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- PDB-4hrw: Identification of function and Mechanistic insights of Guanine de... -

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Basic information

Entry
Database: PDB / ID: 4hrw
TitleIdentification of function and Mechanistic insights of Guanine deaminase from Nitrosomonas europaea
ComponentsCytidine and deoxycytidylate deaminase zinc-binding region
KeywordsHYDROLASE / Cytidine deaminase fold / guanine 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
5-AMINO-1H-[1,2,3]TRIAZOLO[4,5-D]PYRIMIDIN-7-OL / Cytidine and deoxycytidylate deaminase zinc-binding region
Similarity search - Component
Biological speciesNitrosomonas europaea (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsAnand, R. / Bitra, A. / Bhukya, H. / Tanwar, A.S.
CitationJournal: Biochemistry / Year: 2013
Title: Identification of function and mechanistic insights of guanine deaminase from Nitrosomonas europaea: role of the C-terminal loop in catalysis
Authors: Bitra, A. / Hussain, B. / Tanwar, A.S. / Anand, R.
History
DepositionOct 29, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Nov 15, 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 1.3Nov 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_label_asym_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 and deoxycytidylate deaminase zinc-binding region
B: Cytidine and deoxycytidylate deaminase zinc-binding region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3405
Polymers41,0572
Non-polymers2833
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-102 kcal/mol
Surface area14540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.110, 73.250, 109.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 20528.426 Da / Num. of mol.: 2 / Mutation: E79A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas europaea (bacteria) / Strain: ATCC 19718 / NBRC 14298 / Gene: NE0047 / Plasmid: pET 22 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q82Y41
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-AZG / 5-AMINO-1H-[1,2,3]TRIAZOLO[4,5-D]PYRIMIDIN-7-OL / 8-AZAGUANINE


Mass: 152.114 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N6O / Comment: antineoplastic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 1.87 Å3/Da / Density % sol: 34.1 % / Mosaicity: 1.173 °
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M MgCl2, 25% PEG 3350, 0.1M Bis-Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5417 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.43→50 Å / Num. obs: 12160 / % possible obs: 99.5 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.099 / Χ2: 1.408 / Net I/σ(I): 18.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.43-2.537.50.29911931.11199.6
2.53-2.637.70.28211731.1291100
2.63-2.757.80.22512001.1971100
2.75-2.897.90.18811851.1951100
2.89-3.077.80.15512061.298199.9
3.07-3.317.80.12712041.454199.9
3.31-3.647.70.10312021.667199.9
3.64-4.177.60.08512281.697199.3
4.17-5.257.40.06912181.577197.8
5.25-507.20.06313121.743198.3

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Processing

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

2g84


Resolution: 2.43→36 Å / Occupancy max: 1 / Occupancy min: 0.3 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2615 1253 10.3 %
Rwork0.2062 10829 -
obs-12082 99.4 %
Solvent computationBsol: 46.2972 Å2
Displacement parametersBiso max: 98.94 Å2 / Biso mean: 23.4199 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1--5.74 Å2-0 Å20 Å2
2--10.824 Å20 Å2
3----5.084 Å2
Refinement stepCycle: LAST / Resolution: 2.43→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2705 0 13 76 2794
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0059
X-RAY DIFFRACTIONc_angle_d1.19
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3aza.param
X-RAY DIFFRACTION4water.param

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