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- PDB-6a9b: T4 dCMP hydroxymethylase structure solved by I-SAD using a home source -

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Basic information

Entry
Database: PDB / ID: 6a9b
TitleT4 dCMP hydroxymethylase structure solved by I-SAD using a home source
ComponentsDeoxycytidylate 5-hydroxymethyltransferase
KeywordsTRANSFERASE / pyrimidine 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 / PHOSPHATE ION / Deoxycytidylate 5-hydroxymethyltransferase
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.01 Å
AuthorsPark, S.H. / Song, H.K.
CitationJournal: Iucrj / Year: 2019
Title: A cytosine modification mechanism revealed by the structure of a ternary complex of deoxycytidylate hydroxymethylase from bacteriophage T4 with its cofactor and substrate.
Authors: Park, S.H. / Suh, S.W. / Song, H.K.
History
DepositionJul 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deoxycytidylate 5-hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7453
Polymers28,5231
Non-polymers2222
Water3,693205
1
A: Deoxycytidylate 5-hydroxymethyltransferase
hetero molecules

A: Deoxycytidylate 5-hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4906
Polymers57,0462
Non-polymers4444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area5600 Å2
ΔGint-38 kcal/mol
Surface area20300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.603, 74.982, 155.345
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-483-

HOH

21A-605-

HOH

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Components

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


Mass: 28523.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 42 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P08773, deoxycytidylate 5-hydroxymethyltransferase
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O

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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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris-HCl pH 8.5 0.96 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 20840 / % possible obs: 99.8 % / Redundancy: 7 % / Biso Wilson estimate: 29.06 Å2 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.024 / Rrim(I) all: 0.064 / Χ2: 3.183 / Net I/σ(I): 27.3 / Num. measured all: 145060
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.01-2.046.80.20810260.9790.0850.2251.631100
2.04-2.0870.19310260.9810.0770.2081.712100
2.08-2.1270.16410130.9880.0660.1771.801100
2.12-2.1770.14110240.9880.0560.1521.937100
2.17-2.2170.13310260.9920.0540.1442.045100
2.21-2.2670.11810350.9920.0470.1272.21100
2.26-2.3270.10510330.9940.0420.1142.326100
2.32-2.387.10.110300.9940.040.1082.459100
2.38-2.4570.09610190.9950.0390.1042.65799.9
2.45-2.537.10.0910510.9950.0360.0972.85599.9
2.53-2.6270.08110420.9960.0320.0873.024100
2.62-2.7370.07710350.9950.0310.0843.233100
2.73-2.857.10.07210280.9960.0290.0773.545100
2.85-370.06410510.9970.0260.0693.671100
3-3.1970.05810260.9970.0240.0634.12399.9
3.19-3.4470.05310560.9980.0210.0584.194100
3.44-3.786.90.0510610.9980.020.0544.46499.4
3.78-4.336.90.04810610.9980.0190.0514.53499.6
4.33-5.456.90.04610650.9980.0190.054.95999.4
5.45-506.50.04511320.9990.0190.0496.05598.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.01→26.301 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.89
RfactorNum. reflection% reflection
Rfree0.1915 1995 9.61 %
Rwork0.1601 --
obs0.1632 20770 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.85 Å2 / Biso mean: 32.4642 Å2 / Biso min: 16.64 Å2
Refinement stepCycle: final / Resolution: 2.01→26.301 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2009 0 6 205 2220
Biso mean--33.23 38.81 -
Num. residues----246
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0104-2.06070.22341360.18181256139297
2.0607-2.11640.24931400.1611328146899
2.1164-2.17860.18791410.16113301471100
2.1786-2.24890.19931400.148113201460100
2.2489-2.32930.18781400.148813121452100
2.3293-2.42250.18231410.154513371478100
2.4225-2.53260.20791420.172113391481100
2.5326-2.6660.20951410.174913301471100
2.666-2.83290.23011430.179713371480100
2.8329-3.05130.20031430.175113431486100
3.0513-3.35780.18111440.153513601504100
3.3578-3.84240.16871430.14913561499100
3.8424-4.83610.14891470.14041380152799
4.8361-26.30370.22191540.173914471601100

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