PDB-37fc: Crystal Structure of cytidylate kinase from Mycobacterium tuberculosis

ID or keywords:

Entry

Database: PDB / ID: 37fc

Title

Crystal Structure of cytidylate kinase from Mycobacterium tuberculosis

Components

Cytidylate kinase

Keywords

TRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / cytidylate kinase from Mycobacterium tuberculosis

Function / homology

Function and homology information

(d)CMP kinase / CMP kinase activity / dCMP kinase activity / pyrimidine nucleotide metabolic process / nucleobase-containing small molecule interconversion / ATP binding / cytosol
Similarity search - Function

Biological species

Mycobacterium tuberculosis H37Rv (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 1items

Citation

Journal: To be published
Title: Crystal Structure of cytidylate kinase from Mycobacterium tuberculosis
Authors: Ung, A.R. / Lovell, S. / Battaile, K.P.

History

Deposition	Jul 17, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 29, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	37fc.cif.gz	176.9 KB	Display	PDBx/mmCIF format
PDB format	pdb37fc.ent.gz	140 KB	Display	PDB format
PDBx/mmJSON format	37fc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/7f/37fc ftp://data.pdbj.org/pub/pdb/validation_reports/7f/37fc	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: Cytidylate kinase

B: Cytidylate kinase

hetero molecules

48.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, dimeric

Unit cell

Length a, b, c (Å)	124.636, 52.071, 95.162
Angle α, β, γ (deg.)	90.00, 126.62, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-462- HOH
2	1	B-433- HOH

#1: Protein	Cytidylate kinase / CK / Cytidine monophosphate kinase / CMP kinase Mass: 24133.135 Da / Num. of mol.: 2 / Fragment: A7-S226 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: cmk, Rv1712, MTCI125.34 / Plasmid: MytuD.00663.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WPA9, (d)CMP kinase
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.57 Å³/Da / Density % sol: 52.09 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: JCSG+ D11: 70 mM sodium acetate, pH 4.6, 140 mM Calcium Chloride, 14% v/v 2-propanol, 30% v/v glycerol. MytuD.00663.a.B2.PW39481 at 14 mg/mL was combined with 5 mM ATP prior to ...Details: JCSG+ D11: 70 mM sodium acetate, pH 4.6, 140 mM Calcium Chloride, 14% v/v 2-propanol, 30% v/v glycerol. MytuD.00663.a.B2.PW39481 at 14 mg/mL was combined with 5 mM ATP prior to crystallization. No electron density for ATP was observed, plate 20615 D11 drop 3 , Puck: PSL-1708, Cryo: direct PH range: 4.6_exptl_crystal_grow.temp

Crystal

Density Matthews: 2.57 Å³/Da / Density % sol: 52.09 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop
Details: JCSG+ D11: 70 mM sodium acetate, pH 4.6, 140 mM Calcium Chloride, 14% v/v 2-propanol, 30% v/v glycerol. MytuD.00663.a.B2.PW39481 at 14 mg/mL was combined with 5 mM ATP prior to ...
PH range: 4.6_exptl_crystal_grow.temp

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Apr 4, 2026
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 2.05→46.58 Å / Num. obs: 30902 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC_1/2: 0.999 / R_merge(I) obs: 0.062 / R_pim(I) all: 0.026 / R_rim(I) all: 0.067 / Χ²: 1.03 / Net I/σ(I): 15
Reflection shell	Resolution: 2.05→2.11 Å / Redundancy: 7 % / R_merge(I) obs: 1.251 / Num. unique obs: 2376 / CC_1/2: 0.689 / R_pim(I) all: 0.507 / R_rim(I) all: 1.351 / Χ²: 1.03

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Processing

Software

Name	Version	Classification
PHENIX	2.1_6048	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.05→46.58 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.89 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.249	1549	5.02 %
R_work	0.1991	-	-
obs	0.2014	30885	99.57 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.05→46.58 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3187	0	12	132	3331

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	3225
X-RAY DIFFRACTION	f_angle_d	0.566	4388
X-RAY DIFFRACTION	f_dihedral_angle_d	14.336	1170
X-RAY DIFFRACTION	f_chiral_restr	0.043	542
X-RAY DIFFRACTION	f_plane_restr	0.005	581

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 (%)
2.05-2.12	0.3533	141	0.3007	2640	X-RAY DIFFRACTION	99
2.12-2.19	0.3568	156	0.2927	2616	X-RAY DIFFRACTION	99
2.19-2.28	0.3738	140	0.2633	2641	X-RAY DIFFRACTION	100
2.28-2.38	0.3301	144	0.2458	2654	X-RAY DIFFRACTION	100
2.38-2.51	0.3003	142	0.2323	2658	X-RAY DIFFRACTION	100
2.51-2.67	0.3023	129	0.2365	2668	X-RAY DIFFRACTION	100
2.67-2.87	0.3216	167	0.2426	2641	X-RAY DIFFRACTION	100
2.87-3.16	0.2876	132	0.215	2662	X-RAY DIFFRACTION	100
3.16-3.62	0.2355	144	0.196	2694	X-RAY DIFFRACTION	100
3.62-4.56	0.1786	129	0.1535	2688	X-RAY DIFFRACTION	99
4.56-46.58	0.2051	125	0.1818	2774	X-RAY DIFFRACTION	99

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	5.5719	1.9852	3.7393	7.4165	3.2775	3.0764	-0.1942	-0.4847	-0.0438	0.3182	0.3164	0.0591	0.2875	-0.1575	-0.0317	0.439	0.0001	0.0215	0.5924	0.0123	0.4873	-47.0214	10.0659	18.1891
2	7.4099	1.3414	2.3055	2.0175	4.0474	9.0497	-0.1681	-0.2104	-0.2306	-0.1433	0.3517	-0.4327	0.5249	0.9494	-0.1255	0.4822	0.0555	0.0284	0.5039	0.0513	0.5406	-40.5562	3.8003	13.0542
3	2.4647	-0.493	-0.1261	8.0993	-1.9143	2.547	-0.0769	-0.0762	0.4241	0.6833	-0.0445	-0.5125	-0.5399	0.101	0.0969	0.5156	-0.0443	-0.0486	0.4576	-0.0047	0.4193	-40.556	28.7299	11.3903
4	3.2605	-0.5739	0.7279	4.6907	-2.5401	1.4823	-0.1773	0.5168	-0.0939	-0.2394	-0.308	-0.3379	0.2488	-0.1832	0.3935	0.6615	-0.0072	0.0932	0.8128	0.0014	0.6394	-37.0245	15.9586	5.0753
5	4.7209	-0.6681	-1.08	6.7378	-0.6473	7.4648	0.2652	-0.6383	0.1409	1.2181	-0.0055	-0.7192	-0.6018	0.6094	-0.2366	0.5852	-0.0523	-0.113	0.4584	0.0501	0.4349	-35.0367	24.8431	13.3898
6	0.7827	0.0848	-0.5456	2.7377	-2.1905	2.8963	-0.1389	0.1431	-0.0507	0.0026	0.2093	0.1322	-0.1817	-0.2046	-0.0824	0.376	-0.0193	-0.0285	0.4908	0.0167	0.4537	-50.865	15.5501	11.6171
7	4.222	0.0573	-5.0013	5.1789	1.3607	6.316	0.6647	-0.1087	0.3241	-0.1451	-0.1252	-0.2942	-0.3183	-0.0195	-0.5903	0.4669	0.035	-0.0034	0.5656	0.0797	0.4862	-33.1262	14.2663	31.1711
8	4.68	-1.988	4.1924	2.5593	-0.9494	4.1567	-0.3988	0.1377	0.7882	0.0089	0.121	0.4839	-1.4181	-0.539	0.2676	0.6087	0.1276	-0.0356	0.667	-0.0229	0.5712	-44.0238	20.6871	33.2209
9	4.002	1.3078	2.5285	4.4272	1.1534	5.357	0.1331	-0.7718	0.2837	0.1586	-0.2386	0.1818	0.4407	-0.4528	0.145	0.3435	0.031	0.1121	0.6341	0.0694	0.4855	-51.7785	10.3179	24.8316
10	8.556	0.7896	2.215	2.442	2.5855	3.5739	-0.5969	-0.5255	0.0216	0.7878	-0.6868	0.596	1.5409	-0.2626	1.2145	0.7006	-0.0794	0.1874	0.4716	0.0161	0.7096	-46.9326	-2.0525	18.181
11	1.546	1.0042	0.2461	4.6591	1.2656	2.5528	-0.1487	-0.2112	-0.1394	0.1008	0.1326	0.1916	0.1275	0.0031	0.0236	0.3112	0.0249	0.0433	0.4147	0.0123	0.4016	-18.6353	-0.796	12.0784
12	4.2927	-2.8698	-4.2085	4.4663	5.8527	9.2616	-0.0669	0.9669	0.1245	0.9704	-0.1593	0.9892	-0.0176	-0.0065	0.2215	0.4341	0.0291	-0.0215	0.6469	0.012	0.5712	-24.5897	2.4386	4.8822
13	1.7433	0.3158	0.5735	3.2862	1.7153	3.3547	0.014	-0.1302	-0.1103	0.1095	-0.0171	0.0224	0.1953	0.0548	-0.0006	0.3313	0.0158	-0.0075	0.39	0.0052	0.3654	-15.3988	-0.1592	11.0433
14	1.9712	1.0387	0.1703	2.7066	-1.0774	2.2915	0.1426	0.3602	-0.3008	-0.2299	-0.1359	0.064	-0.21	-0.0167	-0.015	0.5573	0.032	-0.0076	0.5118	-0.01	0.4203	-24.993	6.0817	30.5631
15	5.699	-4.7814	-5.5406	7.9733	4.2852	5.4182	-0.4717	-0.5342	-0.6289	-0.3782	0.0111	-0.6121	0.4236	0.6523	0.5078	0.5054	0.0723	0.0403	0.4632	0.0829	0.5352	-15.8719	-1.6584	31.9042
16	5.4651	3.9361	-0.4567	4.5353	-2.8237	4.835	-0.4109	-0.2491	-0.4999	0.1352	0.0585	-0.6143	0.318	-0.2322	0.2317	0.3298	-0.0567	-0.0093	0.4742	-0.0331	0.3802	-6.844	7.9121	22.2832
17	4.5728	-6.423	-3.8354	9.1223	5.5098	3.3657	0.4862	-0.01	1.3315	-0.4794	-0.1752	-1.0523	-1.1356	0.5916	-0.2883	0.7069	-0.1134	-0.0802	0.453	0.0592	0.5842	-13.4637	21.4444	16.2253

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 7 through 18 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 19 through 32 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 33 through 67 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 68 through 80 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 81 through 107 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 108 through 152 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 153 through 172 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 173 through 189 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 190 through 210 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 211 through 224 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 7 through 67 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 68 through 80 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 81 through 152 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 153 through 172 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 173 through 188 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 189 through 210 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 211 through 224 )

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