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- PDB-1b5e: DCMP HYDROXYMETHYLASE FROM T4 -

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Basic information

Entry
Database: PDB / ID: 1b5e
TitleDCMP HYDROXYMETHYLASE FROM T4
ComponentsPROTEIN (DEOXYCYTIDYLATE HYDROXYMETHYLASE)
KeywordsTRANSFERASE / HYDROXYMETHYLASE / DNTP SYNTHESIZING COMPLEX
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
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / Deoxycytidylate 5-hydroxymethyltransferase
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.6 Å
AuthorsSong, H.K. / Sohn, S.H. / Suh, S.W.
CitationJournal: EMBO J. / Year: 1999
Title: Crystal structure of deoxycytidylate hydroxymethylase from bacteriophage T4, a component of the deoxyribonucleoside triphosphate-synthesizing complex.
Authors: Song, H.K. / Sohn, S.H. / Suh, S.W.
History
DepositionJan 6, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (DEOXYCYTIDYLATE HYDROXYMETHYLASE)
B: PROTEIN (DEOXYCYTIDYLATE HYDROXYMETHYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6614
Polymers57,0462
Non-polymers6142
Water2,846158
1
A: PROTEIN (DEOXYCYTIDYLATE HYDROXYMETHYLASE)
B: PROTEIN (DEOXYCYTIDYLATE HYDROXYMETHYLASE)
hetero molecules

A: PROTEIN (DEOXYCYTIDYLATE HYDROXYMETHYLASE)
B: PROTEIN (DEOXYCYTIDYLATE HYDROXYMETHYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,3228
Polymers114,0934
Non-polymers1,2294
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-30 kcal/mol
Surface area18950 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)174.220, 53.120, 75.170
Angle α, β, γ (deg.)90.00, 115.29, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.630999, 0.000917, 0.775783), (0.000776, -1, 0.00055), (0.775783, 0.000255, -0.631)
Vector: -0.0152, 4.7134, 0.1217)

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Components

#1: Protein PROTEIN (DEOXYCYTIDYLATE HYDROXYMETHYLASE) / EC 2.1.2.8 / DEOXYCYTIDYLATE HYDROXYMETHYLASE / DCMP HYDROXYMETHYLASE


Mass: 28523.229 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato
References: UniProt: P08773, deoxycytidylate 5-hydroxymethyltransferase
#2: Chemical ChemComp-DCM / 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE


Mass: 307.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 54 %
Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD.
Crystal growpH: 8 / Details: pH 8.0
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Song, S.H., (1999) Acta Crystallogr. D55, 1061. / pH: 8.73
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19 mg/mlprotein1drop
2dCMP1drop
3100 0.9Tris-HCl1reservoir
40.9 Msodium citrate1reservoirpH8.73

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Apr 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 80033 / % possible obs: 97.3 % / Redundancy: 6.4 % / Rsym value: 0.066

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Processing

Software
NameVersionClassification
CCP4model building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 1.6→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.208 -5 %RANDOM
Rwork0.189 ---
obs0.189 76944 97.3 %-
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3944 0 40 158 4142
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg0.921
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor fileSerial no: 3 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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