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- PDB-1ux0: Bacillus subtilis cytidine deaminase with an Arg56 - Gln substitution -

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Basic information

Entry
Database: PDB / ID: 1ux0
TitleBacillus subtilis cytidine deaminase with an Arg56 - Gln substitution
ComponentsCYTIDINE DEAMINASE
KeywordsHYDROLASE / CYTIDINE DEAMINASE / CDD / TETRAMER / ZINC BINDING / PYRIMIDINE METABOLISM / SALVAGE
Function / homology
Function and homology information


cytidine deaminase / cytidine deamination / 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 ...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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.99 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 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Dec 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2716
Polymers29,6802
Non-polymers5914
Water2,612145
1
A: CYTIDINE DEAMINASE
B: CYTIDINE DEAMINASE
hetero molecules

A: CYTIDINE DEAMINASE
B: CYTIDINE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,54212
Polymers59,3604
Non-polymers1,1838
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
MethodPQS
Unit cell
Length a, b, c (Å)74.880, 66.098, 55.514
Angle α, β, γ (deg.)90.00, 115.64, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999936, 0.001283, -0.011201), (-0.001334, -0.999989, 0.004566), (-0.011195, 0.00458, 0.999927)
Vector: 26.39634, 117.58556, -0.1609)

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Components

#1: Protein CYTIDINE DEAMINASE / CYTIDINE AMINOHYDROLASE / CDA


Mass: 14839.948 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Plasmid: PTRCR56QCDA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JF611 / References: UniProt: P19079, cytidine deaminase
#2: Chemical ChemComp-THU / TETRAHYDRODEOXYURIDINE


Mass: 230.218 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O5
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION ARG 56 GLN IN CHAINS A AND B. THIS ENZYME SCAVENGES EXOGENOUS AND ENDOGENOUS ...ENGINEERED MUTATION ARG 56 GLN IN CHAINS A AND B. THIS ENZYME SCAVENGES EXOGENOUS AND ENDOGENOUS CYTIDINE AND 2'-DEOXYCYTIDINE FOR UMP SYNTHESIS.
Sequence detailsTHIS IS AN R56Q MUTANT ENZYME

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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 %
Crystal growMethod: vapor diffusion / pH: 4.6
Details: VAPOUR DIFFUSION AT RT: PROTEIN: 4.6 MG/ML + 5 MM TETRAHYDRODEOXYURIDINE PRECIPITANT: 17-23 % MPD, 10 MM CALCIUM CHLORIDE 0.1 M SODIUM ACETATE, pH 4.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.968
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 22, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.99→20 Å / Num. obs: 16761 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 16.9
Reflection shellResolution: 1.99→2.04 Å / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 3.2 / % possible all: 99.4

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Processing

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

1jtk


Resolution: 1.99→19.95 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1404991.24 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.207 777 4.6 %RANDOM
Rwork0.191 ---
obs0.191 16757 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.6491 Å2 / ksol: 0.335711 e/Å3
Displacement parametersBiso mean: 24 Å2
Baniso -1Baniso -2Baniso -3
1--5.24 Å20 Å21.08 Å2
2--5.35 Å20 Å2
3----0.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.99→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 34 145 2131
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_mcangle_it1.622
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it2.672.5
LS refinement shellResolution: 1.99→2.11 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.202 85 3.1 %
Rwork0.192 2647 -
obs--98.4 %
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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