB / Gene: Mevan_0710 / Plasmid: pOPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A6UQ44
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.49 Å3/Da / Density % sol: 50.51 % / Description: Teardrop hexagon.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M (NH4)2SO4, 0.1 M HEPES pH 7.5, 35% w/v PAA 2100

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.36→78.04 Å / Num. obs: 22089 / % possible obs: 100 % / Redundancy: 113.8 % / CC1/2: 1 / Net I/σ(I): 22.3
Reflection shellResolution: 2.36→2.45 Å / Num. unique obs: 2259 / CC1/2: 0.306

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PHENIX1.19.2model building
PHASERphasing
xia2data scaling
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TrRosetta

Resolution: 2.36→74.717 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / Cross valid method: FREE R-VALUE / ESU R: 0.318 / ESU R Free: 0.245
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2576 1097 4.996 %
Rwork0.2036 20860 -
all0.206 --
obs-21957 99.524 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.762 Å20.381 Å20 Å2
2--0.762 Å20 Å2
3----2.472 Å2
Refinement stepCycle: LAST / Resolution: 2.36→74.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3245 0 10 18 3273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133305
X-RAY DIFFRACTIONr_bond_other_d0.0350.0173222
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.6324479
X-RAY DIFFRACTIONr_angle_other_deg2.3271.5777506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0385418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63425.118127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.42215615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.215156
X-RAY DIFFRACTIONr_chiral_restr0.0640.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023577
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02589
X-RAY DIFFRACTIONr_nbd_refined0.1960.2654
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2210.22784
X-RAY DIFFRACTIONr_nbtor_refined0.1580.21607
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21409
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.256
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2430.29
X-RAY DIFFRACTIONr_nbd_other0.2290.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1110.26
X-RAY DIFFRACTIONr_mcbond_it6.9918.211678
X-RAY DIFFRACTIONr_mcbond_other6.9938.2071677
X-RAY DIFFRACTIONr_mcangle_it9.33812.3122094
X-RAY DIFFRACTIONr_mcangle_other9.33612.3162095
X-RAY DIFFRACTIONr_scbond_it7.7518.7941627
X-RAY DIFFRACTIONr_scbond_other7.7058.7821620
X-RAY DIFFRACTIONr_scangle_it10.47812.9532385
X-RAY DIFFRACTIONr_scangle_other10.47812.9442378
X-RAY DIFFRACTIONr_lrange_it12.77198.0273521
X-RAY DIFFRACTIONr_lrange_other12.7798.0663522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.4210.384760.4191513X-RAY DIFFRACTION98.8799
2.421-2.4880.462670.4021456X-RAY DIFFRACTION98.9604
2.488-2.560.4740.3271408X-RAY DIFFRACTION99.0642
2.56-2.6390.346760.3151379X-RAY DIFFRACTION99.047
2.639-2.7250.331660.281350X-RAY DIFFRACTION99.2987
2.725-2.8210.352700.241301X-RAY DIFFRACTION99.8543
2.821-2.9270.269620.2021279X-RAY DIFFRACTION99.6285
2.927-3.0470.256550.1941225X-RAY DIFFRACTION99.6885
3.047-3.1820.31630.2041174X-RAY DIFFRACTION99.8386
3.182-3.3380.221600.211124X-RAY DIFFRACTION99.7473
3.338-3.5180.276700.2211057X-RAY DIFFRACTION99.7345
3.518-3.7310.29470.2151043X-RAY DIFFRACTION99.9083
3.731-3.9890.299540.198962X-RAY DIFFRACTION99.9017
3.989-4.3080.257490.179918X-RAY DIFFRACTION100
4.308-4.720.183430.15834X-RAY DIFFRACTION100
4.72-5.2760.241410.161774X-RAY DIFFRACTION100
5.276-6.0920.286400.218687X-RAY DIFFRACTION100
6.092-7.460.259410.217594X-RAY DIFFRACTION100
7.46-10.5450.199290.154480X-RAY DIFFRACTION100
10.545-74.7170.19140.242302X-RAY DIFFRACTION97.8328

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