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

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Basic information

Entry
Database: PDB / ID: 3csv
TitleCrystal structure of a putative aminoglycoside phosphotransferase (YP_614837.1) from Silicibacter sp. TM1040 at 2.15 A resolution
ComponentsAminoglycoside phosphotransferase
KeywordsTRANSFERASE / YP_614837.1 / Putative Aminoglycoside Phosphotransferase / Phosphotransferase enzyme family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


kinase activity / 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
Aminoglycoside phosphotransferase
Similarity search - Component
Biological speciesSilicibacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative aminoglycoside phosphotransferase (YP_614837.1) from Silicibacter sp. TM1040 at 2.15 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / 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: pdbx_struct_special_symmetry / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminoglycoside phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,09916
Polymers38,1961
Non-polymers90315
Water3,585199
1
A: Aminoglycoside phosphotransferase
hetero molecules

A: Aminoglycoside phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,19732
Polymers76,3922
Non-polymers1,80530
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area6230 Å2
ΔGint-119.3 kcal/mol
Surface area28730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.680, 55.940, 61.220
Angle α, β, γ (deg.)90.000, 102.900, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-333-

ZN

21A-427-

HOH

31A-520-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Aminoglycoside phosphotransferase


Mass: 38195.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter sp. (bacteria) / Strain: TM1040 / Gene: YP_614837.1, TM1040_2843 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q1GCP1

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Non-polymers , 6 types, 214 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.48 Å3/Da / Density % sol: 50.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: NANODROP, 2.0M (NH4)2SO4, 0.2M NaCl, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97915 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 17, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.15→29.735 Å / Num. obs: 20496 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.356 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.33
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.15-2.230.3222.476624013196.5
2.23-2.320.2423.276063952197.6
2.32-2.420.1943.970613663197.9
2.42-2.550.1684.678524075198.7
2.55-2.710.1226.175643907198.9
2.71-2.920.0937.877323989198.6
2.92-3.210.06111.275533883199.1
3.21-3.670.03716.976513931198.7
3.67-4.610.02622.877633968198.8
4.61-29.7350.02624.177163938197.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→29.735 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.92 / SU B: 8.559 / SU ML: 0.118 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.19
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. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. ZN IS MODELED BASED ON AN X-RAY FLOURESCENCE SCAN, ANOMALOUS DIFFERENCE FOURIERS, AND COORDINATION GEOMETRY. 5. NA, CL, SO4, AND EDO ARE MODELED BASED ON CRYSTALLIZATION AND CRYO CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1050 5.1 %RANDOM
Rwork0.168 ---
obs0.171 20494 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.368 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å2-0.19 Å2
2--1.11 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.15→29.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2531 0 52 199 2782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222654
X-RAY DIFFRACTIONr_bond_other_d0.0010.021822
X-RAY DIFFRACTIONr_angle_refined_deg1.1741.9623590
X-RAY DIFFRACTIONr_angle_other_deg0.90634386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5885328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15623.088136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22215415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0641527
X-RAY DIFFRACTIONr_chiral_restr0.070.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022985
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02567
X-RAY DIFFRACTIONr_nbd_refined0.2060.2562
X-RAY DIFFRACTIONr_nbd_other0.1960.21918
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21263
X-RAY DIFFRACTIONr_nbtor_other0.0840.21381
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2161
X-RAY DIFFRACTIONr_metal_ion_refined0.0110.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2580.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.216
X-RAY DIFFRACTIONr_mcbond_it1.3531622
X-RAY DIFFRACTIONr_mcbond_other0.3213646
X-RAY DIFFRACTIONr_mcangle_it2.42552590
X-RAY DIFFRACTIONr_scbond_it4.45581056
X-RAY DIFFRACTIONr_scangle_it6.40511996
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 66 -
Rwork0.188 1414 -
all-1480 -
obs--98.47 %
Refinement TLS params.Method: refined / Origin x: 14.22 Å / Origin y: 30.193 Å / Origin z: 18.446 Å
111213212223313233
T-0.0741 Å20.0115 Å2-0.0243 Å2--0.0707 Å2-0.0069 Å2---0.1464 Å2
L0.5622 °20.1701 °2-0.3121 °2-0.229 °2-0.2843 °2--0.7762 °2
S-0.015 Å °-0.0172 Å °0.0014 Å °-0.0377 Å °0.035 Å °-0.005 Å °0.0433 Å °0.0351 Å °-0.02 Å °

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