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- PDB-2ar7: Crystal structure of human adenylate kinase 4, AK4 -

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Basic information

Entry
Database: PDB / ID: 2ar7
TitleCrystal structure of human adenylate kinase 4, AK4
ComponentsAdenylate kinase 4
KeywordsTRANSFERASE / AK4 / nucleotide kinase / nucleotide binding / human / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


ribonucleoside diphosphate biosynthetic process / nucleoside triphosphate adenylate kinase activity / nucleoside-phosphate kinase / nucleoside monophosphate kinase activity / dAMP kinase activity / CMP kinase activity / dCMP kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process ...ribonucleoside diphosphate biosynthetic process / nucleoside triphosphate adenylate kinase activity / nucleoside-phosphate kinase / nucleoside monophosphate kinase activity / dAMP kinase activity / CMP kinase activity / dCMP kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / regulation of oxidative phosphorylation / AMP kinase activity / nucleobase-containing small molecule interconversion / nucleoside-diphosphate kinase / Interconversion of nucleotide di- and triphosphates / GTP metabolic process / nucleoside diphosphate kinase activity / ATP metabolic process / cellular response to hypoxia / mitochondrial matrix / GTP binding / mitochondrion / ATP binding / cytoplasm
Similarity search - Function
Adenylate kinase 4, mitochondrial / Adenylate kinase 3/4, mitochondrial / Adenylate kinase, active site lid domain superfamily / Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / Adenylate kinase ...Adenylate kinase 4, mitochondrial / Adenylate kinase 3/4, mitochondrial / Adenylate kinase, active site lid domain superfamily / Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / 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
Adenylate kinase 4, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsFilippakopoulos, P. / Turnbull, A.P. / Fedorov, O. / Weigelt, J. / Bunkoczi, G. / Ugochukwu, E. / Debreczeni, J. / Niesen, F. / von Delft, F. / Edwards, A. ...Filippakopoulos, P. / Turnbull, A.P. / Fedorov, O. / Weigelt, J. / Bunkoczi, G. / Ugochukwu, E. / Debreczeni, J. / Niesen, F. / von Delft, F. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human adenylate kinase 4, AK4
Authors: Filippakopoulos, P. / Turnbull, A.P. / Fedorov, O. / Weigelt, J. / Bunkoczi, G. / Ugochukwu, E. / Debreczeni, J. / Niesen, F. / von Delft, F. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Knapp, S.
History
DepositionAug 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenylate kinase 4
B: Adenylate kinase 4


Theoretical massNumber of molelcules
Total (without water)55,9522
Polymers55,9522
Non-polymers00
Water5,657314
1
A: Adenylate kinase 4


Theoretical massNumber of molelcules
Total (without water)27,9761
Polymers27,9761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adenylate kinase 4


Theoretical massNumber of molelcules
Total (without water)27,9761
Polymers27,9761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Adenylate kinase 4
B: Adenylate kinase 4

A: Adenylate kinase 4
B: Adenylate kinase 4


Theoretical massNumber of molelcules
Total (without water)111,9044
Polymers111,9044
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area7410 Å2
ΔGint-35 kcal/mol
Surface area41780 Å2
MethodPISA
4
A: Adenylate kinase 4
B: Adenylate kinase 4

A: Adenylate kinase 4
B: Adenylate kinase 4


Theoretical massNumber of molelcules
Total (without water)111,9044
Polymers111,9044
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area7750 Å2
ΔGint-40 kcal/mol
Surface area41440 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-10 kcal/mol
Surface area22580 Å2
MethodPISA
6
A: Adenylate kinase 4

A: Adenylate kinase 4


Theoretical massNumber of molelcules
Total (without water)55,9522
Polymers55,9522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2900 Å2
ΔGint-15 kcal/mol
Surface area21660 Å2
MethodPISA
7
B: Adenylate kinase 4

B: Adenylate kinase 4


Theoretical massNumber of molelcules
Total (without water)55,9522
Polymers55,9522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area2570 Å2
ΔGint-8 kcal/mol
Surface area22050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.738, 95.514, 140.873
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Adenylate kinase 4 / ATP-AMP transphosphorylase / Adenylate kinase isoenzyme 4 / AK4


Mass: 27975.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AK3, AK4 / Plasmid: pLIC-SGC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P27144, adenylate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: sodium succinate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.968 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 23, 2005
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.15→47.95 Å / Num. all: 32401 / Num. obs: 32401 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Net I/σ(I): 19.5
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 2704 / % possible all: 82.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2BBW

2bbw


Resolution: 2.15→47.95 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.398 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22995 1635 5 %RANDOM
Rwork0.16617 ---
all0.16934 30746 --
obs0.16934 30746 97.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.15→47.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3470 0 0 314 3784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223590
X-RAY DIFFRACTIONr_bond_other_d0.0010.023313
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.9664887
X-RAY DIFFRACTIONr_angle_other_deg0.86837693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1185452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.10123.54161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29615610
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2411527
X-RAY DIFFRACTIONr_chiral_restr0.0820.2547
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023993
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02712
X-RAY DIFFRACTIONr_nbd_refined0.2030.2701
X-RAY DIFFRACTIONr_nbd_other0.1780.23223
X-RAY DIFFRACTIONr_nbtor_refined0.170.21708
X-RAY DIFFRACTIONr_nbtor_other0.0840.22057
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2231
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2680.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2250.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.232
X-RAY DIFFRACTIONr_mcbond_it4.21232451
X-RAY DIFFRACTIONr_mcbond_other1.2123896
X-RAY DIFFRACTIONr_mcangle_it5.18553610
X-RAY DIFFRACTIONr_scbond_it7.64981481
X-RAY DIFFRACTIONr_scangle_it9.668111271
LS refinement shellResolution: 2.15→2.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 108 -
Rwork0.224 1845 -
obs--79.94 %
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)
10.7831-0.4542-0.03441.9988-1.32681.11240.05420.0418-0.03180.06210.0132-0.08860.14060.0156-0.06740.1305-0.0106-0.02370.21290.01940.061215.193921.325836.5322
24.16830.5564-0.80852.0856-0.08022.71340.05470.12540.17980.1139-0.10410.231-0.1472-0.36610.04940.00540.05540.02810.1-0.0211-0.0009-15.023637.567160.7332
30.8895-0.4939-0.07051.5926-0.12283.63460.0763-0.1135-0.0518-0.13660.0998-0.0170.0006-0.1925-0.17610.0591-0.06110.01840.13910.05440.038511.594728.304632.3858
423.1169-2.98423.66518.72325.43685.91090.460.66720.40810.23470.6312-0.90050.50090.2156-1.09120.4621-0.0239-0.00980.2520.07170.077314.25927.966221.8101
51.7759-0.47630.9911.4448-0.64212.55280.01760.02110.03410.0063-0.0372-0.00110.0269-0.00540.01960.0640.014-0.00350.09040.02150.000823.945611.661169.1897
60.328-0.12090.05564.57981.55362.41580.00440.14670.03760.01850.00630.05040.12890.0953-0.01070.00130.03470.02180.0597-0.0098-0.052730.6432-8.732848.5041
72.5437-0.3159-1.09062.37590.56097.7384-0.2678-0.1539-0.0717-0.08660.00110.02350.619-0.09990.26670.145-0.0122-0.02510.04920.04640.03925.874313.444369.0659
82.88081.2002-0.78255.4003-1.65713.4205-0.23240.24240.131-0.33620.20090.16430.0523-0.1840.03150.0831-0.0336-0.08050.09840.0079-0.017328.39539.605873.8304
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 12526 - 147
2X-RAY DIFFRACTION2AA126 - 159148 - 181
3X-RAY DIFFRACTION3AA160 - 211182 - 233
4X-RAY DIFFRACTION4AA212 - 224234 - 246
5X-RAY DIFFRACTION5BB4 - 12526 - 147
6X-RAY DIFFRACTION6BB126 - 168148 - 190
7X-RAY DIFFRACTION7BB169 - 193191 - 215
8X-RAY DIFFRACTION8BB194 - 224216 - 246

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