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- PDB-1b5d: DCMP Hydroxymethylase from T4 (Intact) -

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Basic information

Entry
Database: PDB / ID: 1b5d
TitleDCMP Hydroxymethylase from T4 (Intact)
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 / MIR / Resolution: 2.2 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 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Feb 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
Water2,720151
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 area6520 Å2
ΔGint-32 kcal/mol
Surface area19590 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)176.230, 53.290, 75.860
Angle α, β, γ (deg.)90.00, 115.54, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.628872, -6.0E-6, 0.777509), (2.0E-5, -1, -2.4E-5), (0.777509, 3.0E-5, -0.628872)
Vector: 0.0039, 4.733, -0.018)

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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.: 151 / 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: 2.65 Å3/Da / Density % sol: 54 %
Crystal growpH: 8 / Details: pH 8.0
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
3100 0.9Tris-HCl1reservoir
40.9 Msodium citrate1reservoirpH8.73
2dCMP1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jun 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 28632 / % possible obs: 90 %

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Processing

Software
NameVersionClassification
X-PLOR3.843refinement
MADNESSdata reduction
FSSCALEdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.2→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.208 -5 %RANDOM
Rwork0.16 ---
obs0.16 28632 90 %-
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4018 0 40 151 4209
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg0.868
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

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