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- PDB-2c95: Structure of adenylate kinase 1 in complex with P1,P4-di(adenosin... -

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Basic information

Entry
Database: PDB / ID: 2c95
TitleStructure of adenylate kinase 1 in complex with P1,P4-di(adenosine) tetraphosphate
ComponentsADENYLATE KINASE 1
KeywordsTRANSFERASE / AP4A / NUCLEOTIDE KINASE / TRANSFERASE ATP-BINDING
Function / homology
Function and homology information


nucleoside-phosphate kinase / dAMP kinase activity / outer dense fiber / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / adenylate kinase / AMP kinase activity / nucleobase-containing small molecule interconversion / nucleoside-diphosphate kinase ...nucleoside-phosphate kinase / dAMP kinase activity / outer dense fiber / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / adenylate kinase / AMP kinase activity / nucleobase-containing small molecule interconversion / nucleoside-diphosphate kinase / Interconversion of nucleotide di- and triphosphates / nucleoside diphosphate kinase activity / ATP metabolic process / extracellular exosome / ATP binding / cytosol / cytoplasm
Similarity search - Function
Adenylate kinase isoenzyme 1 / Adenylate kinase, isozyme 1/5 / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / Adenylate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BIS(ADENOSINE)-5'-TETRAPHOSPHATE / MALONATE ION / Adenylate kinase isoenzyme 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsBunkoczi, G. / Filippakopoulos, P. / Jansson, A. / Longman, E. / von Delft, F. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Knapp, S.
CitationJournal: To be Published
Title: Structure of Adenylate Kinase 1 in Complex with P1, P4-Di(Adenosine)Tetraphosphate
Authors: Bunkoczi, G. / Filippakopoulos, P. / Jansson, A. / Longman, E. / von Delft, F. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Weigelt, J. / Knapp, S.
History
DepositionDec 9, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADENYLATE KINASE 1
B: ADENYLATE KINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5536
Polymers43,6762
Non-polymers1,8774
Water6,846380
1
A: ADENYLATE KINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7763
Polymers21,8381
Non-polymers9382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADENYLATE KINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7763
Polymers21,8381
Non-polymers9382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.535, 69.998, 88.558
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A0 - 194
2115B0 - 194

NCS oper: (Code: given
Matrix: (0.99992, -0.00611, -0.01096), (0.00608, 0.99998, -0.00307), (0.01098, 0.003, 0.99994)
Vector: -2.17906, 34.70399, -0.38201)

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Components

#1: Protein ADENYLATE KINASE 1 / ATP-AMP TRANSPHOSPHORYLASE / AK1 / MYOKINASE


Mass: 21837.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PLIC-SGC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00568, adenylate kinase
#2: Chemical ChemComp-B4P / BIS(ADENOSINE)-5'-TETRAPHOSPHATE


Mass: 836.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28N10O19P4
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE FOR THE PROTEIN BELOW IS FROM A SYNTHETIC CONSTRUCT (GENBANK ID AAQ02450) AND ACCOUNTS ...THE SEQUENCE FOR THE PROTEIN BELOW IS FROM A SYNTHETIC CONSTRUCT (GENBANK ID AAQ02450) AND ACCOUNTS FOR THE SEQUENCE CONFLICTS BELOW. HOWEVER, UNIPROT ENTRY P00568 REMAINS THE CLOSEST MATCH TO THIS SEQUENCE.

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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: 2.2 Å3/Da / Density % sol: 44.3 %
Crystal growpH: 7 / Details: 3.4 M NAMALONATE 1 MM ZNSO4, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Aug 10, 2005
RadiationMonochromator: OSMIC HR MULTILAYER OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.71→32.55 Å / Num. obs: 37771 / % possible obs: 88.5 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.51
Reflection shellResolution: 1.71→1.81 Å / Redundancy: 0.93 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 4.06 / % possible all: 41.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Z83

1z83


Resolution: 1.71→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.249 / SU ML: 0.091 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1891 5 %RANDOM
Rwork0.176 ---
obs0.178 35815 88.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 4.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2--0.71 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.71→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2983 0 120 380 3483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223205
X-RAY DIFFRACTIONr_bond_other_d0.0010.022177
X-RAY DIFFRACTIONr_angle_refined_deg1.5932.0324354
X-RAY DIFFRACTIONr_angle_other_deg0.99535333
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7675403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52624.328134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69215577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5731524
X-RAY DIFFRACTIONr_chiral_restr0.0830.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023499
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02613
X-RAY DIFFRACTIONr_nbd_refined0.2150.2630
X-RAY DIFFRACTIONr_nbd_other0.1970.22269
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21527
X-RAY DIFFRACTIONr_nbtor_other0.0840.21595
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2264
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3250.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.237
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.65632009
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.18453141
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.04781365
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.478111205
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1128medium positional0.320.5
1319loose positional0.535
1128medium thermal0.842
1319loose thermal1.5910
LS refinement shellResolution: 1.71→1.76 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.412 48
Rwork0.291 821
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)
11.0643-0.0476-0.00231.0176-0.41141.5352-0.0241-0.063-0.04150.07950.0230.0569-0.0644-0.06860.0012-0.0931-0.01150.0021-0.1187-0.0082-0.094815.468617.186610.4825
21.20740.10370.14740.688-0.38291.9302-0.0238-0.0681-0.02580.03780.01460.0294-0.0267-0.01630.0091-0.0848-0.00280.0092-0.1306-0.0138-0.080713.397851.838210.3093
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 194
2X-RAY DIFFRACTION2B0 - 194

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