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- PDB-1qh4: CRYSTAL STRUCTURE OF CHICKEN BRAIN-TYPE CREATINE KINASE AT 1.41 A... -

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Basic information

Entry
Database: PDB / ID: 1qh4
TitleCRYSTAL STRUCTURE OF CHICKEN BRAIN-TYPE CREATINE KINASE AT 1.41 ANGSTROM RESOLUTION
ComponentsCREATINE KINASE
KeywordsTRANSFERASE / BRAIN-TYPE CREATINE KINASE / CANCER / CELLULAR ENERGY METABOLISM / GUANIDINO KINASE / NEURODEGENERATIVE DISORDERS
Function / homology
Function and homology information


Creatine metabolism / extracellular membrane-bounded organelle / creatine kinase / phosphocreatine biosynthetic process / creatine kinase activity / ATP biosynthetic process / kinase activity / ubiquitin protein ligase binding / extracellular space / ATP binding / cytosol
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
ACETATE ION / Creatine kinase B-type
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsEder, M. / Schlattner, U. / Becker, A. / Wallimann, T. / Kabsch, W. / Fritz-Wolf, K.
Citation
Journal: Protein Sci. / Year: 1999
Title: Crystal structure of brain-type creatine kinase at 1.41 A resolution.
Authors: Eder, M. / Schlattner, U. / Becker, A. / Wallimann, T. / Kabsch, W. / Fritz-Wolf, K.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Transition State Structure of Arginine Kinase: Implications for Catalysis of Bimolecular Reactions
Authors: Zhou, G. / Somasundaram, T. / Blanc, E. / Parthasarathy, G. / Ellington, W.R. / Chapman, M.S.
#2: Journal: Nature / Year: 1996
Title: Structure of Mitochondrial Creatine Kinase.
Authors: Fritz-Wolf, K. / Schnyder, T. / Wallimann, T. / Kabsch, W.
History
DepositionMay 11, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Nov 19, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification / _software.name
Revision 1.4Aug 16, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: CREATINE KINASE
B: CREATINE KINASE
C: CREATINE KINASE
D: CREATINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,59211
Polymers171,1984
Non-polymers3947
Water26,4281467
1
A: CREATINE KINASE
B: CREATINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7765
Polymers85,5992
Non-polymers1773
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-8 kcal/mol
Surface area31080 Å2
MethodPISA
2
C: CREATINE KINASE
D: CREATINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8166
Polymers85,5992
Non-polymers2174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-7 kcal/mol
Surface area30640 Å2
MethodPISA
3
C: CREATINE KINASE
D: CREATINE KINASE
hetero molecules

A: CREATINE KINASE
B: CREATINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,59211
Polymers171,1984
Non-polymers3947
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area10280 Å2
ΔGint-37 kcal/mol
Surface area59730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.430, 175.990, 95.400
Angle α, β, γ (deg.)90.00, 95.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CREATINE KINASE / / BB-CK / BRAIN-TYPE CREATINE KINASE


Mass: 42799.523 Da / Num. of mol.: 4 / Fragment: B CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Cellular location: CYTOPLASM / Gene: EMBL-NR. X03509 / Organ: BRAIN / Plasmid: PRF23 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P05122, creatine kinase
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1467 / 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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growpH: 6.5
Details: 0.1M MES, 0.4M CA(OAC)2, 15% PE 2MM DTT, PH 6.5, 8 MG/ML PROTEIN
Crystal
*PLUS
Density % sol: 48 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
225 mMMES1drop
33 mMdithiothreitol1drop
41 mM1dropNaN3
50.4 M1reservoirCa(OAc)2
615 %PEG80001reservoir
70.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.84
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 22, 1998 / Details: BENT CRYSTAL
RadiationMonochromator: GE SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.84 Å / Relative weight: 1
ReflectionResolution: 1.41→38 Å / Num. obs: 301191 / % possible obs: 99.1 % / Redundancy: 4 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 17.2
Reflection shellResolution: 1.41→1.5 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 5 / % possible all: 97.1
Reflection shell
*PLUS
% possible obs: 97.1 % / Num. unique obs: 49959

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Processing

Software
NameVersionClassification
SHELXL-97refinement
CNSrefinement
SHELXL-97model building
AMoREphasing
XDSV. 99data reduction
XDSV. 99data scaling
CNSphasing
SHELXL-97phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CRK, MITOCHONDRIAL CREATINE KINASE

1crk


Resolution: 1.41→6 Å / Num. parameters: 12204 / Num. restraintsaints: 14868 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: X-PLOR AND CNS WERE USED FOR INITIAL REFINEMENT. ANISOTROPIC REFINEMENT IN SHELX REDUCED FREE R (NO CUTOFF) BY 2.6% DISORDERED RESIDUES 321 - 330 (CHAIN A-D) WERE MODELED
RfactorNum. reflection% reflectionSelection details
Rfree0.1881 14886 5.3 %RANDOM
all0.1365 282461 --
obs0.1338 -99.1 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 15 / Occupancy sum hydrogen: 11644 / Occupancy sum non hydrogen: 13358
Refinement stepCycle: LAST / Resolution: 1.41→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12067 0 25 1467 13559
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.022
X-RAY DIFFRACTIONs_zero_chiral_vol0.059
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.067
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.014
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.055
X-RAY DIFFRACTIONs_approx_iso_adps0.079
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 6 Å / σ(F): 0 / % reflection Rfree: 5.3 % / Rfactor obs: 0.134 / Rfactor Rwork: 0.1338
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.022
X-RAY DIFFRACTIONs_chiral_restr0.059

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