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- PDB-3r8c: Crystal structure of cytidylate kinase (Cmk) from Mycobacterium a... -

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Basic information

Entry
Database: PDB / ID: 3r8c
TitleCrystal structure of cytidylate kinase (Cmk) from Mycobacterium abscessus
ComponentsCytidylate kinase
KeywordsTRANSFERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Mycobacterium / tuberculosis / water contaminant / chronic lung disease / rapid growing mycobacterium / pyrimidine nucleoside monophosphate kinase / phosphotransferase
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
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 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
DepositionMar 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 11, 2015Group: Database references
Revision 1.3Apr 15, 2015Group: Database references
Revision 1.4Sep 13, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytidylate kinase
B: Cytidylate kinase


Theoretical massNumber of molelcules
Total (without water)47,7312
Polymers47,7312
Non-polymers00
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-7 kcal/mol
Surface area18780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.130, 70.490, 92.320
Angle α, β, γ (deg.)90.000, 91.950, 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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Strain: ATCC 19977 / DSM 44196 / Gene: cmk, MAB_2371 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: B1MB31, UMP/CMP kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.33 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: protein at 27.9 mg/mL 12.5% PEG 1000, 12.5% PEG 2250, 12.5% MPD, 0.1 M MOPS/NaHepes, 30 mM MgCl2, 30 mM CaCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 23, 2011 / Details: VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 22360 / Num. obs: 21148 / % possible obs: 94.6 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 29.545 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 15.76
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
2.2-2.263.10.2016.4546651673152190.9
2.26-2.320.1866.434477143491
2.32-2.390.1497.124678145893.3
2.39-2.460.1258.154602143893.8
2.46-2.540.1128.794362135494
2.54-2.630.1049.334325136094.2
2.63-2.730.09210.974104128295.5
2.73-2.840.07911.544117129195.1
2.84-2.970.06813.823798118295.5
2.97-3.110.0615.383764118896.2
3.11-3.280.05118.453470108996.6
3.28-3.480.04522.143324105496.1
3.48-3.720.03926.473152100496.6
3.72-4.020.03628.14285692296.2
4.02-4.40.0330.91266284795.8
4.4-4.920.03330.13244478696.3
4.92-5.680.03328.05215268798
5.68-6.960.03326.34182358697.5
6.96-9.840.02733.84133844395.1
9.840.02337.9565822282.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 55.91 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å19.35 Å
Translation3 Å19.35 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2h92

2h92


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.893 / WRfactor Rfree: 0.2366 / WRfactor Rwork: 0.2003 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8173 / SU B: 14.63 / SU ML: 0.164 / SU R Cruickshank DPI: 0.3083 / SU Rfree: 0.2268 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2538 1056 5 %RANDOM
Rwork0.2143 ---
obs0.2162 21127 94.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 88.52 Å2 / Biso mean: 27.7739 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20 Å2-1.29 Å2
2---2.68 Å20 Å2
3---1.22 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2871 0 0 200 3071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222907
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.9743975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1975402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23124.434106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43415444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6981524
X-RAY DIFFRACTIONr_chiral_restr0.0920.2507
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212158
X-RAY DIFFRACTIONr_mcbond_it0.6781.52010
X-RAY DIFFRACTIONr_mcangle_it1.21423211
X-RAY DIFFRACTIONr_scbond_it2.0943897
X-RAY DIFFRACTIONr_scangle_it3.3464.5762
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 86 -
Rwork0.283 1429 -
all-1515 -
obs--90.61 %
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)
12.37220.4744-1.34755.331-0.01124.9852-0.0165-0.19030.1061-0.18780.0765-0.18090.08440.0777-0.060.08590.0064-0.00780.0689-0.03910.090315.0533-7.9295-2.0019
20.7153-0.1267-0.2461.71330.37523.37250.042-0.0666-0.1008-0.10550.0094-0.0179-0.18530.0612-0.05140.0442-0.00040.02690.11140.02220.154819.95824.238213.5016
31.47560.8358-0.376.52282.56594.1306-0.0564-0.06740.2158-0.2291-0.18630.2771-0.2643-0.3520.24270.03410.0567-0.01350.1054-0.00910.15087.82522.07082.0279
42.2555-2.7605-0.35494.14831.79343.4451-0.2176-0.1311-0.06770.35440.02520.15480.4108-0.19650.19250.1474-0.04660.02650.0741-0.03670.101410.439-17.20493.8395
50.8520.54131.05921.39561.38772.82040.04530.0511-0.0840.23050.1274-0.1340.0472-0.0184-0.17270.154-0.0024-0.04560.06310.02360.128328.9986-0.11539.708
61.18530.42811.7452.00730.85942.64710.0507-0.0901-0.01310.3333-0.05840.08130.1106-0.20450.00770.1261-0.02270.03120.10560.00940.100924.03842.032243.2325
73.90874.27811.83284.89771.25136.8144-0.90190.53250.6338-0.79140.68720.7357-0.61930.12350.21460.4358-0.0309-0.13260.23910.11290.211417.742514.873240.4848
82.23724.6706-1.57579.7823-3.77149.1527-0.0162-0.0928-0.0783-0.1148-0.1254-0.1838-0.1236-0.12830.14160.29410.008-0.11910.0464-0.05780.14731.703119.519452.5699
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 28
2X-RAY DIFFRACTION2A29 - 103
3X-RAY DIFFRACTION3A104 - 139
4X-RAY DIFFRACTION4A140 - 218
5X-RAY DIFFRACTION5B-1 - 79
6X-RAY DIFFRACTION6B80 - 147
7X-RAY DIFFRACTION7B148 - 196
8X-RAY DIFFRACTION8B197 - 217

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