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- PDB-4f3w: Crystal structure of cytidine deaminase Cdd from Mycobacterium marinum -

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Basic information

Entry
Database: PDB / ID: 4f3w
TitleCrystal structure of cytidine deaminase Cdd from Mycobacterium marinum
ComponentsCytidine deaminase Cdd
KeywordsHYDROLASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / mycobacterium / ortholog / cytidine / uridine / zinc binding enzyme
Function / homology
Function and homology information


cytidine deamination / cytidine deaminase activity / zinc ion binding / cytosol
Similarity search - Function
: / Cytidine and deoxycytidylate deaminase zinc-binding region / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / 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 Cdd
Similarity search - Component
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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
DepositionMay 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Apr 15, 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_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_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 Cdd
B: Cytidine deaminase Cdd
C: Cytidine deaminase Cdd
D: Cytidine deaminase Cdd
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3468
Polymers56,0844
Non-polymers2624
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8000 Å2
ΔGint-219 kcal/mol
Surface area17090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.470, 48.710, 53.920
Angle α, β, γ (deg.)100.190, 110.420, 98.390
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Cytidine deaminase Cdd


Mass: 14021.043 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (bacteria) / Strain: ATCC BAA-535 / M / Gene: cdd, MMAR_1204 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: B2HDU6, cytidine deaminase
#2: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 299 / 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 Å3/Da / Density % sol: 38.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: MymaA.00495.a.A1 PS00823 at 20 mg/mL against JCSG+ A8 0.2 M sodium formate, 20% PEG 3350, crystal tracking ID 232847a8, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 40341 / Num. obs: 39961 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 24.135 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 25.76
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.8-1.850.1815.988904286096.1
1.85-1.90.1556.819091282897
1.9-1.950.1298.779200278798.5
1.95-2.010.10910.399265273499.7
2.01-2.080.09112.789408268199.4
2.08-2.150.07716.369895253799.8
2.15-2.230.06720.5911344247799.6
2.23-2.320.05923.5211541238599.2
2.32-2.430.05525.4411525228299.4
2.43-2.550.05128.6911641217699.9
2.55-2.680.05229.5212028208599.8
2.68-2.850.04635.7212927195299.7
2.85-3.040.0441.2513456185499.5
3.04-3.290.03545.9312347170899.6
3.29-3.60.03449.411435159499.7
3.6-4.020.03152.1110247142799.6
4.02-4.650.02955.868922125499.4
4.65-5.690.02954.677807107199.6
5.69-8.050.03152.81604382899
8.050.02757.13308644198.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å46.61 Å
Translation3 Å46.61 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3ijf

3ijf


Resolution: 1.8→48.98 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.2166 / WRfactor Rwork: 0.1798 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8655 / SU B: 5.229 / SU ML: 0.082 / SU R Cruickshank DPI: 0.1335 / SU Rfree: 0.1257 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2181 1977 4.9 %RANDOM
Rwork0.1801 ---
obs0.182 39960 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 47.61 Å2 / Biso mean: 18.0363 Å2 / Biso min: 8.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20.31 Å20.42 Å2
2--0.08 Å20.04 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3437 0 4 299 3740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193518
X-RAY DIFFRACTIONr_bond_other_d0.0010.022345
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.9864800
X-RAY DIFFRACTIONr_angle_other_deg0.94135694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5145481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.7322.239134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43315493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4591534
X-RAY DIFFRACTIONr_chiral_restr0.0860.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214068
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02718
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 130 -
Rwork0.217 2726 -
all-2856 -
obs--96.39 %
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)
10.473-0.2219-0.20860.4082-0.431.0391-0.0876-0.0101-0.03260.030.05560.01070.0693-0.05550.0320.03090.00170.02860.0276-0.00280.05250.5229-5.5335-20.01
20.9376-0.2316-0.80510.1872-0.05651.2736-0.04530.1849-0.01170.0308-0.0235-0.04510.0169-0.17030.06880.0126-0.0047-0.00860.0653-0.03310.04083.03353.4655-40.7792
30.6669-0.1248-0.34570.2616-0.2020.7010.04680.00070.0474-0.0155-0.0401-0.00810.02420.0287-0.00660.02450.00290.00080.01770.01380.044221.928417.1536-30.2317
40.4089-0.1365-0.02460.4497-0.37510.9896-0.01680.0085-0.02270.07020.0325-0.019-0.0603-0.0158-0.01570.0580.0119-0.01550.0113-0.00030.01849.00216.65-11.3739
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 122
2X-RAY DIFFRACTION1A201
3X-RAY DIFFRACTION1A301 - 373
4X-RAY DIFFRACTION2B2 - 122
5X-RAY DIFFRACTION2B201
6X-RAY DIFFRACTION2B301 - 379
7X-RAY DIFFRACTION3C4 - 122
8X-RAY DIFFRACTION3C201
9X-RAY DIFFRACTION3C301 - 372
10X-RAY DIFFRACTION4D3 - 122
11X-RAY DIFFRACTION4D201
12X-RAY DIFFRACTION4D301 - 375

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