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- PDB-4z9m: Crystal structure of human sarcomeric mitochondrial creatine kinase -

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Basic information

Entry
Database: PDB / ID: 4z9m
TitleCrystal structure of human sarcomeric mitochondrial creatine kinase
ComponentsCreatine kinase S-type, mitochondrial
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


creatine kinase / creatine metabolic process / Creatine metabolism / phosphocreatine biosynthetic process / creatine kinase activity / muscle contraction / kinase activity / mitochondrial inner membrane / mitochondrion / ATP binding
Similarity search - Function
Transferase Creatine Kinase; Chain A, domain 1 / ATP:guanido phosphotransferase, N-terminal domain / 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 ...Transferase Creatine Kinase; Chain A, domain 1 / ATP:guanido phosphotransferase, N-terminal domain / 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 / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase/guanido kinase, catalytic domain / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Creatine kinase S-type, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsRabeh, W.M. / Tempel, W. / Nedyalkova, L. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of human sarcomeric mitochondrial creatine kinase
Authors: Rabeh, W.M. / Tempel, W. / Nedyalkova, L. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bochkarev, A. / Park, H.
History
DepositionApr 10, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionApr 22, 2015ID: 2GL6
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_assembly ...entity_src_gen / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Creatine kinase S-type, mitochondrial
B: Creatine kinase S-type, mitochondrial
C: Creatine kinase S-type, mitochondrial
D: Creatine kinase S-type, mitochondrial
E: Creatine kinase S-type, mitochondrial
F: Creatine kinase S-type, mitochondrial
G: Creatine kinase S-type, mitochondrial
H: Creatine kinase S-type, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)360,91387
Polymers357,4968
Non-polymers3,41879
Water15,295849
1
A: Creatine kinase S-type, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1149
Polymers44,6871
Non-polymers4278
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Creatine kinase S-type, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1148
Polymers44,6871
Non-polymers4277
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Creatine kinase S-type, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1148
Polymers44,6871
Non-polymers4277
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Creatine kinase S-type, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,11410
Polymers44,6871
Non-polymers4279
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Creatine kinase S-type, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,11417
Polymers44,6871
Non-polymers42716
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Creatine kinase S-type, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,11413
Polymers44,6871
Non-polymers42712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Creatine kinase S-type, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1147
Polymers44,6871
Non-polymers4276
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Creatine kinase S-type, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,11415
Polymers44,6871
Non-polymers42714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.057, 106.058, 114.932
Angle α, β, γ (deg.)70.120, 84.570, 68.610
Int Tables number1
Space group name H-MP1
DetailsAuthors have indicated that the extent of the biological unit was not examined in this experiment.

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Components

#1: Protein
Creatine kinase S-type, mitochondrial / Basic-type mitochondrial creatine kinase / Mib-CK / Sarcomeric mitochondrial creatine kinase / S-MtCK


Mass: 44686.938 Da / Num. of mol.: 8 / Fragment: unp residues 27-416
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CKMT2 / Plasmid: p28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE-3)-RIL / References: UniProt: P17540, creatine kinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 71 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 849 / 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: 2.78 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 17% PEG-3350, 10mM DTT, 0.2M diammonium citrate, 0.1M Bis-TRIS, protein buffer also contained magnesium chloride, creatine, ADP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.00003 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2→49.09 Å / Num. obs: 247985 / % possible obs: 95.4 % / Redundancy: 2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.077 / Net I/σ(I): 8.5 / Num. measured all: 494536
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2-2.0320.897124658123460.3180.89495.5
10.95-49.091.90.01936273514350.9980.01990.3

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Processing

Software
NameVersionClassification
Aimless0.5.1data scaling
REFMACrefinement
PDB_EXTRACT3.15data extraction
XDSdata scaling
RefinementStarting model: 2GL6

2gl6
PDB Unreleased entry


Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.184 / FOM work R set: 0.8007 / SU B: 5.59 / SU ML: 0.142 / SU R Cruickshank DPI: 0.1937 / SU Rfree: 0.1689 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: MOLREP had previously been used for molecular replacement with coordinates from PDB entry 1CRK, and ARP/WARP for solvent picking. Whereas PDB entry 2GL6 was refined against merged data ...Details: MOLREP had previously been used for molecular replacement with coordinates from PDB entry 1CRK, and ARP/WARP for solvent picking. Whereas PDB entry 2GL6 was refined against merged data collected on two crystals, the current model was refined against data from only one of these crystals.
RfactorNum. reflection% reflectionSelection details
Rfree0.2362 4357 2 %THIN SHELLS (SFTOOLS)
Rwork0.2023 209937 --
obs0.203 214294 95.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.2 Å2 / Biso mean: 38.291 Å2 / Biso min: 7.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20.37 Å2-0.84 Å2
2---0.14 Å2-0.49 Å2
3---0.58 Å2
Refinement stepCycle: final / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21843 0 306 849 22998
Biso mean--41.36 35.17 -
Num. residues----2818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01922843
X-RAY DIFFRACTIONr_bond_other_d0.0030.0221173
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.97131068
X-RAY DIFFRACTIONr_angle_other_deg0.903348535
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.74952850
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67323.0951076
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.095153723
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.36915229
X-RAY DIFFRACTIONr_chiral_restr0.0690.23399
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02125982
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025349
X-RAY DIFFRACTIONr_mcbond_it2.493.84211309
X-RAY DIFFRACTIONr_mcbond_other2.493.84211308
X-RAY DIFFRACTIONr_mcangle_it3.8295.74314119
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 347 -
Rwork0.292 15560 -
all-15907 -
obs--95.52 %

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