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- PDB-2w4l: Human dCMP deaminase -

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Basic information

Entry
Database: PDB / ID: 2w4l
TitleHuman dCMP deaminase
ComponentsDEOXYCYTIDYLATE DEAMINASE
KeywordsHYDROLASE / PYRIMIDINE METABOLISM / NUCLEOTIDE BIOSYNTHESIS / ZINC / HEXAMER / METAL-BINDING / PHOSPHOPROTEIN / ALLOSTERIC ENZYME
Function / homology
Function and homology information


dCMP deaminase / dCMP deaminase activity / 5-hydroxymethyl-dUMP N-hydrolase activity / nucleoside salvage / pyrimidine nucleotide metabolic process / dUMP biosynthetic process / Interconversion of nucleotide di- and triphosphates / dTMP biosynthetic process / zinc ion binding / identical protein binding ...dCMP deaminase / dCMP deaminase activity / 5-hydroxymethyl-dUMP N-hydrolase activity / nucleoside salvage / pyrimidine nucleotide metabolic process / dUMP biosynthetic process / Interconversion of nucleotide di- and triphosphates / dTMP biosynthetic process / zinc ion binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Deoxycytidylate deaminase / Deoxycytidylate deaminase domain / Deoxycytidylate deaminase-related / Cytidine and deoxycytidylate deaminase zinc-binding region / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. ...Deoxycytidylate deaminase / Deoxycytidylate deaminase domain / Deoxycytidylate deaminase-related / Cytidine and deoxycytidylate deaminase zinc-binding region / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Deoxycytidylate deaminase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSiponen, M.I. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. ...Siponen, M.I. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Nilsson, M.E. / Nyman, T. / Persson, C. / Sagemark, J. / Schuler, H. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Wikstrom, M. / Wisniewska, M. / Nordlund, P.
CitationJournal: To be Published
Title: The Crystal Structure of Human Dcmp Deaminase
Authors: Siponen, M.I. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / ...Authors: Siponen, M.I. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Nilsson, M.E. / Nyman, T. / Persson, C. / Sagemark, J. / Schuler, H. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Wikstrom, M. / Wisniewska, M. / Nordlund, P.
History
DepositionNov 28, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DEOXYCYTIDYLATE DEAMINASE
B: DEOXYCYTIDYLATE DEAMINASE
C: DEOXYCYTIDYLATE DEAMINASE
D: DEOXYCYTIDYLATE DEAMINASE
E: DEOXYCYTIDYLATE DEAMINASE
F: DEOXYCYTIDYLATE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,44716
Polymers120,9136
Non-polymers53410
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25220 Å2
ΔGint-159.6 kcal/mol
Surface area48130 Å2
MethodPQS
Unit cell
Length a, b, c (Å)66.230, 80.070, 96.240
Angle α, β, γ (deg.)90.00, 94.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DEOXYCYTIDYLATE DEAMINASE / DCMP DEAMINSE


Mass: 20152.150 Da / Num. of mol.: 6 / Fragment: 5-173
Source method: isolated from a genetically manipulated source
Details: CONSTRUCT HAS C-TERMINAL HISTAG / Source: (gene. exp.) HOMO SAPIENS (human) / Description: MGC / Plasmid: PNIC-CH2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) R3 PRARE / References: UniProt: P32321, dCMP deaminase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsWE HAVE A C-TERMINAL HIS-TAG AND A TWO AMINOACID LINKER RESIDUES -SAHHHHHH

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.55 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 58496 / % possible obs: 99.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.55
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HVW

2hvw


Resolution: 2.1→29.7 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.816 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2924 5 %RANDOM
Rwork0.2 ---
obs0.202 55550 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.01 Å2
2---0.03 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7248 0 10 252 7510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227436
X-RAY DIFFRACTIONr_bond_other_d0.0010.025036
X-RAY DIFFRACTIONr_angle_refined_deg1.0341.95310054
X-RAY DIFFRACTIONr_angle_other_deg0.826312315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3975930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4724.679327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.239151277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5321531
X-RAY DIFFRACTIONr_chiral_restr0.0630.21104
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028240
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021488
X-RAY DIFFRACTIONr_nbd_refined0.1870.21476
X-RAY DIFFRACTIONr_nbd_other0.180.25119
X-RAY DIFFRACTIONr_nbtor_refined0.1710.23706
X-RAY DIFFRACTIONr_nbtor_other0.0840.23860
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2254
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2540.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6331.54811
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.09627495
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.18633061
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.874.52552
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.286 213
Rwork0.226 4045

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