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- PDB-4n57: Crystal structure of aminoglycoside phosphotransferase APH(2'')-I... -

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Basic information

Entry
Database: PDB / ID: 4n57
TitleCrystal structure of aminoglycoside phosphotransferase APH(2'')-IVa ADP complex
ComponentsAPH(2'')-Id
KeywordsTRANSFERASE / aminoglycoside / phosphotransferase antibiotic resistance / nucleoside diphosphate
Function / homology
Function and homology information


nucleotide binding / metal ion binding
Similarity search - Function
: / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / 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
ADENOSINE-5'-DIPHOSPHATE / APH(2'')-Id
Similarity search - Component
Biological speciesEnterococcus casseliflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsKaplan, E. / Leban, N. / Chaloin, L. / Guichou, J.-F. / Lionne, C.
CitationJournal: To be Published
Title: Crystal structure of aminoglycoside phosphotransferase APH(2'')-IVa ADP complex
Authors: Kaplan, E. / Leban, N. / Chaloin, L. / Guichou, J.-F. / Lionne, C.
History
DepositionOct 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Advisory / Data collection / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.name / _software.version
Revision 1.2Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: APH(2'')-Id
B: APH(2'')-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1438
Polymers75,1922
Non-polymers9526
Water4,324240
1
A: APH(2'')-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0724
Polymers37,5961
Non-polymers4763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: APH(2'')-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0724
Polymers37,5961
Non-polymers4763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.051, 65.802, 76.731
Angle α, β, γ (deg.)90.00, 92.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein APH(2'')-Id


Mass: 37595.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus casseliflavus (bacteria) / Gene: aph(2'')-Id / Production host: Escherichia coli (E. coli) / References: UniProt: O68183
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 75 mM Ammonium citrate 12% PEG3350, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 4, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.35→49.98 Å / Num. all: 30155 / Num. obs: 30125 / % possible obs: 99.9 % / Observed criterion σ(F): 22 / Observed criterion σ(I): 10.9 / Redundancy: 4.3 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067
Reflection shellResolution: 2.35→49.98 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.067 / Mean I/σ(I) obs: 10.9 / Rsym value: 0.067 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
AMoREphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
DNAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N4V

3n4v


Resolution: 2.35→49.931 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.869 / SU ML: 0.31 / σ(F): 1.34 / Phase error: 25.15 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2477 1666 5.25 %
Rwork0.1819 --
obs0.1852 31723 99.9 %
all-30155 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.579 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å2-0 Å2-0.03 Å2
2---2.44 Å2-0 Å2
3---1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.35→49.931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4914 0 58 240 5212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095123
X-RAY DIFFRACTIONf_angle_d1.1896921
X-RAY DIFFRACTIONf_dihedral_angle_d17.6151963
X-RAY DIFFRACTIONf_chiral_restr0.045728
X-RAY DIFFRACTIONf_plane_restr0.006885
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.41920.30171440.24042457X-RAY DIFFRACTION100
2.4192-2.49720.29591530.2352454X-RAY DIFFRACTION100
2.4972-2.58650.32371470.22562486X-RAY DIFFRACTION100
2.5865-2.690.27861580.21342466X-RAY DIFFRACTION100
2.69-2.81250.2891480.21632510X-RAY DIFFRACTION100
2.8125-2.96070.29251490.21692489X-RAY DIFFRACTION100
2.9607-3.14620.29591080.21512518X-RAY DIFFRACTION100
3.1462-3.38910.28481470.20142479X-RAY DIFFRACTION100
3.3891-3.730.28881300.18022512X-RAY DIFFRACTION100
3.73-4.26950.20991410.15952529X-RAY DIFFRACTION100
4.2695-5.37810.18381300.1372530X-RAY DIFFRACTION100
5.3781-49.94230.1641110.15392627X-RAY DIFFRACTION100
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)
13.478-0.79143.02212.5703-2.1345.3448-0.0605-0.30820.00510.4114-0.0402-0.0553-0.1399-0.18340.11040.31980.01910.08430.2229-0.01860.1993-5.1882-1.4247.3085
25.8687-0.3764-2.52711.2365-0.07141.8632-0.0666-0.34830.0007-0.08930.0096-0.2320.13340.29720.04930.30250.0153-0.01540.2287-0.03790.23570.61.185826.4204
32.7124-0.3213-1.96322.74420.10025.13320.0937-0.026-0.0143-0.20920.0042-0.5472-0.0540.2893-0.07620.1254-0.0075-0.00660.20180.01140.352146.989612.4596-1.7715
45.41860.26274.0943.37491.82986.3878-0.22330.47110.7215-0.764-0.06980.84610.2079-0.37030.28610.556-0.0715-0.04610.34320.1560.573419.833822.598-0.1574
56.9748-2.51950.3056.6342-0.99942.28610.0474-0.2618-0.44150.31840.08650.37910.1467-0.2111-0.11120.2142-0.0196-0.01120.2103-0.00250.154236.097311.843112.4163
68.97443.04185.92268.31242.60677.12810.15521.0356-0.4581-1.58610.30771.00190.69170.055-0.46390.8557-0.063-0.15710.38160.07520.6319.29639.6722-0.9357
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 132 )
2X-RAY DIFFRACTION2chain 'A' and (resid 133 through 297 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 132 )
4X-RAY DIFFRACTION4chain 'B' and (resid 133 through 194 )
5X-RAY DIFFRACTION5chain 'B' and (resid 195 through 256 )
6X-RAY DIFFRACTION6chain 'B' and (resid 257 through 297 )

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