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- PDB-6l18: XFEL structure of T4dCH D179N mutant complex with natively expres... -

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Basic information

Entry
Database: PDB / ID: 6l18
TitleXFEL structure of T4dCH D179N mutant complex with natively expressed dTMP
ComponentsDeoxycytidylate 5-hydroxymethyltransferase
KeywordsTRANSFERASE / XFEL / Room temperature / dTMP / Complex / Natively inhibited / Hydroxymethylase
Function / homology
Function and homology information


deoxycytidylate 5-hydroxymethyltransferase / deoxycytidylate 5-hydroxymethyltransferase activity
Similarity search - Function
Deoxycytidylate hydroxymethylase / Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / THYMIDINE-5'-PHOSPHATE / Deoxycytidylate 5-hydroxymethyltransferase
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsPark, S.H. / Song, H.K.
CitationJournal: Sci Rep / Year: 2019
Title: A host dTMP-bound structure of T4 phage dCMP hydroxymethylase mutant using an X-ray free electron laser.
Authors: Park, S.H. / Park, J. / Lee, S.J. / Yang, W.S. / Park, S. / Kim, K. / Park, Z.Y. / Song, H.K.
History
DepositionSep 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine / refine_hist / refine_ls_shell / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.ls_d_res_low / _refine.ls_number_reflns_obs / _refine_hist.d_res_low / _refine_ls_shell.d_res_low / _refine_ls_shell.percent_reflns_obs / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deoxycytidylate 5-hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3424
Polymers29,8701
Non-polymers4723
Water1,08160
1
A: Deoxycytidylate 5-hydroxymethyltransferase
hetero molecules

A: Deoxycytidylate 5-hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6848
Polymers59,7392
Non-polymers9446
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7030 Å2
ΔGint-56 kcal/mol
Surface area20950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.860, 74.970, 157.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

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Components

#1: Protein Deoxycytidylate 5-hydroxymethyltransferase / Deoxycytidylate hydroxymethylase / dCMP hydroxymethylase / dCMP HMase


Mass: 29869.676 Da / Num. of mol.: 1 / Mutation: D179N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 42 / Production host: Escherichia coli (E. coli)
References: UniProt: P08773, deoxycytidylate 5-hydroxymethyltransferase
#2: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
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: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 293 K / Method: small tubes / pH: 8.5
Details: 2 ul of 1.0 M Tris-HCl pH 8.5 2 ul of 1.0 M NaI 17 ul of C6H5Na3 2H2O 10 ul of 40mg/ml D179N mutant protein

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Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: PAL-XFEL / Beamline: NCI / Wavelength: 1.2782 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Sep 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2782 Å / Relative weight: 1
ReflectionResolution: 1.88→40 Å / Num. obs: 27244 / % possible obs: 100 % / Redundancy: 595.9 % / R split: 0.1914 / Net I/σ(I): 4.87
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 176.2 % / Mean I/σ(I) obs: 2.51 / Num. unique obs: 2687 / R split: 0.3795 / % possible all: 100
Serial crystallography measurementPulse duration: 30 fsec. / Pulse energy: 9.7 µJ
Serial crystallography data reductionFrames total: 22925

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.17 Å44.79 Å
Translation4.17 Å44.79 Å

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Processing

Software
NameVersionClassification
PHASER2.8.1phasing
XDSdata reduction
PHENIX1.13-2998refinement
PDB_EXTRACT3.25data extraction
CrystFELdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B5E

1b5e


Resolution: 1.9→37.4923 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.1905 1360 -
Rwork0.1691 --
obs-26554 100 %
Displacement parametersBiso max: 138 Å2 / Biso mean: 58.2769 Å2 / Biso min: 38.42 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.4923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2009 0 23 60 2092
LS refinement shellResolution: 1.9→1.9679 Å /
Rfactor% reflection
Rfree0.229 -
Rwork0.2108 -
obs-100 %
Refinement TLS params.Method: refined / Origin x: 8.186 Å / Origin y: 9.8896 Å / Origin z: 24.1111 Å
111213212223313233
T0.4424 Å2-0.0021 Å2-0.0019 Å2-0.4524 Å20.0053 Å2--0.4593 Å2
L0.9958 °20.4005 °20.1428 °2-0.9264 °20.0247 °2--1.4578 °2
S-0.0478 Å °0.0688 Å °0.1443 Å °-0.1335 Å °0.0312 Å °0.0394 Å °-0.1138 Å °0.0272 Å °0.0228 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 246
2X-RAY DIFFRACTION1allA301 - 460

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