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- PDB-4r85: Crystal structure of 5-methylcytosine deaminase from Klebsiella p... -

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Basic information

Entry
Database: PDB / ID: 4r85
TitleCrystal structure of 5-methylcytosine deaminase from Klebsiella pneumoniae liganded with 5-methylcytosine
ComponentsCytosine deaminase
KeywordsHYDROLASE / Amidohydrolase fold / 5-methylcytosine deaminase / 5-methylcytosine
Function / homology
Function and homology information


cytosine catabolic process / isoguanine deaminase activity / cytosine deaminase / : / cytosine deaminase activity / metal ion binding
Similarity search - Function
Amidohydrolase 3 / Amidohydrolase family / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Metal-dependent hydrolase, composite domain superfamily / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel ...Amidohydrolase 3 / Amidohydrolase family / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Metal-dependent hydrolase, composite domain superfamily / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
5-methylcytosine / : / Cytosine deaminase / Cytosine deaminase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Hitchcock, D.S. / Raushel, F.M. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal structure of 5-methylcytosine deaminase from Klebsiella pneumoniae liganded with 5-methylcytosine
Authors: Fedorov, A.A. / Fedorov, E.V. / Hitchcock, D.S. / Raushel, F.M. / Almo, S.C.
History
DepositionAug 29, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionSep 17, 2014ID: 4JNP
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_seq_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: Cytosine deaminase
B: Cytosine deaminase
C: Cytosine deaminase
D: Cytosine deaminase
E: Cytosine deaminase
F: Cytosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,14836
Polymers288,4056
Non-polymers2,74430
Water30,8781714
1
A: Cytosine deaminase
D: Cytosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,95711
Polymers96,1352
Non-polymers8229
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-11 kcal/mol
Surface area27890 Å2
MethodPISA
2
B: Cytosine deaminase
F: Cytosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,14213
Polymers96,1352
Non-polymers1,00711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-14 kcal/mol
Surface area28250 Å2
MethodPISA
3
C: Cytosine deaminase
E: Cytosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,04912
Polymers96,1352
Non-polymers91510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-13 kcal/mol
Surface area28090 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29020 Å2
ΔGint-42 kcal/mol
Surface area74740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.481, 137.669, 112.093
Angle α, β, γ (deg.)90.00, 118.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cytosine deaminase


Mass: 48067.453 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: 30660/NJST258_1 / Gene: KPNJ1_03949 / Production host: Escherichia coli (E. coli)
References: UniProt: W8V4R8, UniProt: A0A0E1CHI1*PLUS, cytosine deaminase
#2: Chemical
ChemComp-17E / 5-methylcytosine / 4-amino-5-methylpyrimidin-2(1H)-one


Mass: 125.129 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H7N3O
#3: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1714 / 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: 2.63 Å3/Da / Density % sol: 53.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG 3350, 0.15M DL-MALIC ACID, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2013
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.802→40.174 Å / Num. obs: 265794 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
CBASSdata collection
BALBESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4JNP

4jnp
PDB Unreleased entry


Resolution: 1.802→40.174 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 20.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1869 8064 3.03 %
Rwork0.1585 --
obs0.1594 265794 96.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.802→40.174 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19317 0 168 1714 21199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00719881
X-RAY DIFFRACTIONf_angle_d1.06126905
X-RAY DIFFRACTIONf_dihedral_angle_d13.6117418
X-RAY DIFFRACTIONf_chiral_restr0.072986
X-RAY DIFFRACTIONf_plane_restr0.0053563
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.802-1.82210.30332480.27198140X-RAY DIFFRACTION92
1.8221-1.84360.29512920.26188607X-RAY DIFFRACTION97
1.8436-1.86610.28852970.2528573X-RAY DIFFRACTION97
1.8661-1.88970.27172710.24178658X-RAY DIFFRACTION97
1.8897-1.91450.282930.23398512X-RAY DIFFRACTION97
1.9145-1.94080.28132820.22768564X-RAY DIFFRACTION97
1.9408-1.96850.27363040.21918617X-RAY DIFFRACTION97
1.9685-1.99790.25222730.21218598X-RAY DIFFRACTION97
1.9979-2.02910.2452800.19088571X-RAY DIFFRACTION97
2.0291-2.06240.21672420.17818633X-RAY DIFFRACTION97
2.0624-2.09790.19342610.17758541X-RAY DIFFRACTION97
2.0979-2.13610.20252780.16868594X-RAY DIFFRACTION97
2.1361-2.17710.19912870.16278525X-RAY DIFFRACTION97
2.1771-2.22160.18892810.1518580X-RAY DIFFRACTION97
2.2216-2.26990.20192750.1598529X-RAY DIFFRACTION96
2.2699-2.32270.19192670.15628503X-RAY DIFFRACTION96
2.3227-2.38080.19732680.15498529X-RAY DIFFRACTION96
2.3808-2.44510.17092510.14848468X-RAY DIFFRACTION96
2.4451-2.51710.19062630.1488507X-RAY DIFFRACTION96
2.5171-2.59830.18552260.15048607X-RAY DIFFRACTION96
2.5983-2.69110.17442730.14948455X-RAY DIFFRACTION96
2.6911-2.79890.19682820.15068526X-RAY DIFFRACTION96
2.7989-2.92620.21672700.15568487X-RAY DIFFRACTION96
2.9262-3.08040.17042530.15668572X-RAY DIFFRACTION96
3.0804-3.27330.15712360.15228625X-RAY DIFFRACTION96
3.2733-3.52590.18512490.14088641X-RAY DIFFRACTION97
3.5259-3.88050.14742690.13578740X-RAY DIFFRACTION98
3.8805-4.44140.13432670.12098891X-RAY DIFFRACTION99
4.4414-5.59330.15682460.13538961X-RAY DIFFRACTION100
5.5933-40.18390.14472800.15188976X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6469-0.1069-0.09310.62190.07760.61010.00120.08450.0269-0.08090.0048-0.1108-0.0570.1093-0.00860.1401-0.04570.00570.14330.0080.1017142.57318.613111.9046
20.82680.17660.22170.73570.07410.7069-0.04650.00940.0855-0.03320.00010.13-0.0945-0.09310.03130.11810.0214-0.02550.10790.00960.119191.54098.520817.1395
30.47490.04390.21890.5688-0.07311.0552-0.001-0.09020.03070.0685-0.00650.0165-0.0507-0.01420.00940.1226-0.0019-0.00610.1099-0.01350.0841122.10918.279159.0867
40.6590.1114-0.05840.6327-0.0590.49090.01490.0671-0.0464-0.07050.0075-0.1150.03640.114-0.02020.11630.025-0.00610.1426-0.03680.1238145.1796-24.488216.4023
50.5067-0.01940.09110.65550.27820.84790.0255-0.088-0.04690.1207-0.00520.03650.1415-0.0435-0.01740.1537-0.0085-0.00980.11190.02840.093116.2947-24.359958.9441
60.7642-0.0770.36870.5445-0.00080.79050.01920.021-0.0506-0.0195-0.0070.06470.0499-0.1003-0.01940.1121-0.0183-0.01750.111-0.00680.100793.8702-24.118412.0751
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F

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