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- PDB-3r2n: Crystal structure of cytidine deaminase from Mycobacterium leprae -

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Basic information

Entry
Database: PDB / ID: 3r2n
TitleCrystal structure of cytidine deaminase from Mycobacterium leprae
ComponentsCytidine deaminase
KeywordsHYDROLASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / tuberculosis / cytidine deaminase / CDA / pyrimidine salvage / homotetramer / drug resistance / zinc binding protein / catalytic zinc
Function / homology
Function and homology information


cytidine deaminase / : / 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
Cytidine deaminase / Cytidine deaminase
Similarity search - Component
Biological speciesMycobacterium leprae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionMar 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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: Cytidine deaminase
B: Cytidine deaminase
C: Cytidine deaminase
D: Cytidine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,84013
Polymers58,2384
Non-polymers6029
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8990 Å2
ΔGint-194 kcal/mol
Surface area16900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.840, 79.740, 104.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 4 / Auth seq-ID: 3 - 120 / Label seq-ID: 7 - 124

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Cytidine deaminase


Mass: 14559.457 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium leprae (bacteria) / Strain: Br4923 / Gene: cdd, MLBr02174 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: B8ZST1, UniProt: A0A0H3MRL9*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.03 Å3/Da / Density % sol: 39.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MyleA.00495.a.A1 PS00720 at 66.15 mg/mL against JCSG+ screen condition D6, 0.2 M MgCl2, 0.1 M Tris pH 8.5, 20% PEG 8000 with 25% ethylene glycol as cryo-protectant, crystal tracking ID ...Details: MyleA.00495.a.A1 PS00720 at 66.15 mg/mL against JCSG+ screen condition D6, 0.2 M MgCl2, 0.1 M Tris pH 8.5, 20% PEG 8000 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 217493d6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 21771 / Num. obs: 21604 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 39.824 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 16.65
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.3-2.365.60.4753.9885771584154497.5
2.36-2.420.4634.228686150898.1
2.42-2.490.3914.998672147798.2
2.49-2.570.3126.248792145598.9
2.57-2.660.2896.858571139799.1
2.66-2.750.2228.418451137199.3
2.75-2.850.186108287132699.7
2.85-2.970.16511.247974127199.8
2.97-3.10.1214.637533120099.5
3.1-3.250.10216.757427118299.9
3.25-3.430.07521.516946112099.5
3.43-3.640.06424.976539106499.8
3.64-3.890.05427.26606999999.9
3.89-4.20.04731.35572594899.9
4.2-4.60.04235.875160863100
4.6-5.140.04236.15474580899.9
5.14-5.940.04532.74403069099.7
5.94-7.270.03535.13735612100
7.27-10.290.02542.4282748299.8
10.290.02143.67154128798

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 49.09 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å46.28 Å
Translation3 Å46.28 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
BOSdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MPZ

3mpz


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.201 / WRfactor Rwork: 0.1688 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8573 / SU B: 15.263 / SU ML: 0.163 / SU R Cruickshank DPI: 0.3362 / SU Rfree: 0.2211 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.336 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2232 1078 5 %RANDOM
Rwork0.1824 ---
obs0.1844 21515 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 70.21 Å2 / Biso mean: 35.3068 Å2 / Biso min: 11.07 Å2
Baniso -1Baniso -2Baniso -3
1-4.48 Å20 Å20 Å2
2---0.71 Å20 Å2
3----3.76 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3486 0 26 110 3622
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223583
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.974873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4555485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.28124.245139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.20915522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9341520
X-RAY DIFFRACTIONr_chiral_restr0.0980.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212748
X-RAY DIFFRACTIONr_mcbond_it0.5441.52379
X-RAY DIFFRACTIONr_mcangle_it0.98223765
X-RAY DIFFRACTIONr_scbond_it1.71431204
X-RAY DIFFRACTIONr_scangle_it2.5654.51104
Refine LS restraints NCS

Ens-ID: 1 / Number: 849 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.250.5
2BMEDIUM POSITIONAL0.250.5
3CMEDIUM POSITIONAL0.30.5
4DMEDIUM POSITIONAL0.240.5
1AMEDIUM THERMAL0.942
2BMEDIUM THERMAL0.862
3CMEDIUM THERMAL0.962
4DMEDIUM THERMAL0.862
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 82 -
Rwork0.235 1455 -
all-1537 -
obs--97.28 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.25880.297-0.78371.6156-0.07681.5490.1562-0.0975-0.00520.0047-0.03180.0457-0.19040.1799-0.12440.0593-0.04840.01480.0907-0.00160.024922.52911.290321.8587
20.89140.63460.15841.2633-0.47771.8823-0.0201-0.03540.0028-0.12320.0431-0.10490.2655-0.0677-0.0230.1421-0.0320.01380.0216-0.00870.023615.2327-11.1568-1.3382
30.99610.8517-0.21311.6383-0.08391.1146-0.0102-0.0083-0.029-0.06540.0354-0.0406-0.0277-0.0063-0.02520.0206-0.01020.02030.08080.00250.024224.25229.6164-4.0116
40.31090.6853-0.04651.9571-0.31492.00530.0573-0.02780.0915-0.0380.03540.10910.1903-0.1771-0.09280.0699-0.04250.03040.09650.01160.07162.59840.078219.4966
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 121
2X-RAY DIFFRACTION1A135 - 136
3X-RAY DIFFRACTION2B1 - 121
4X-RAY DIFFRACTION2B135 - 136
5X-RAY DIFFRACTION3C3 - 121
6X-RAY DIFFRACTION3C135 - 136
7X-RAY DIFFRACTION4D0 - 121
8X-RAY DIFFRACTION4D135 - 136

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