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- PDB-3r20: Crystal structure of cytidylate kinase from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 3r20
TitleCrystal structure of cytidylate kinase from Mycobacterium smegmatis
ComponentsCytidylate kinase
KeywordsTRANSFERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / cytidylate kinase / ADP / dCMP / dCDP
Function / homology
Function and homology information


(d)CMP kinase / (d)CMP kinase activity / pyrimidine nucleotide metabolic process / ATP binding / cytoplasm
Similarity search - Function
Cytidylate kinase / Cytidylate kinase domain / Cytidylate kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DIPHOSPHATE / Cytidylate kinase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Citation
Journal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
#1: Journal: J Biomol Screen / Year: 2016
Title: Mycobacterium Cytidylate Kinase Appears to Be an Undruggable Target.
Authors: Craig, J.K. / Risler, J.K. / Loesch, K.A. / Dong, W. / Baker, D. / Barrett, L.K. / Subramanian, S. / Samudrala, R. / Van Voorhis, W.C.
History
DepositionMar 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Oct 12, 2016Group: Database references
Revision 1.4Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Cytidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3285
Polymers23,9611
Non-polymers3684
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cytidylate kinase
hetero molecules

A: Cytidylate kinase
hetero molecules

A: Cytidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,98515
Polymers71,8823
Non-polymers1,10312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area5910 Å2
ΔGint-52 kcal/mol
Surface area28550 Å2
MethodPISA
3
A: Cytidylate kinase
hetero molecules

A: Cytidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,65710
Polymers47,9222
Non-polymers7358
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_676x-y+1,-y+2,-z+11
Buried area3300 Å2
ΔGint-28 kcal/mol
Surface area19660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.220, 96.220, 43.150
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-378-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytidylate kinase / / CK / Cytidine monophosphate kinase


Mass: 23960.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: cmk, MSMEG_3739 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QYQ0, UMP/CMP kinase

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Non-polymers , 5 types, 211 molecules

#2: Chemical ChemComp-DPO / DIPHOSPHATE / Pyrophosphate


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MysmA.00663.a.A1 PS00600 at 37.2 mg/mL against JCSG+ screen condition E2. 0.2 M NaCl, 0.1 M sodium cacodylate pH 6.5, 2 M ammonium sulfate with 25% ethylene glycol as cryo-protectant, ...Details: MysmA.00663.a.A1 PS00600 at 37.2 mg/mL against JCSG+ screen condition E2. 0.2 M NaCl, 0.1 M sodium cacodylate pH 6.5, 2 M ammonium sulfate with 25% ethylene glycol as cryo-protectant, crystal tracking ID 215891e2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 15827 / Num. obs: 15632 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 28.667 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 21.82
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2-2.055.20.4163.9466921182111494.2
2.05-2.110.355.3176471101107697.7
2.11-2.170.3255.927939107998.1
2.17-2.240.2587.458016105399.2
2.24-2.310.2198.87868101298.6
2.31-2.390.18210.727976100198.8
2.39-2.480.16811.97765494899.4
2.48-2.580.13514.69764393199.4
2.58-2.70.11916.54734789699.7
2.7-2.830.10119.93725785499.8
2.83-2.980.08223.24676980499.9
2.98-3.160.06529649476499.6
3.16-3.380.04636.68619873599.7
3.38-3.650.04142.76577968599.7
3.65-40.03649.59524063099.7
4-4.470.03354.36468956799.6
4.47-5.160.03454.12417050799.8
5.16-6.330.03546.38345542998.6
6.33-8.940.02559.84288434598.6
8.940.02364.69153320297.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 53.41 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å48.11 Å
Translation3 Å48.11 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3R8C

3r8c


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.1796 / WRfactor Rwork: 0.1497 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8616 / SU B: 8.346 / SU ML: 0.105 / SU R Cruickshank DPI: 0.1676 / SU Rfree: 0.1498 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21 776 5 %RANDOM
Rwork0.1683 ---
obs0.1705 15571 98.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 64.4 Å2 / Biso mean: 24.2344 Å2 / Biso min: 7.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å2-0.47 Å20 Å2
2---0.94 Å20 Å2
3---1.41 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1572 0 19 207 1798
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221601
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.9862182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7815216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.923.18266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.84115247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8291519
X-RAY DIFFRACTIONr_chiral_restr0.0850.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211201
X-RAY DIFFRACTIONr_mcbond_it0.6921.51077
X-RAY DIFFRACTIONr_mcangle_it1.21221721
X-RAY DIFFRACTIONr_scbond_it2.1873524
X-RAY DIFFRACTIONr_scangle_it3.6474.5461
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 58 -
Rwork0.19 1054 -
all-1112 -
obs--94.08 %
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)
10.0594-0.34440.04193.46640.48720.43030.04010.02460.0429-0.149-0.0717-0.22480.03380.04260.03160.04910.01840.02950.06150.00820.076820.190867.557614.4201
21.0238-0.21670.00323.26560.4710.9641-0.00460.00420.0116-0.14280.0579-0.36050.05730.0012-0.05340.04350.0040.0490.007-0.00870.101623.173273.956113.5015
31.0729-0.809-0.01132.1104-1.21742.14180.05020.0766-0.0114-0.2228-0.06710.08840.0352-0.01280.01680.07950.0149-0.00990.0522-0.00950.013613.81360.97488.4516
46.19151.40141.80797.87493.54435.2295-0.0083-0.03190.0532-0.04270.2882-0.94070.21080.4361-0.280.06380.0576-0.00030.0717-0.0380.127223.062763.37232.7571
50.3947-0.31880.24591.69411.06991.3033-0.0084-0.06260.00890.0864-0.00920.05080.0398-0.080.01760.0668-0.02230.02450.08450.00070.05749.841963.786226.5575
610.9132.77017.25237.5569.303412.95020.2031-0.1747-0.26010.2025-0.19640.03930.2907-0.3059-0.00670.03810.0048-0.00710.02520.02140.170621.096746.156520.2226
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 60
2X-RAY DIFFRACTION2A61 - 110
3X-RAY DIFFRACTION3A111 - 149
4X-RAY DIFFRACTION4A150 - 171
5X-RAY DIFFRACTION5A172 - 207
6X-RAY DIFFRACTION6A208 - 221

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