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- PDB-3ndp: Crystal structure of human AK4(L171P) -

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Basic information

Entry
Database: PDB / ID: 3ndp
TitleCrystal structure of human AK4(L171P)
ComponentsAdenylate kinase isoenzyme 4
KeywordsTRANSFERASE / PARALLEL BETA-SHEET / ALPHA-HELICES
Function / homology
Function and homology information


ribonucleoside diphosphate biosynthetic process / nucleoside monophosphate kinase activity / nucleoside-triphosphate-adenylate kinase / nucleoside triphosphate adenylate kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / adenylate kinase activity / nucleoside-diphosphate kinase / nucleobase-containing small molecule interconversion ...ribonucleoside diphosphate biosynthetic process / nucleoside monophosphate kinase activity / nucleoside-triphosphate-adenylate kinase / nucleoside triphosphate adenylate kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / adenylate kinase activity / nucleoside-diphosphate kinase / nucleobase-containing small molecule interconversion / regulation of oxidative phosphorylation / Interconversion of nucleotide di- and triphosphates / GTP metabolic process / nucleoside diphosphate kinase activity / ATP metabolic process / cellular response to hypoxia / mitochondrial matrix / phosphorylation / 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 / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP 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 / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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: 2.3 Å
AuthorsLiu, R. / Wang, Y. / Wei, Z. / Gong, W.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Crystal structure of human adenylate kinase 4 (L171P) suggests the role of hinge region in protein domain motion
Authors: Liu, R. / Xu, H. / Wei, Z. / Wang, Y. / Lin, Y. / Gong, W.
History
DepositionJun 7, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenylate kinase isoenzyme 4
B: Adenylate kinase isoenzyme 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,48710
Polymers52,7182
Non-polymers7698
Water5,080282
1
A: Adenylate kinase isoenzyme 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7435
Polymers26,3591
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Adenylate kinase isoenzyme 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7435
Polymers26,3591
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Adenylate kinase isoenzyme 4
B: Adenylate kinase isoenzyme 4
hetero molecules

A: Adenylate kinase isoenzyme 4
B: Adenylate kinase isoenzyme 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,97420
Polymers105,4374
Non-polymers1,53716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area6640 Å2
ΔGint-25 kcal/mol
Surface area36710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.790, 77.790, 144.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Adenylate kinase isoenzyme 4 / Adenylate kinase 3-like / ATP-AMP transphosphorylase


Mass: 26359.139 Da / Num. of mol.: 2 / Mutation: L171P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AK4 / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P27144, adenylate kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.08 Å3/Da / Density % sol: 40.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.22-1.28M (NH4)2SO4, 0.1M TRISHCL, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 20375 / % possible obs: 99.6 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.111
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.465 / % possible all: 99.4

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Processing

Software
NameVersionClassification
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Solved Model by SAD

Resolution: 2.3→28.21 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2710518 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1037 5.1 %RANDOM
Rwork0.226 ---
obs0.226 20311 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.87 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 23.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20 Å2
2--0.74 Å20 Å2
3----1.48 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3290 0 40 282 3612
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.23
X-RAY DIFFRACTIONc_mcangle_it2.03
X-RAY DIFFRACTIONc_scbond_it1.89
X-RAY DIFFRACTIONc_scangle_it2.78
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.342 173 5.3 %
Rwork0.272 3090 -
obs--98.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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