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- PDB-1vrp: The 2.1 Structure of T. californica Creatine Kinase Complexed wit... -

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Basic information

Entry
Database: PDB / ID: 1vrp
TitleThe 2.1 Structure of T. californica Creatine Kinase Complexed with the Transition-State Analogue Complex, ADP-Mg 2+ /NO3-/Creatine
ComponentsCreatine Kinase, M chain
KeywordsTRANSFERASE / Creatine kinase / transition-state analogue complex / guanidino kinases / phosphocreatine / arginine kinases
Function / homology
Function and homology information


creatine kinase / phosphocreatine biosynthetic process / creatine kinase activity / ATP binding / cytoplasm
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 / (DIAMINOMETHYL-METHYL-AMINO)-ACETIC ACID / NITRATE ION / Creatine kinase M-type
Similarity search - Component
Biological speciesTorpedo californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLahiri, S.D. / Wang, P.F. / Babbitt, P.C. / McLeish, M.J. / Kenyon, G.L. / Allen, K.N.
CitationJournal: Biochemistry / Year: 2002
Title: The 2.1 A Structure of Torpedo californica Creatine Kinase Complexed with the ADP-Mg(2+)-NO3(-)-Creatine Transition-State Analogue Complex
Authors: Lahiri, S.D. / Wang, P.F. / Babbitt, P.C. / McLeish, M.J. / Kenyon, G.L. / Allen, K.N.
History
DepositionApr 25, 2005Deposition site: RCSB / Processing site: RCSB
SupersessionMay 3, 2005ID: 1N16
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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.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_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

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Assembly

Deposited unit
A: Creatine Kinase, M chain
B: Creatine Kinase, M chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0968
Polymers85,9982
Non-polymers1,0986
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.634, 87.189, 127.596
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Creatine Kinase, M chain / / M-CK


Mass: 42999.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Torpedo californica (Pacific electric ray)
Gene: FSCCKPA / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P04414, creatine kinase

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Non-polymers , 5 types, 157 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-IOM / (DIAMINOMETHYL-METHYL-AMINO)-ACETIC ACID


Mass: 133.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H11N3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.01M nickel, chloride hexahydrate, 0.1 M Tris, pH 8.0, and 16% w/v PEG 2000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 22, 2002 / Details: Bent conical Si-mirror (Rh coating)
RadiationMonochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→50.42 Å / Num. obs: 42682 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.043 / Net I/σ(I): 21.9
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 10 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 10 / Num. unique all: 1034 / Rsym value: 0.21 / % possible all: 94

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QH4

1qh4


Resolution: 2.1→50.42 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.278 4303 -RANDOM
Rwork0.242 ---
all0.26 46742 --
obs0.26 42682 91.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.28 Å2 / ksol: 0.3978 e/Å3
Displacement parametersBiso mean: 27.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.27 Å20 Å20 Å2
2---3.25 Å20 Å2
3----0.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.1→50.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5884 0 69 151 6104
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_d1.7
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_mcbond_it2.5451.5
X-RAY DIFFRACTIONc_mcangle_it3.8772
X-RAY DIFFRACTIONc_scbond_it3.0242
X-RAY DIFFRACTIONc_scangle_it5.262.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2adp.par
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4crt.par
X-RAY DIFFRACTION5ion.param

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