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- PDB-3dxp: Crystal structure of a putative aminoglycoside phosphotransferase... -

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Basic information

Entry
Database: PDB / ID: 3dxp
TitleCrystal structure of a putative aminoglycoside phosphotransferase (reut_a1007) from ralstonia eutropha jmp134 at 2.32 A resolution
Componentsputative acyl-CoA dehydrogenase
KeywordsTRANSFERASE / Protein kinase-like fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


transferase activity / metal ion binding
Similarity search - Function
: / Acyl-CoA dehydrogenase family member 10/11, N-terminal / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / Alpha-Beta Complex ...: / Acyl-CoA dehydrogenase family member 10/11, N-terminal / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Aminoglycoside phosphotransferase
Similarity search - Component
Biological speciesRalstonia eutropha JMP134 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.32 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative acyl-CoA dehydrogenase (YP_295230.1) from RALSTONIA EUTROPHA JMP134 at 2.32 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: 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 1.5Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3594
Polymers41,1981
Non-polymers1613
Water1,72996
1
A: putative acyl-CoA dehydrogenase
hetero molecules

A: putative acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7188
Polymers82,3962
Non-polymers3226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area1600 Å2
ΔGint-29 kcal/mol
Surface area28370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.088, 127.522, 51.509
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsTHIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE PROTOMER MAY FORM A DIMER BASED ON CRYSTAL PACKING ANALYSIS. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).

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Components

#1: Protein putative acyl-CoA dehydrogenase


Mass: 41197.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha JMP134 (bacteria) / Gene: YP_295230.1, Reut_A1007 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q473P7
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.47 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.17
Details: 20.0% polyethylene glycol 8000, 0.3M calcium acetate, 0.1M MES pH 6.17, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97971,0.97956
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 26, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979711
30.979561
ReflectionResolution: 2.32→28.989 Å / Num. obs: 18395 / % possible obs: 99.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 33.49 Å2 / Rmerge(I) obs: 0.129 / Rsym value: 0.129 / Net I/σ(I): 5.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.32-2.383.50.7181.1467413290.718100
2.38-2.453.50.561.4461913220.56100
2.45-2.523.50.5461.4432912430.546100
2.52-2.593.50.4511.7439212500.451100
2.59-2.683.50.3852416311800.385100
2.68-2.773.50.362.1403611500.36100
2.77-2.883.50.2792.7400011420.279100
2.88-33.50.222.8368910590.22100
3-3.133.50.1924363810500.192100
3.13-3.283.50.1554.934449890.155100
3.28-3.463.50.1186.233109530.118100
3.46-3.673.50.0947.531479050.094100
3.67-3.923.40.0798.928708340.079100
3.92-4.243.40.0669.827518030.066100
4.24-4.643.40.05910.324897350.059100
4.64-5.193.30.0611.622546790.06100
5.19-5.993.30.06810.319815960.068100
5.99-7.343.30.0611.817155210.0699.9
7.34-10.383.10.04614.213124190.04699.8
10.38-28.992.80.0596.96512360.05995.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3.004data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.32→28.989 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.895 / SU B: 11.451 / SU ML: 0.254 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.39 / ESU R Free: 0.28
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION 3. CALCIUM, ACETATE AND 1,2-ETHANEDIOL WERE MODELED BASED ON CRYSTALLIZATION AND CRYOPROTECTION CONDITIONS. 4. DUE TO A STRONG ICE RING, 991 REFLECTIONS BETWEEN 2.656-2.586 ANGSTROMS WERE OMITTED FROM THE FINAL REFINEMENT. 5. THERE ARE TWO REGIONS OF UNMODELED DENSITY IN THE SOLVENT STRUCTURE NEAR AMINO ACIDS A90 AND A94. 6. RESIDUES A267 AND A268 ARE RAMACHANDRAN OUTLIERS IN A REGION WHERE THE ELECTRON DENSITY IS DIFFICULT TO INTERPRET.
RfactorNum. reflection% reflectionSelection details
Rfree0.287 898 5.2 %RANDOM
Rwork0.235 ---
obs0.238 17366 94.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.949 Å2
Baniso -1Baniso -2Baniso -3
1--3.58 Å20 Å20 Å2
2---3.53 Å20 Å2
3---7.1 Å2
Refinement stepCycle: LAST / Resolution: 2.32→28.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2563 0 9 96 2668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222670
X-RAY DIFFRACTIONr_bond_other_d0.0010.021799
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.9483628
X-RAY DIFFRACTIONr_angle_other_deg0.93934356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9465336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.0223.415123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92215420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6861518
X-RAY DIFFRACTIONr_chiral_restr0.0910.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023025
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02569
X-RAY DIFFRACTIONr_nbd_refined0.2010.2657
X-RAY DIFFRACTIONr_nbd_other0.1930.21820
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21333
X-RAY DIFFRACTIONr_nbtor_other0.0870.21262
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.284
X-RAY DIFFRACTIONr_metal_ion_refined0.1650.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1280.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1660.214
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0390.24
X-RAY DIFFRACTIONr_mcbond_it1.7231733
X-RAY DIFFRACTIONr_mcbond_other0.2773673
X-RAY DIFFRACTIONr_mcangle_it2.77652644
X-RAY DIFFRACTIONr_scbond_it4.27181141
X-RAY DIFFRACTIONr_scangle_it5.79111980
LS refinement shellResolution: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.45 71 -
Rwork0.347 1257 -
all-1328 -
obs--100 %

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