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- PDB-1ux1: Bacillus subtilis cytidine deaminase with a Cys53His and an Arg56... -

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Basic information

Entry
Database: PDB / ID: 1ux1
TitleBacillus subtilis cytidine deaminase with a Cys53His and an Arg56Gln substitution
ComponentsCYTIDINE DEAMINASE
KeywordsHYDROLASE / CYTIDINE DEAMINASE / CDD / TETRAMER / ZINC BINDING / PYRIMIDINE METABOLISM / SALVAGE
Function / homology
Function and homology information


cytidine deaminase / cytidine deamination / deoxycytidine deaminase activity / cytidine deaminase activity / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
Cytidine deaminase, homotetrameric / 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
TETRAHYDRODEOXYURIDINE / Cytidine deaminase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsJohansson, E. / Neuhard, J. / Willemoes, M. / Larsen, S.
CitationJournal: Biochemistry / Year: 2004
Title: Structural, Kinetic, and Mutational Studies of the Zinc Ion Environment in Tetrameric Cytidine Deaminase
Authors: Johansson, E. / Neuhard, J. / Willemoes, M. / Larsen, S.
History
DepositionFeb 18, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 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 / struct_site
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 / _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

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Assembly

Deposited unit
A: CYTIDINE DEAMINASE
B: CYTIDINE DEAMINASE
C: CYTIDINE DEAMINASE
D: CYTIDINE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,80413
Polymers59,5004
Non-polymers1,3059
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)62.484, 62.484, 221.604
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-2002-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.260457, 0.954156, 0.147471), (0.95353, -0.278176, 0.11575), (0.151467, 0.11047, -0.98227)-7.0863, -18.56337, 178.45891
2given(-0.980847, 0.004784, -0.194722), (0.011362, -0.996591, -0.08172), (-0.194449, -0.082367, 0.977448)62.99423, 28.70962, 7.33272
3given(-0.286679, -0.957326, 0.036628), (-0.95697, 0.284359, -0.05786), (0.044975, -0.051639, -0.997653)36.29831, 34.82265, 183.99223

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Components

#1: Protein
CYTIDINE DEAMINASE / / CYTIDINE AMINOHYDROLASE / CDA


Mass: 14874.952 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Plasmid: PTRCC53H/R56QCDA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SO5201 / References: UniProt: P19079, cytidine deaminase
#2: Chemical
ChemComp-THU / TETRAHYDRODEOXYURIDINE


Mass: 230.218 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O5
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION ARG 56 GLN IN CHAINS A B C D ENGINEERED MUTATION CYS 53 HIS IN CHAINS A B C D ...ENGINEERED MUTATION ARG 56 GLN IN CHAINS A B C D ENGINEERED MUTATION CYS 53 HIS IN CHAINS A B C D THIS ENZYME SCAVENGES EXOGENOUS AND ENDOGENOUS CYTIDINE AND 2'-DEOXYCYTIDINE FOR UMP SYNTHESIS.

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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: 2.1 Å3/Da / Density % sol: 41.4 %
Crystal growMethod: vapor diffusion / pH: 7.5
Details: VAPOUR DIFFUSION AT RT: PROTEIN: 4.6 MG/ML, + 5 MM TETRAHYDRODEOXYURIDINE, PRECIPITANT: 30 % PEG400, 0.2M MAGNESIUM CHLORIDE, 0.1 M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 23, 2002 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.36→25 Å / Num. obs: 21401 / % possible obs: 98.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 29.8
Reflection shellResolution: 2.36→2.41 Å / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 6.9 / % possible all: 83.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JTK

1jtk


Resolution: 2.36→24.66 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2004857.7 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1071 5 %RANDOM
Rwork0.213 ---
obs0.213 21345 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.6894 Å2 / ksol: 0.346096 e/Å3
Displacement parametersBiso mean: 32.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20.34 Å20 Å2
2---0.96 Å20 Å2
3---1.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.36→24.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3940 0 76 98 4114
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.292
X-RAY DIFFRACTIONc_scbond_it2.162
X-RAY DIFFRACTIONc_scangle_it3.162.5
LS refinement shellResolution: 2.36→2.51 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 163 4.9 %
Rwork0.241 3166 -
obs--94.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4THU_PARTHU_TOP

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