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- PDB-3h86: Crystal structure of adenylate kinase from Methanococcus maripaludis -

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Basic information

Entry
Database: PDB / ID: 3h86
TitleCrystal structure of adenylate kinase from Methanococcus maripaludis
ComponentsAdenylate kinase
KeywordsTRANSFERASE / mesophile / kinase / adenylate kinase / phosphotransferase / ATP-binding / Cytoplasm / Nucleotide-binding
Function / homology
Function and homology information


adenylate kinase / adenylate kinase activity / ATP binding / cytoplasm
Similarity search - Function
Adenylate kinase AdkA / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BIS(ADENOSINE)-5'-PENTAPHOSPHATE / Adenylate kinase
Similarity search - Component
Biological speciesMethanococcus maripaludis (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMilya, D.G. / Yousif, S.
CitationJournal: Proteins / Year: 2009
Title: Crystal structure of a trimeric archaeal adenylate kinase from the mesophile Methanococcus maripaludis with an unusually broad functional range and thermal stability.
Authors: Davlieva, M. / Shamoo, Y.
History
DepositionApr 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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 / 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 1.4Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Adenylate kinase
A: Adenylate kinase
C: Adenylate kinase
G: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0388
Polymers84,3734
Non-polymers3,6654
Water77543
1
B: Adenylate kinase
A: Adenylate kinase
C: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0296
Polymers63,2803
Non-polymers2,7493
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9120 Å2
ΔGint-44 kcal/mol
Surface area23920 Å2
MethodPISA
2
G: Adenylate kinase
hetero molecules

G: Adenylate kinase
hetero molecules

G: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0296
Polymers63,2803
Non-polymers2,7493
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area9140 Å2
ΔGint-49 kcal/mol
Surface area23270 Å2
MethodPISA
3
G: Adenylate kinase
hetero molecules

G: Adenylate kinase
hetero molecules

G: Adenylate kinase
hetero molecules

B: Adenylate kinase
A: Adenylate kinase
C: Adenylate kinase
hetero molecules

B: Adenylate kinase
A: Adenylate kinase
C: Adenylate kinase
hetero molecules

B: Adenylate kinase
A: Adenylate kinase
C: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,11524
Polymers253,11912
Non-polymers10,99612
Water21612
TypeNameSymmetry operationNumber
crystal symmetry operation4_555x+2/3,y+1/3,z+1/31
crystal symmetry operation5_555-y+2/3,x-y+1/3,z+1/31
crystal symmetry operation6_555-x+y+2/3,-x+1/3,z+1/31
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area44640 Å2
ΔGint-256 kcal/mol
Surface area86880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.840, 102.840, 228.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11G-195-

HOH

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Components

#1: Protein
Adenylate kinase / / AK / ATP-AMP transphosphorylase


Mass: 21093.244 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis (archaea) / Strain: ATCC 43000D / Gene: adk, adkA, MMP1031 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: Q6LYG0, adenylate kinase
#2: Chemical
ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H29N10O22P5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: 3.4 M ammonium chloride, 0.1 M sodium acetate, 3% ethylene glycol (v/v)., pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 28, 2008 / Details: Rigaku Osmic Mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.609
11-H-K, K, -L20.391
ReflectionResolution: 2.5→29.69 Å / Num. all: 31194 / Num. obs: 31158 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 2.44 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 9.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3109 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERfor MRphasing
PHENIX5.5.0070refinement
REFMAC5.5.0070refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KHT

1kht


Resolution: 2.5→19.7 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.684 / SU ML: 0.15 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23911 3138 10.1 %RANDOM
Rwork0.18268 ---
obs0.18821 27970 99.86 %-
all-31158 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.467 Å2
Baniso -1Baniso -2Baniso -3
1-9.05 Å20 Å20 Å2
2--9.05 Å20 Å2
3----18.1 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5848 0 228 43 6119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_refined_d0.0220.0226160
X-RAY DIFFRACTIONf_bond_other_d
X-RAY DIFFRACTIONf_angle_refined_deg2.1512.038368
X-RAY DIFFRACTIONf_angle_other_deg
X-RAY DIFFRACTIONf_dihedral_angle_1_deg7.1195760
X-RAY DIFFRACTIONf_dihedral_angle_2_deg32.94425.246244
X-RAY DIFFRACTIONf_dihedral_angle_3_deg20.275151136
X-RAY DIFFRACTIONf_dihedral_angle_4_deg20.3691540
X-RAY DIFFRACTIONf_chiral_restr0.1240.2976
X-RAY DIFFRACTIONf_gen_planes_refined0.0090.0214388
X-RAY DIFFRACTIONf_gen_planes_other
X-RAY DIFFRACTIONf_nbd_refined
X-RAY DIFFRACTIONf_nbd_other
X-RAY DIFFRACTIONf_nbtor_refined
X-RAY DIFFRACTIONf_nbtor_other
X-RAY DIFFRACTIONf_xyhbond_nbd_refined
X-RAY DIFFRACTIONf_xyhbond_nbd_other
X-RAY DIFFRACTIONf_metal_ion_refined
X-RAY DIFFRACTIONf_metal_ion_other
X-RAY DIFFRACTIONf_symmetry_vdw_refined
X-RAY DIFFRACTIONf_symmetry_vdw_other
X-RAY DIFFRACTIONf_symmetry_hbond_refined
X-RAY DIFFRACTIONf_symmetry_hbond_other
X-RAY DIFFRACTIONf_symmetry_metal_ion_refined
X-RAY DIFFRACTIONf_symmetry_metal_ion_other
X-RAY DIFFRACTIONf_mcbond_it1.121.53792
X-RAY DIFFRACTIONf_mcbond_other
X-RAY DIFFRACTIONf_mcangle_it1.99526140
X-RAY DIFFRACTIONf_scbond_it3.00232368
X-RAY DIFFRACTIONf_scangle_it4.5474.52228
X-RAY DIFFRACTIONf_rigid_bond_restr
X-RAY DIFFRACTIONf_sphericity_free
X-RAY DIFFRACTIONf_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 211 -
Rwork0.185 2066 -
obs-2066 99.82 %

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