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- PDB-4die: Crystal structure of a cytidylate kinase CmK from Mycobacterium a... -

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Basic information

Entry
Database: PDB / ID: 4die
TitleCrystal structure of a cytidylate kinase CmK from Mycobacterium abscessus bound to cytidine-5'-monophosphate
ComponentsCytidylate kinase
KeywordsTRANSFERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / kinase / Mycobacterium / Cytidine monophosphate kinase / CK
Function / homology
Function and homology information


(d)CMP kinase / CMP kinase activity / dCMP kinase activity / pyrimidine nucleotide metabolic process / phosphorylation / 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
CYTIDINE-5'-MONOPHOSPHATE / PHOSPHATE ION / Cytidylate kinase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: 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.
History
DepositionJan 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Sep 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
B: Cytidylate kinase
C: Cytidylate kinase
D: Cytidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,13512
Polymers95,4624
Non-polymers1,6738
Water2,594144
1
A: Cytidylate kinase
B: Cytidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5686
Polymers47,7312
Non-polymers8364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Cytidylate kinase
D: Cytidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5686
Polymers47,7312
Non-polymers8364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Cytidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2843
Polymers23,8661
Non-polymers4182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Cytidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2843
Polymers23,8661
Non-polymers4182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: Cytidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2843
Polymers23,8661
Non-polymers4182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: Cytidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2843
Polymers23,8661
Non-polymers4182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.760, 96.520, 78.790
Angle α, β, γ (deg.)90.000, 97.220, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 23865.596 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Strain: ATCC 19977 / Gene: cmk, MAB_2371 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: B1MB31, (d)CMP kinase
#2: Chemical
ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE / Cytidine monophosphate


Mass: 323.197 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N3O8P
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.8 Å3/Da / Density % sol: 56.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MyabA.00663.a.A1 PW30208 at 27.9 mg/mL with 4 mM C5P and 4 mM ADP against JCSG+ screen condition E1, 0.1 M sodium cacodylate pH 6.5, 1 M trisodium citrate with 25% ethylene glycol as cryo- ...Details: MyabA.00663.a.A1 PW30208 at 27.9 mg/mL with 4 mM C5P and 4 mM ADP against JCSG+ screen condition E1, 0.1 M sodium cacodylate pH 6.5, 1 M trisodium citrate with 25% ethylene glycol as cryo-protectant, crystal tracking ID 220703e1, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. all: 30667 / Num. obs: 30247 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 42.885 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 16.56
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.65-2.720.5413.079732224298.2
2.72-2.790.4833.419755216799.7
2.79-2.870.3774.269421210599.3
2.87-2.960.3354.739410208999.5
2.96-3.060.2855.69059201699.6
3.06-3.170.2067.58621191599.4
3.17-3.290.1728.978497189999.5
3.29-3.420.12911.497882177498.6
3.42-3.570.09315.277150170698.4
3.57-3.750.07118.826254156293.3
3.75-3.950.05922.956054149694.8
3.95-4.190.04926.66577148999.1
4.19-4.480.04130.636172140199.4
4.48-4.840.03833.045700130199.6
4.84-5.30.04229.285268120899.3
5.3-5.930.04826.114742110099.2
5.93-6.840.04329.09404195299.5
6.84-8.380.02543.01352282299.5
8.38-11.850.01661.57285064999.7
11.850.01663.45148735496.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 47.5 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å48.33 Å
Translation3 Å48.33 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: 2.65→50 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.2301 / WRfactor Rwork: 0.1942 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7626 / SU B: 23.447 / SU ML: 0.249 / SU R Cruickshank DPI: 0.715 / SU Rfree: 0.335 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.715 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1520 5 %RANDOM
Rwork0.231 ---
obs0.233 30247 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 165.82 Å2 / Biso mean: 39.0239 Å2 / Biso min: 13.69 Å2
Baniso -1Baniso -2Baniso -3
1--3.02 Å20 Å2-0.08 Å2
2---0.66 Å20 Å2
3---3.67 Å2
Refinement stepCycle: LAST / Resolution: 2.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5758 0 104 144 6006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195931
X-RAY DIFFRACTIONr_bond_other_d0.0050.023659
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.9948132
X-RAY DIFFRACTIONr_angle_other_deg1.18239013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9975815
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.98124.493207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60715863
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7741546
X-RAY DIFFRACTIONr_chiral_restr0.0680.21036
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216721
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021069
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 120 -
Rwork0.374 2052 -
all-2172 -
obs--98.1 %
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)
12.54980.21460.50351.81610.27170.37020.0076-0.11010.18320.08-0.02030.04510.0829-0.07380.01270.03210.0024-0.00980.07720.00510.0342-18.037233.3539-0.5169
25.06834.02480.51534.89060.74261.1117-0.24630.46370.3614-0.28560.12950.1931-0.1446-0.21370.11680.0384-0.0025-0.04830.14670.0680.1152-19.504542.7616-8.5599
33.5783-2.57784.4257.5762-2.77655.53740.61460.1698-0.148-0.3274-0.351-0.70730.77960.1295-0.26360.1516-0.02490.0020.16890.01270.1857-0.961932.3538-10.267
42.08240.47662.56192.83562.10054.2588-0.2077-0.00940.4518-0.1820.0834-0.5201-0.1626-0.07160.12430.1249-0.0486-0.04730.13420.04590.27910.476348.2475-3.6988
51.55190.83510.07192.1397-0.2050.4277-0.021-0.1284-0.1103-0.0383-0.0392-0.1124-0.01520.0690.06030.02040.00770.01840.04920.00540.0731-17.7314-0.0678-4.0371
642.0227-16.137510.763220.3168-9.84665.081.5276-0.24051.98440.6207-1.22160.8633-0.0310.3934-0.30590.6513-0.08850.22090.2637-0.08550.4981-39.91595.6075-4.8993
72.52290.8984.33020.6410.98248.4128-0.83391.31610.1791-0.5580.88680.1191-0.23911.0858-0.05281.6209-0.70720.0172.29760.21921.0643-27.58017.9501-16.8213
85.6386-0.7982-4.50283.872-0.80858.4105-0.30910.1499-0.2456-0.00160.12150.1992-0.0824-0.0520.18760.0561-0.04680.00150.1103-0.01650.0559-33.9366-10.6533-8.207
94.42870.15161.12463.2097-1.0443.0355-0.17220.31980.2103-0.09690.0787-0.13140.13460.07430.09350.0184-0.0133-0.00550.0257-0.00060.1641-20.753534.0867-39.463
101.0935-0.4493-0.33032.5793-0.33870.4061-0.04980.20490.0352-0.0322-0.0485-0.27650.038-0.0510.09830.0516-0.01430.00490.06750.01570.0705-8.769117.8096-39.202
114.0853-3.2024-1.32834.1915-0.05791.554-0.2112-0.27960.36490.4630.1272-0.544-0.04660.06910.08410.0842-0.0213-0.07850.0564-0.01930.1648-10.160632.0766-31.5182
123.64030.24272.69852.0659-0.86833.07260.10910.079-0.08330.1610.07120.36160.0920.2562-0.18030.04470.06430.00960.1391-0.02380.1802-28.903528.2145-32.0459
132.3702-1.3323-0.02762.72650.42080.1337-0.0365-0.0042-0.23560.0870.08720.0391-0.02570.0203-0.05080.036-0.00540.02130.04070.00470.0835-13.0511-10.8138-34.6502
1418.0147-0.3038-12.587220.63387.116744.5940.89671.3389-0.2848-0.2883-1.0431-2.0466-0.8353-1.17610.14640.12230.06510.0270.17050.02530.39039.2133-5.1263-30.7575
1518.19844.3978-1.515839.2067-7.69621.53541.5028-0.95470.8751.7934-1.5648-0.261-0.38980.35440.0620.4903-0.0750.04910.535-0.29890.4934-0.5228-1.6723-21.2199
163.31770.0869-1.55664.40180.47880.7917-0.3872-0.1913-0.16220.50340.3713-0.52940.2430.13380.01590.12390.0832-0.05820.0959-0.01020.12742.2387-20.1696-29.4203
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 103
2X-RAY DIFFRACTION2A104 - 140
3X-RAY DIFFRACTION3A141 - 194
4X-RAY DIFFRACTION4A195 - 218
5X-RAY DIFFRACTION5B-1 - 146
6X-RAY DIFFRACTION6B147 - 173
7X-RAY DIFFRACTION7B174 - 187
8X-RAY DIFFRACTION8B188 - 218
9X-RAY DIFFRACTION9C-1 - 28
10X-RAY DIFFRACTION10C29 - 103
11X-RAY DIFFRACTION11C104 - 139
12X-RAY DIFFRACTION12C140 - 218
13X-RAY DIFFRACTION13D-1 - 144
14X-RAY DIFFRACTION14D145 - 174
15X-RAY DIFFRACTION15D175 - 183
16X-RAY DIFFRACTION16D184 - 218

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