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- PDB-3gmt: Crystal structure of adenylate kinase from burkholderia pseudomallei -

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Basic information

Entry
Database: PDB / ID: 3gmt
TitleCrystal structure of adenylate kinase from burkholderia pseudomallei
ComponentsAdenylate kinase
KeywordsTRANSFERASE / SSGCID / ADENYLATE KINASE / BURKHOLDERIA PSEUDOMALLEI / ATP-binding / Kinase / Nucleotide biosynthesis / Nucleotide-binding / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


adenylate kinase / adenylate kinase activity / AMP salvage / ATP binding / cytoplasm
Similarity search - Function
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 ...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
Biological speciesBurkholderia pseudomallei 1710b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsAbendroth, J. / Staker, B.L. / Robinson, H. / Buchko, G.W. / Hewitt, S.N. / Napuli, A.J. / Van Voorhis, W. / Stacy, R. / Myler, P.J. / Stewart, L. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2010
Title: Structural characterization of Burkholderia pseudomallei adenylate kinase (Adk): profound asymmetry in the crystal structure of the 'open' state.
Authors: Buchko, G.W. / Robinson, H. / Abendroth, J. / Staker, B.L. / Myler, P.J.
#1: Journal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionMar 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,9276
Polymers51,5432
Non-polymers3844
Water3,891216
1
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9643
Polymers25,7721
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9643
Polymers25,7721
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.230, 66.000, 63.760
Angle α, β, γ (deg.)90.00, 113.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 25771.525 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei 1710b (bacteria)
Strain: 1719B / Gene: adk, BURPS1710b_1080 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3JVB1, adenylate kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.27 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8
Details: HAMPTON SCREEN, B5: 30% PEG 4000, 200MM LI2SO4, 100MM TRIS PH 8,, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9791 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM Q315r / Detector: CCD / Date: Jan 31, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 27839 / Num. obs: 27703 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 42.51 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 17.02
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2051 / Rsym value: 0.618 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SHARPphasing
PARROTphasing
ARP/wARPmodel building
REFMAC5.5.0088refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.901 / SU B: 6.724 / SU ML: 0.179 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.253 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1395 5 %RANDOM
Rwork0.235 ---
all0.238 27715 --
obs0.238 26320 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å2-0.19 Å2
2--1.7 Å2-0 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3084 0 20 216 3320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223157
X-RAY DIFFRACTIONr_bond_other_d0.0010.022203
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.9924265
X-RAY DIFFRACTIONr_angle_other_deg0.87435366
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.195400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.29223.731134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.88115546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3871525
X-RAY DIFFRACTIONr_chiral_restr0.0790.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213505
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02618
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8021.51996
X-RAY DIFFRACTIONr_mcbond_other0.1731.5820
X-RAY DIFFRACTIONr_mcangle_it1.47823192
X-RAY DIFFRACTIONr_scbond_it2.57831161
X-RAY DIFFRACTIONr_scangle_it4.0244.51073
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 89 -
Rwork0.275 1953 -
obs--99.95 %

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