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- PDB-8ci4: Crystal structure of doubly S-methanethiolated rabbit M-type crea... -

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Basic information

Entry
Database: PDB / ID: 8ci4
TitleCrystal structure of doubly S-methanethiolated rabbit M-type creatine kinase
ComponentsCreatine kinase M-type
KeywordsCYTOSOLIC PROTEIN / anaerobic metabolism / chemically inactivated
Function / homology
Function and homology information


creatine kinase / phosphocreatine biosynthetic process / creatine kinase activity / response to heat / phosphorylation / extracellular space / ATP binding
Similarity search - Function
ATP:guanido phosphotransferase, N-terminal / ATP:guanido phosphotransferase, N-terminal domain superfamily / ATP:guanido phosphotransferase, N-terminal domain / Phosphagen kinase N-terminal domain profile. / ATP:guanido phosphotransferase active site / Phosphagen kinase active site signature. / ATP:guanido phosphotransferase / ATP:guanido phosphotransferase, catalytic domain / ATP:guanido phosphotransferase, C-terminal catalytic domain / Phosphagen kinase C-terminal domain profile. / Glutamine synthetase/guanido kinase, catalytic domain
Similarity search - Domain/homology
CITRATE ANION / Creatine kinase M-type
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsJoergensen, M.H. / Andersen, D.G. / Andersen, G.R.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF20OC0065238 Denmark
CitationJournal: Adv Mater / Year: 2024
Title: Chemical Zymogens and Transmembrane Activation of Transcription in Synthetic Cells.
Authors: Andersen, D.G. / Pedersen, A.B. / Jorgensen, M.H. / Montasell, M.C. / Sogaard, A.B. / Chen, G. / Schroeder, A. / Andersen, G.R. / Zelikin, A.N.
History
DepositionFeb 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Creatine kinase M-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8414
Polymers43,2731
Non-polymers5673
Water3,243180
1
A: Creatine kinase M-type
hetero molecules

A: Creatine kinase M-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6818
Polymers86,5472
Non-polymers1,1356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
Unit cell
Length a, b, c (Å)198.760, 198.760, 71.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-401-

FLC

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Components

#1: Protein Creatine kinase M-type / Creatine kinase M chain / Creatine phosphokinase M-type / CPK-M / M-CK


Mass: 43273.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: CKM / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: P00563, creatine kinase
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.09 Å3/Da / Density % sol: 69.94 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 1.35 M sodium citrate, 0.1 M HEPES pH 7.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE CdTe 16M / Detector: PIXEL / Date: Apr 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.01→100 Å / Num. obs: 47490 / % possible obs: 99.8 % / Redundancy: 13.5 % / Biso Wilson estimate: 45.17 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.54
Reflection shellResolution: 2.012→2.084 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 1 / Num. unique obs: 4616 / CC1/2: 0.435 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→62.85 Å / SU ML: 0.3267 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.9544
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2248 1704 3.59 %
Rwork0.2061 45749 -
obs0.2068 47453 99.76 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.22 Å2
Refinement stepCycle: LAST / Resolution: 2.01→62.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2956 0 43 180 3179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01013060
X-RAY DIFFRACTIONf_angle_d1.19374122
X-RAY DIFFRACTIONf_chiral_restr0.0605434
X-RAY DIFFRACTIONf_plane_restr0.0097540
X-RAY DIFFRACTIONf_dihedral_angle_d9.6326411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.070.40981380.40133703X-RAY DIFFRACTION98.26
2.07-2.140.36331390.35053759X-RAY DIFFRACTION99.9
2.14-2.210.30171420.30433756X-RAY DIFFRACTION99.92
2.21-2.30.37371410.29183788X-RAY DIFFRACTION99.92
2.3-2.410.31091400.26033775X-RAY DIFFRACTION99.95
2.41-2.540.29771410.24413781X-RAY DIFFRACTION99.95
2.54-2.690.24711410.22933785X-RAY DIFFRACTION99.7
2.69-2.90.25491410.23393826X-RAY DIFFRACTION99.92
2.9-3.190.25041430.22133813X-RAY DIFFRACTION100
3.19-3.660.21141430.19213840X-RAY DIFFRACTION99.97
3.66-4.610.16731440.15513875X-RAY DIFFRACTION99.98
4.61-62.850.18711510.17974048X-RAY DIFFRACTION99.72
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)
16.20988976147-0.05004084017322.148542833393.598016104330.4140032271822.91956489096-0.0597215753246-0.06110333222070.06947711975230.3171897146090.05517562794330.0154343733190.125687714852-0.20198849453-0.08537719383440.45454336914-0.0009542448698980.01656467614850.4075599170540.07605245679790.42336142724834.7730439834147.59846350446.5248289849
21.211819216240.01321991729070.3726203324890.635980980440.03852551086381.06431503590.05209280451710.152789069219-0.0158160342882-0.05132153173810.03635923685480.08732020031480.0266580638217-0.14939338042-0.08031283100540.364279088940.04104450268530.03101966852750.4397313015570.05007275689410.43031801863226.7655743739153.90038474619.5912496857
34.94486189712-1.80056966399-0.5622978856761.868754420850.4728201623430.9443313650660.1071192830230.05058673353690.083481858474-0.00566019675581-0.06015764062880.249558481178-0.0124848842863-0.281516704527-0.06669814477370.386204128485-0.01372470127360.01178924677470.5774583471810.08382137122780.5815102908582.60234118335152.42897015921.7694239804
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 6 through 42 )6 - 421 - 37
22chain 'A' and (resid 43 through 286 )43 - 28638 - 281
33chain 'A' and (resid 287 through 381 )287 - 381282 - 369

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