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- PDB-5xkq: Crystal structure of Msmeg3575 in complex with ammeline -

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Basic information

Entry
Database: PDB / ID: 5xkq
TitleCrystal structure of Msmeg3575 in complex with ammeline
ComponentsCMP/dCMP deaminase, zinc-binding protein
KeywordsHYDROLASE / CDA fold / deaminase / ammeline
Function / homology
Function and homology information


cytidine metabolic process / pyrimidine-containing compound salvage / cytosine deaminase activity / cytosine metabolic process / metal ion binding / cytoplasm
Similarity search - Function
Cytidine and deoxycytidylate deaminase zinc-binding region / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like
Similarity search - Domain/homology
4,6-diamino-1,3,5-triazin-2-ol / ACETATE ION / Cytidine/deoxycytidylate deaminase, zinc-binding region
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGaded, V.M. / Anand, R.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science and Technology, Government of IndiaEMR/2015/002121 and DST/TM/WTI/2K16/252 India
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Selective Deamination of Mutagens by a Mycobacterial Enzyme
Authors: Gaded, V. / Anand, R.
History
DepositionMay 9, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Nov 22, 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 / struct_conn / struct_ncs_dom_lim
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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CMP/dCMP deaminase, zinc-binding protein
B: CMP/dCMP deaminase, zinc-binding protein
C: CMP/dCMP deaminase, zinc-binding protein
D: CMP/dCMP deaminase, zinc-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,06715
Polymers69,0544
Non-polymers1,01311
Water61334
1
A: CMP/dCMP deaminase, zinc-binding protein
B: CMP/dCMP deaminase, zinc-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0047
Polymers34,5272
Non-polymers4775
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-27 kcal/mol
Surface area12840 Å2
MethodPISA
2
C: CMP/dCMP deaminase, zinc-binding protein
D: CMP/dCMP deaminase, zinc-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0638
Polymers34,5272
Non-polymers5366
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-64 kcal/mol
Surface area12640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.679, 61.392, 109.406
Angle α, β, γ (deg.)90.00, 89.95, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 2 - 159 / Label seq-ID: 2 - 159

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
CMP/dCMP deaminase, zinc-binding protein / Cytidine/deoxycytidylate deaminase / zinc-binding region


Mass: 17263.387 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_3575, MSMEI_3493 / Plasmid: pET28a / Cell line (production host): Bl21 DE3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: A0QY90

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Non-polymers , 5 types, 45 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-6AM / 4,6-diamino-1,3,5-triazin-2-ol / Ammeline


Mass: 127.105 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N5O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.47 Å3/Da / Density % sol: 50.29 % / Description: Flat plate like crystals
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 0.2 M magnesium acetate tetrahydrate, 0.1 M TRis HCl pH 6.4 and 20% PEG 8000
PH range: 6.0 - 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.68→109.41 Å / Num. obs: 19362 / % possible obs: 99.1 % / Redundancy: 4.1 % / Rsym value: 0.094 / Net I/σ(I): 12.9
Reflection shellResolution: 2.68→2.75 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XKO

5xko


Resolution: 2.7→109.41 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.893 / SU B: 13.221 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25327 832 4.5 %RANDOM
Rwork0.19307 ---
obs0.19567 17737 95.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.03 Å2
2---0.05 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.7→109.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4605 0 56 34 4695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194786
X-RAY DIFFRACTIONr_bond_other_d0.0060.024371
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.9296537
X-RAY DIFFRACTIONr_angle_other_deg1.4212.9999927
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7265611
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36522.3200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.37215626
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1691541
X-RAY DIFFRACTIONr_chiral_restr0.0780.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215490
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021131
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1244.4282469
X-RAY DIFFRACTIONr_mcbond_other3.1244.4272467
X-RAY DIFFRACTIONr_mcangle_it4.8486.6273071
X-RAY DIFFRACTIONr_mcangle_other4.8486.6283072
X-RAY DIFFRACTIONr_scbond_it3.2934.7882317
X-RAY DIFFRACTIONr_scbond_other3.2924.7872318
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2467.0583467
X-RAY DIFFRACTIONr_long_range_B_refined7.7236.2595217
X-RAY DIFFRACTIONr_long_range_B_other7.71236.2595217
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A164880.11
12B164880.11
21A171180.05
22C171180.05
31A164840.1
32D164840.1
41B162840.11
42C162840.11
51B179800.03
52D179800.03
61C162860.1
62D162860.1
LS refinement shellResolution: 2.696→2.766 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 35 -
Rwork0.264 886 -
obs--65.04 %

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