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- PDB-3dmo: 1.6 A crystal structure of cytidine deaminase from Burkholderia p... -

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Basic information

Entry
Database: PDB / ID: 3dmo
Title1.6 A crystal structure of cytidine deaminase from Burkholderia pseudomallei
ComponentsCytidine deaminase
KeywordsHYDROLASE / BURKHOLDERIA / PSEUDOMALLEI / CYTIDINE / DEAMINASE / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / SSGCID
Function / homology
Function and homology information


cytidine deaminase / cytidine deaminase activity / zinc ion binding
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
PHOSPHATE ION / Cytidine deaminase / Cytidine deaminase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: 1.6 A crystal structure of cytidine deaminase from Burkholderia pseudomallei
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionJul 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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
B: Cytidine deaminase
C: Cytidine deaminase
D: Cytidine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,52813
Polymers58,6994
Non-polymers8299
Water6,521362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11020 Å2
ΔGint-216 kcal/mol
Surface area17380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.495, 72.308, 83.327
Angle α, β, γ (deg.)90.00, 111.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cytidine deaminase


Mass: 14674.748 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710B / Gene: cdd, BPSS1959 / Plasmid: BG1861rc / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q63IV7, UniProt: Q3JJN0*PLUS, cytidine deaminase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.89 Å3/Da / Density % sol: 57.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 6.2
Details: 35% MPD, 0.1M Na/K PHOSPHATE, pH 6.2, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 4, 2008 / Details: ADJUSTABLE FOCUSING MIRRORS
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 88018 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.091 / Χ2: 1.391 / Net I/σ(I): 6.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.6-1.663.70.77987251.047100
1.66-1.723.70.59187921.066100
1.72-1.83.80.45887551.013100
1.8-1.93.80.34688181.13100
1.9-2.023.70.25587931.36899.9
2.02-2.173.70.18987871.54599.9
2.17-2.393.70.14387851.75899.9
2.39-2.743.80.1188111.78299.9
2.74-3.453.80.07588521.78699.8
3.45-503.70.04789001.39998.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 50.04 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å34.55 Å
Translation2.5 Å34.55 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→34.54 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.77 / SU B: 2.437 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.224 4417 5 %RANDOM
Rwork0.199 ---
obs0.2 87989 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 49.94 Å2 / Biso mean: 24.804 Å2 / Biso min: 15 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å2-0.02 Å2
2---0.09 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.6→34.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3854 0 41 362 4257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223973
X-RAY DIFFRACTIONr_angle_refined_deg1.1521.9585411
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8185530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.33923.827162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.07215589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1171520
X-RAY DIFFRACTIONr_chiral_restr0.0750.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023032
X-RAY DIFFRACTIONr_nbd_refined0.1910.21842
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22695
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2326
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1140.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.215
X-RAY DIFFRACTIONr_mcbond_it0.5261.52640
X-RAY DIFFRACTIONr_mcangle_it0.89724116
X-RAY DIFFRACTIONr_scbond_it1.4831456
X-RAY DIFFRACTIONr_scangle_it2.4944.51288
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 307 -
Rwork0.401 6094 -
all-6401 -
obs--99.04 %

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