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- PDB-4ld2: Crystal structure of NE0047 in complex with cytidine -

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Basic information

Entry
Database: PDB / ID: 4ld2
TitleCrystal structure of NE0047 in complex with cytidine
ComponentsCytidine and deoxycytidylate deaminase zinc-binding region
KeywordsHYDROLASE / CDA fold / deaminase
Function / homology
Function and homology information


guanosine deaminase activity / purine nucleoside catabolic process / zinc ion binding
Similarity search - Function
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
4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / Cytidine and deoxycytidylate deaminase zinc-binding region
Similarity search - Component
Biological speciesNitrosomonas europaea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsBitra, A. / Biswas, A. / Anand, R.
CitationJournal: Biochemistry / Year: 2013
Title: Structural basis of the substrate specificity of cytidine deaminase superfamily Guanine deaminase
Authors: Bitra, A. / Biswas, A. / Anand, R.
History
DepositionJun 24, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytidine and deoxycytidylate deaminase zinc-binding region
B: Cytidine and deoxycytidylate deaminase zinc-binding region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6717
Polymers41,1732
Non-polymers4985
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-98 kcal/mol
Surface area14640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.210, 74.550, 110.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytidine and deoxycytidylate deaminase zinc-binding region


Mass: 20586.463 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas europaea (bacteria) / Strain: ATCC 19718 / NBRC 14298 / Gene: NE0047 / Production host: Escherichia coli (E. coli)
References: UniProt: Q82Y41, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CTN / 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / CYTIDINE


Mass: 243.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N3O5
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 1.9 Å3/Da / Density % sol: 35.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.225M MgCl2, 25% PEG 3350, 0.1M Bis-Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.55→27.53 Å / Num. all: 46602 / Num. obs: 46602 / % possible obs: 100 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 13.6
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 4.4 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3.11data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G84

2g84


Resolution: 1.55→27.53 Å / Occupancy max: 1 / Occupancy min: 0.3 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2181 2315 5 %
Rwork0.1986 --
obs-46534 100 %
Solvent computationBsol: 35.2375 Å2
Displacement parametersBiso max: 69.57 Å2 / Biso mean: 16.1116 Å2 / Biso min: 1.44 Å2
Baniso -1Baniso -2Baniso -3
1--2.81 Å2-0 Å20 Å2
2--3.91 Å20 Å2
3----1.1 Å2
Refinement stepCycle: LAST / Resolution: 1.55→27.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2691 0 27 227 2945
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0039
X-RAY DIFFRACTIONc_angle_d1.17
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0.086 / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.272 70
Rwork0.227 -
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3cytidine.param
X-RAY DIFFRACTION4water.param
X-RAY DIFFRACTION5edo.param

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