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- PDB-3n4v: apo APH(2")-IVa form III -

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Basic information

Entry
Database: PDB / ID: 3n4v
Titleapo APH(2")-IVa form III
ComponentsAPH(2'')-Id
KeywordsUNKNOWN FUNCTION / aminoglycoside / phosphotransferase / resistance
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
Biological speciesEnterococcus casseliflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSmith, C.A. / Toth, M. / Frase, H. / Vakulenko, S.B.
CitationJournal: Protein Sci. / Year: 2010
Title: Crystal structure and kinetic mechanism of aminoglycoside phosphotransferase-2''-IVa.
Authors: Toth, M. / Frase, H. / Antunes, N.T. / Smith, C.A. / Vakulenko, S.B.
History
DepositionMay 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: APH(2'')-Id
B: APH(2'')-Id


Theoretical massNumber of molelcules
Total (without water)70,6502
Polymers70,6502
Non-polymers00
Water3,891216
1
A: APH(2'')-Id


Theoretical massNumber of molelcules
Total (without water)35,3251
Polymers35,3251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: APH(2'')-Id


Theoretical massNumber of molelcules
Total (without water)35,3251
Polymers35,3251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.966, 65.119, 78.458
Angle α, β, γ (deg.)90.00, 91.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 35325.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus casseliflavus (bacteria) / Gene: aph(2'')-Id / References: UniProt: O68183
#2: Water ChemComp-HOH / 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: 2.75 Å3/Da / Density % sol: 55.2 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→42.183 Å / Num. all: 28901 / Num. obs: 28901 / % possible obs: 95.6 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 15.6
Reflection shellResolution: 2.4→2.5 Å / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 1.9 / % possible all: 72

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
PHENIX(phenix.refine: 1.5_2)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→42.183 Å / SU ML: 0.39 / σ(F): 1.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2631 1417 5.07 %
Rwork0.1929 --
obs0.1965 27974 92.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.362 Å2 / ksol: 0.302 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.3301 Å2-0 Å2-2.5078 Å2
2---6.6972 Å20 Å2
3---2.3672 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4916 0 0 216 5132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085063
X-RAY DIFFRACTIONf_angle_d1.1536835
X-RAY DIFFRACTIONf_dihedral_angle_d19.8881897
X-RAY DIFFRACTIONf_chiral_restr0.084723
X-RAY DIFFRACTIONf_plane_restr0.005886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.48580.3456770.23951464X-RAY DIFFRACTION51
2.4858-2.58530.31341160.24812202X-RAY DIFFRACTION78
2.5853-2.70290.33391370.24472806X-RAY DIFFRACTION98
2.7029-2.84540.34821600.24522843X-RAY DIFFRACTION100
2.8454-3.02360.29061510.2242843X-RAY DIFFRACTION100
3.0236-3.2570.29011690.21762836X-RAY DIFFRACTION100
3.257-3.58460.29371650.19082848X-RAY DIFFRACTION100
3.5846-4.1030.23961290.15032895X-RAY DIFFRACTION100
4.103-5.16780.16971490.12292873X-RAY DIFFRACTION100
5.1678-42.18910.20841640.16292947X-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)
11.5704-1.435-0.50342.7492-0.39940.6961-0.19110.1512-0.05280.16830.1270.12940.0681-0.03460.04640.141-0.02740.02860.1507-0.01870.0666-8.12461.405350.7228
20.43610.07090.75430.8912-0.03321.3407-0.0255-0.0113-0.11730.02820.0676-0.07510.02750.17380.02160.11280.0185-0.04560.2271-0.0040.236812.30810.739840.8312
31.6304-1.07270.13410.9982-0.5780.76770.36970.1495-0.3655-0.6576-0.07630.09840.3761-0.0322-0.23040.3215-0.0227-0.08540.1679-0.06370.2142-4.5027-4.379916.1396
40.06760.17860.27420.83940.28311.6406-0.0526-0.0098-0.13060.00350.0907-0.0252-0.1237-0.0185-0.00050.09930.0041-0.0170.16460.01280.183711.22372.316337.3266
50.82780.02160.25920.14560.13151.0347-0.01050.14780.2222-0.32060.0741-0.1317-0.45720.15390.0620.32780.0354-0.05560.18440.04880.2094-2.2445.02222.657
61.1842-0.0670.52312.11471.04221.14390.0997-0.1003-0.02570.1036-0.2061-0.18190.07820.05750.07820.0851-0.01230.00560.16530.06510.159649.174715.437480.6995
71.1003-0.4452-0.1221.38090.07360.12890.11840.13180.0086-0.2981-0.0080.05180.1067-0.0874-0.040.29930.01970.02530.24620.00190.11232.540314.18965.2985
80.2982-0.385-0.01960.55220.22010.5402-0.0743-0.1109-0.24280.3335-0.13420.39470.4674-0.06390.20640.3808-0.03220.21160.1717-0.01210.445415.84619.820789.8651
91.58440.2866-0.41061.3616-0.88710.67250.0851-0.09530.18860.0347-0.11710.1284-0.0827-0.06870.02420.16540.0554-0.02780.1769-0.01730.129229.627816.168867.4867
101.1996-0.78150.22010.85870.25640.4510.2009-0.00630.06860.2851-0.12640.2876-0.0034-0.1473-0.09590.25240.02290.11030.1867-0.03670.288820.847419.363585.1466
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 1:99
2X-RAY DIFFRACTION2chain A and resid 100:145
3X-RAY DIFFRACTION3chain A and resid 146:189
4X-RAY DIFFRACTION4chain A and resid 190:255
5X-RAY DIFFRACTION5chain A and resid 256:298
6X-RAY DIFFRACTION6chain B and resid 1:99
7X-RAY DIFFRACTION7chain B and resid 100:145
8X-RAY DIFFRACTION8chain B and resid 146:189
9X-RAY DIFFRACTION9chain B and resid 190:255
10X-RAY DIFFRACTION10chain B and resid 256:298

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