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- PDB-3umf: Schistosoma mansoni adenylate kinase -

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Basic information

Entry
Database: PDB / ID: 3umf
TitleSchistosoma mansoni adenylate kinase
ComponentsAdenylate kinase
KeywordsTRANSFERASE / Rossmann fold
Function / homology
Function and homology information


adenylate kinase activity / ATP binding
Similarity search - Function
Adenylate kinase / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP 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
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.047 Å
AuthorsMarques, I. / DeMarco, R. / Pereira, H.M.
CitationJournal: Mol.Biochem.Parasitol. / Year: 2012
Title: Structural and kinetic studies of Schistosoma mansoni adenylate kinases.
Authors: Marques, I. / Romanello, L. / Demarco, R. / Pereira, H.D.
History
DepositionNov 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Sep 13, 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

Downloads & links

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Assembly

Deposited unit
A: Adenylate kinase


Theoretical massNumber of molelcules
Total (without water)24,5111
Polymers24,5111
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.695, 82.695, 66.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Adenylate kinase


Mass: 24511.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: Smp_071390 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: C4QGH8, UniProt: G4V9S0*PLUS, adenylate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris, pH 8.5, 1.4 M ammonium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97627 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 9, 2010
RadiationMonochromator: Si(111), Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 2.047→43.978 Å / Num. all: 15116 / Num. obs: 14849 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Biso Wilson estimate: 41.906 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.047-2.170.6082.3910414228695.5
2.17-2.320.3734.239852222199.2
2.32-2.510.2516.49200208399
2.51-2.740.169.759035193099.5
2.74-3.070.09515.17911175999
3.07-3.540.0623.276884155398.5
3.54-4.330.04231.865760133899
4.33-6.090.03535.344337104897.3
6.090.03137.33247663195.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
XSCALEdata scaling
PHASERphasing
DMphasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
DNAdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ADK

3adk


Resolution: 2.047→43.978 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.38 / σ(F): 2.02 / Phase error: 20.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2277 743 5 %RANDOM
Rwork0.1886 ---
obs0.1906 14847 98.23 %-
all-15116 --
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.427 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso max: 90.23 Å2 / Biso mean: 41.3668 Å2 / Biso min: 17.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.047→43.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1463 0 0 131 1594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031484
X-RAY DIFFRACTIONf_angle_d0.731993
X-RAY DIFFRACTIONf_chiral_restr0.047229
X-RAY DIFFRACTIONf_plane_restr0.003257
X-RAY DIFFRACTIONf_dihedral_angle_d14.619563
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.047-2.20540.30411420.24342700284296
2.2054-2.42730.26391470.20912787293499
2.4273-2.77850.23911480.19572821296999
2.7785-3.50030.21821500.18782838298899
3.5003-43.9780.21021560.17442958311498
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)
12.06230.2805-1.02221.6253-0.11781.6775-0.02480.0166-0.32990.0181-0.01160.28560.3152-0.1448-0.00120.264-0.0077-0.03190.2410.05390.37318.8709-5.89736.9994
23.5459-2.5085-1.06782.6953-0.06561.0139-0.0172-0.6219-0.0040.00370.4470.53370.0179-0.1654-0.04270.3134-0.04550.01210.30930.04010.372424.3032-18.39516.1145
36.0559-0.09170.61021.16630.89733.8744-0.60610.2291-0.4264-0.74450.3537-0.44770.38560.19470.00330.3224-0.00110.08010.28590.01550.261437.5867-24.4202-1.0712
48.593-1.9968-0.82793.61871.35023.77810.3801-0.0164-0.6461-0.7747-0.15510.2460.4667-0.1122-0.11490.4964-0.0553-0.06490.257-00.28822.1259-18.6412-3.2199
54.0307-0.1171-1.1394.0941-1.10494.72450.1410.2772-0.2908-0.1939-0.02230.1035-0.08840.0447-0.06650.31420.0215-0.02490.33680.01280.3221.5104-9.6385-3.0902
62.0037-0.0321-0.52481.0674-0.89940.9034-0.05390.3063-0.1407-0.1030.03390.07290.0447-0.04580.07360.2322-0.007-0.04120.2245-0.00650.237321.4455-0.63270.8993
71.69690.4378-0.35242.18510.90275.6169-0.0854-0.00980.11940.16130.1195-0.2559-0.10940.36240.07070.1927-0.0038-0.00910.21250.01010.19740.37914.18511.0758
81.2976-0.61010.3240.6620.23831.2984-0.07070.15620.3061-0.12090.01210.1086-0.0380.21880.05920.2972-0.0341-0.02470.28660.03330.263724.18064.2128-3.1603
95.03130.6922.4434.23642.07335.8207-0.0417-0.40270.0899-0.0287-0.10190.6101-0.188-0.45560.15530.21710.0180.00810.209-0.00810.298314.64194.034410.1917
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 4:33)A4 - 33
2X-RAY DIFFRACTION2chain 'A' and (resseq 34:50)A34 - 50
3X-RAY DIFFRACTION3chain 'A' and (resseq 51:69)A51 - 69
4X-RAY DIFFRACTION4chain 'A' and (resseq 70:84)A70 - 84
5X-RAY DIFFRACTION5chain 'A' and (resseq 85:109)A85 - 109
6X-RAY DIFFRACTION6chain 'A' and (resseq 110:122)A110 - 122
7X-RAY DIFFRACTION7chain 'A' and (resseq 123:156)A123 - 156
8X-RAY DIFFRACTION8chain 'A' and (resseq 157:176)A157 - 176
9X-RAY DIFFRACTION9chain 'A' and (resseq 177:197)A177 - 197

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