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- PDB-3b8f: Crystal structure of the cytidine deaminase from Bacillus anthracis -

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Basic information

Entry
Database: PDB / ID: 3b8f
TitleCrystal structure of the cytidine deaminase from Bacillus anthracis
ComponentsPutative Blasticidin S deaminase
KeywordsHYDROLASE / cytidine deaminase / Bacillus anthracis / Structural genomics / PSI-2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homologyCytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / Cytidine deaminase-like / catalytic activity / 3-Layer(aba) Sandwich / Alpha Beta / Blasticidin S deaminase / Blasticidin S deaminase
Function and homology information
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsZhang, R. / Joachimiak, G. / Wu, R. / Patterson, S. / Gornicki, P. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the cytidine deaminase from Bacillus anthracis.
Authors: Zhang, R. / Joachimiak, G. / Wu, R. / Patterson, S. / Gornicki, P. / Joachimiak, A.
History
DepositionNov 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative Blasticidin S deaminase
B: Putative Blasticidin S deaminase
C: Putative Blasticidin S deaminase
D: Putative Blasticidin S deaminase


Theoretical massNumber of molelcules
Total (without water)65,4304
Polymers65,4304
Non-polymers00
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.078, 98.479, 61.360
Angle α, β, γ (deg.)90.00, 111.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative Blasticidin S deaminase


Mass: 16357.528 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / isolate Porton / Gene: BAS3426, BA_3696, GBAA3696 / Plasmid: pDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q81Y61, UniProt: A0A6H3AIE5*PLUS, adenosine deaminase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 1.4M Tri-sodium citrate dihydrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 3, 2007 / Details: Mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.9→57.26 Å / Num. all: 47234 / Num. obs: 45458 / % possible obs: 96.24 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 22.2
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 1.43 / Num. unique all: 3625 / % possible all: 83.56

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→57.26 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 5.948 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.145 / ESU R Free: 0.127
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19589 2417 5 %RANDOM
Rwork0.1676 ---
obs0.16908 45458 96.24 %-
all-45458 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.654 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20.73 Å2
2--0.3 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.9→57.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4565 0 0 413 4978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224685
X-RAY DIFFRACTIONr_bond_other_d0.0010.023126
X-RAY DIFFRACTIONr_angle_refined_deg1.3641.9386369
X-RAY DIFFRACTIONr_angle_other_deg0.9373.0027650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2535563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84525.238231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19215814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4781519
X-RAY DIFFRACTIONr_chiral_restr0.0840.2696
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025176
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02891
X-RAY DIFFRACTIONr_nbd_refined0.2260.21057
X-RAY DIFFRACTIONr_nbd_other0.20.23314
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22242
X-RAY DIFFRACTIONr_nbtor_other0.0880.22250
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2323
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2640.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2080.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.215
X-RAY DIFFRACTIONr_mcbond_it1.2121.53638
X-RAY DIFFRACTIONr_mcbond_other0.211.51128
X-RAY DIFFRACTIONr_mcangle_it1.44424587
X-RAY DIFFRACTIONr_scbond_it2.50232217
X-RAY DIFFRACTIONr_scangle_it3.5364.51782
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 154 -
Rwork0.213 2875 -
obs-3029 83.56 %
Refinement TLS params.Method: refined / Origin x: 8.584 Å / Origin y: 14.513 Å / Origin z: 67.403 Å
111213212223313233
T0.0206 Å2-0.0131 Å20.0138 Å2--0.0703 Å2-0.025 Å2---0.0693 Å2
L0.6695 °20.0063 °2-0.1498 °2-0.4521 °2-0.146 °2--0.3117 °2
S0.007 Å °-0.0181 Å °0.0397 Å °-0.0343 Å °-0.0007 Å °-0.0108 Å °0.0169 Å °0.0082 Å °-0.0064 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 502 - 50
2X-RAY DIFFRACTION1AA51 - 10051 - 100
3X-RAY DIFFRACTION1AA101 - 142101 - 142
4X-RAY DIFFRACTION1BB1 - 501 - 50
5X-RAY DIFFRACTION1BB51 - 10051 - 100
6X-RAY DIFFRACTION1BB101 - 142101 - 142
7X-RAY DIFFRACTION1CC2 - 502 - 50
8X-RAY DIFFRACTION1CC51 - 10051 - 100
9X-RAY DIFFRACTION1CC101 - 141101 - 141
10X-RAY DIFFRACTION1DD1 - 501 - 50
11X-RAY DIFFRACTION1DD51 - 10051 - 100
12X-RAY DIFFRACTION1DD101 - 142101 - 142

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