PDB-4r88: Crystal structure of 5-methylcytosine deaminase from Klebsiella p...

ID or keywords:

Entry

Database: PDB / ID: 4r88

Title

Crystal structure of 5-methylcytosine deaminase from Klebsiella pneumoniae liganded with 5-fluorocytosine

Components

Cytosine deaminase

Keywords

HYDROLASE / Amidohydrolase fold / 5-methylcytosine deaminase / 5-fluorocytosine

Function / homology

Function and homology information

cytosine catabolic process / isoguanine deaminase activity / cytosine deaminase / : / cytosine deaminase activity / metal ion binding
Similarity search - Function

Biological species

Klebsiella pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.952 Å

Authors

Fedorov, A.A. / Fedorov, E.V. / Hitchcock, D.S. / Raushel, F.M. / Almo, S.C.

Citation

Journal: To be Published
Title: Crystal structure of 5-methylcytosine deaminase from Klebsiella pneumoniae liganded with 5-fluorocytosine
Authors: Fedorov, A.A. / Fedorov, E.V. / Hitchcock, D.S. / Raushel, F.M. / Almo, S.C.

History

Deposition	Aug 29, 2014	Deposition site: RCSB / Processing site: RCSB
Supersession	Sep 17, 2014	ID: 4JNR
Revision 1.0	Sep 17, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4r88.cif.gz	1003.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4r88.ent.gz	836.7 KB	Display	PDB format
PDBx/mmJSON format	4r88.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4r88_validation.pdf.gz	578.1 KB	Display	wwPDB validaton report
Full document	4r88_full_validation.pdf.gz	600.1 KB	Display
Data in XML	4r88_validation.xml.gz	97.2 KB	Display
Data in CIF	4r88_validation.cif.gz	136.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r8/4r88 ftp://data.pdbj.org/pub/pdb/validation_reports/r8/4r88	HTTPS FTP

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Related structure data

Related structure data	4jnr PDB Unreleased entryS 4r7w 4r85 S: Starting model for refinement
Similar structure data	4r85-1 6dnp-d 4r85-2 4r85-3 3r0d-2 5dri-d 1vg9-2 4r7w-2 4r7w-3 3zdn-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4jnr
PDB Unreleased entryS

4r7w

4r85

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (3) #158 - Feb 2013 Proton-Gated Urea Channel similarity (2) #111 - Mar 2009 Hydrogenase similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #244 - Apr 2020 Photosynthetic Supercomplexes similarity (1) #4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1) #147 - Mar 2012 Rhodopsin similarity (1) #61 - Jan 2005 Phenylalanine Hydroxylase similarity (1) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#215 - Nov 2017
Aspartate Transcarbamoylase
similarity (3)
#158 - Feb 2013
Proton-Gated Urea Channel
similarity (2)
#111 - Mar 2009
Hydrogenase
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#244 - Apr 2020
Photosynthetic Supercomplexes
similarity (1)
#4 - Apr 2000
Collagen
similarity (1)
#116 - Aug 2009
Sulfotransferases
similarity (1)
#147 - Mar 2012
Rhodopsin
similarity (1)
#61 - Jan 2005
Phenylalanine Hydroxylase
similarity (1)
#129 - Sep 2010
Isocitrate Dehydrogenase
similarity (1)
#154 - Oct 2012
Citric Acid Cycle
similarity (1)
#191 - Nov 2015
Glutamate-gated Chloride Receptors
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)

Deposited unit

A: Cytosine deaminase

B: Cytosine deaminase

C: Cytosine deaminase

D: Cytosine deaminase

E: Cytosine deaminase

F: Cytosine deaminase

hetero molecules

293 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Cytosine deaminase

B: Cytosine deaminase

hetero molecules

defined by author&software
97.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Cytosine deaminase

E: Cytosine deaminase

hetero molecules

defined by author&software
97.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

D: Cytosine deaminase

F: Cytosine deaminase

hetero molecules

defined by author&software
97.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	101.954, 162.419, 184.047
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 6 molecules ABCDEF

#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

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Non-polymers , 8 types, 1206 molecules

#2: Chemical	ChemComp-1LD / 5-fluorocytosine / 4-amino-5-fluoropyrimidin-2(1H)-one Mass: 129.092 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₄H₄FN₃O / Comment: medication, antifungal*YM
#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: Chemical	ChemComp-ACY / ACETIC ACID Mass: 60.052 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₂H₄O₂
#6: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C₂H₆O₂
#7: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#8: Chemical	ChemComp-FLC / CITRATE ANION Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₅O₇
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1148 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.64 Å³/Da / Density % sol: 53.44 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 30% PEG 4000, 0.1M SODIUM CITRATE, 0.2M AMMONIUM ACETATE, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 26, 2013
Radiation	Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.075 Å / Relative weight: 1
Reflection	Resolution: 1.952→46.663 Å / Num. obs: 211096 / % possible obs: 95.41 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software

Name	Version	Classification
CBASS		data collection
BALBES		phasing
PHENIX	(phenix.refine: 1.8_1069)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 4JNR

4jnr
PDB Unreleased entry

Resolution: 1.952→46.663 Å / SU ML: 0.2 / σ(F): 0 / Phase error: 20.76 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2008	6377	3.02 %
R_work	0.1646	-	-
obs	0.1657	211096	95.41 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.952→46.663 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19320	0	295	1148	20763

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	20022
X-RAY DIFFRACTION	f_angle_d	1.057	27050
X-RAY DIFFRACTION	f_dihedral_angle_d	14.088	7483
X-RAY DIFFRACTION	f_chiral_restr	0.071	2990
X-RAY DIFFRACTION	f_plane_restr	0.005	3585

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.952-1.974	0.3011	201	0.2547	6360	X-RAY DIFFRACTION	90
1.974-1.9972	0.2875	250	0.2488	6640	X-RAY DIFFRACTION	94
1.9972-2.0216	0.2779	195	0.2372	6650	X-RAY DIFFRACTION	94
2.0216-2.0471	0.2738	188	0.2248	6671	X-RAY DIFFRACTION	94
2.0471-2.0741	0.3018	210	0.2236	6666	X-RAY DIFFRACTION	94
2.0741-2.1025	0.2377	175	0.2129	6669	X-RAY DIFFRACTION	94
2.1025-2.1325	0.2459	242	0.2039	6637	X-RAY DIFFRACTION	94
2.1325-2.1644	0.2442	183	0.2061	6689	X-RAY DIFFRACTION	94
2.1644-2.1982	0.276	185	0.1999	6666	X-RAY DIFFRACTION	94
2.1982-2.2342	0.2334	183	0.1924	6645	X-RAY DIFFRACTION	93
2.2342-2.2727	0.2386	211	0.195	6627	X-RAY DIFFRACTION	93
2.2727-2.3141	0.2451	218	0.1871	6632	X-RAY DIFFRACTION	93
2.3141-2.3586	0.2095	212	0.1848	6616	X-RAY DIFFRACTION	93
2.3586-2.4067	0.256	216	0.1717	6610	X-RAY DIFFRACTION	93
2.4067-2.4591	0.2123	219	0.1706	6644	X-RAY DIFFRACTION	93
2.4591-2.5162	0.2148	217	0.163	6663	X-RAY DIFFRACTION	94
2.5162-2.5792	0.2132	222	0.1591	6699	X-RAY DIFFRACTION	94
2.5792-2.6489	0.1958	207	0.1627	6724	X-RAY DIFFRACTION	95
2.6489-2.7268	0.2218	216	0.1668	6840	X-RAY DIFFRACTION	95
2.7268-2.8148	0.2391	204	0.1679	6838	X-RAY DIFFRACTION	96
2.8148-2.9154	0.2218	233	0.1675	6909	X-RAY DIFFRACTION	97
2.9154-3.0321	0.2104	196	0.162	6936	X-RAY DIFFRACTION	97
3.0321-3.1701	0.1751	220	0.156	7003	X-RAY DIFFRACTION	98
3.1701-3.3372	0.181	215	0.1494	7067	X-RAY DIFFRACTION	98
3.3372-3.5462	0.1684	235	0.1403	7138	X-RAY DIFFRACTION	99
3.5462-3.8199	0.1512	225	0.1389	7107	X-RAY DIFFRACTION	99
3.8199-4.2041	0.169	189	0.131	7232	X-RAY DIFFRACTION	99
4.2041-4.8119	0.1448	223	0.1267	7268	X-RAY DIFFRACTION	100
4.8119-6.0604	0.177	243	0.1619	7300	X-RAY DIFFRACTION	100
6.0604-46.6763	0.1887	244	0.164	7573	X-RAY DIFFRACTION	100

Refinement TLS params.

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

ID	L11 (°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)
1	0.6216	0.2331	-0.1	0.6137	-0.2791	0.6091	0.0021	0.0277	0.0524	0.011	0.0017	-0.0288	-0.0206	0.0265	-0.0019	0.0943	0.0089	-0.0099	0.1172	-0.0084	0.1137	39.5866	24.6852	18.8476
2	0.6116	0.2407	0.0751	0.7082	0.0614	0.7068	-0.0082	0.0589	0.0071	-0.0549	0.0302	-0.0877	-0.0436	0.1273	-0.0164	0.1126	-0.0008	0.0042	0.1874	-0.0101	0.1036	34.1004	11.9987	-11.612
3	1.2173	-0.1469	0.1529	0.4679	0.0528	0.7039	-0.0235	-0.1623	0.0269	0.0696	0.0294	0.1211	-0.0294	-0.148	-0.0021	0.1308	0.0145	0.0229	0.1811	0.0036	0.1362	-6.1461	9.4852	37.4078
4	0.4816	-0.1791	-0.0484	0.8517	0.1582	0.6544	-0.0251	-0.0001	-0.0899	0.0246	0.0485	-0.0176	0.1636	0.0489	-0.0134	0.1588	0.0258	0.0031	0.1423	-0.0073	0.1125	33.1584	-24.2831	34.9078
5	0.9967	-0.3596	-0.1402	0.531	0.1373	0.411	-0.0001	0.0331	-0.0385	-0.009	0.0052	0.0869	0.0455	-0.029	-0.0017	0.1083	-0.0199	-0.0173	0.1429	0.0093	0.1378	-14.5229	6.0494	5.3912
6	0.7336	-0.272	0.1514	0.8298	-0.0302	0.806	0.0062	0.0493	-0.1879	0.0166	0.0363	0.0435	0.2341	0.0128	-0.0286	0.2142	-0.0096	-0.0107	0.1288	-0.0419	0.1765	18.5895	-33.939	6.3228

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A
2	X-RAY DIFFRACTION	2	chain B
3	X-RAY DIFFRACTION	3	chain C
4	X-RAY DIFFRACTION	4	chain D
5	X-RAY DIFFRACTION	5	chain E
6	X-RAY DIFFRACTION	6	chain F

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