PDB Short entry for 3N4U HEADER UNKNOWN FUNCTION 22-MAY-10 3N4U TITLE APP APH(2")-IVA FORM II COMPND MOL_ID: 1; COMPND 2 MOLECULE: APH(2'')-ID; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROCOCCUS CASSELIFLAVUS; SOURCE 3 ORGANISM_COMMON: ENTEROCOCCUS FLAVESCENS; SOURCE 4 ORGANISM_TAXID: 37734; SOURCE 5 GENE: APH(2'')-ID KEYWDS AMINOGLYCOSIDE, PHOSPHOTRANSFERASE, RESISTANCE, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR C.A.SMITH,M.TOTH,H.FRASE,S.B.VAKULENKO REVDAT 3 21-FEB-24 3N4U 1 REMARK REVDAT 2 22-SEP-10 3N4U 1 JRNL REVDAT 1 30-JUN-10 3N4U 0 JRNL AUTH M.TOTH,H.FRASE,N.T.ANTUNES,C.A.SMITH,S.B.VAKULENKO JRNL TITL CRYSTAL STRUCTURE AND KINETIC MECHANISM OF AMINOGLYCOSIDE JRNL TITL 2 PHOSPHOTRANSFERASE-2''-IVA. JRNL REF PROTEIN SCI. V. 19 1565 2010 JRNL REFN ISSN 0961-8368 JRNL PMID 20556826 JRNL DOI 10.1002/PRO.437 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 14542 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 727 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.8255 - 3.7552 0.97 2843 150 0.1606 0.2451 REMARK 3 2 3.7552 - 2.9839 0.99 2803 147 0.1564 0.2506 REMARK 3 3 2.9839 - 2.6077 1.00 2764 146 0.1883 0.2839 REMARK 3 4 2.6077 - 2.3697 0.99 2776 146 0.2014 0.3186 REMARK 3 5 2.3697 - 2.2000 0.96 2629 138 0.2147 0.3193 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.28 REMARK 3 B_SOL : 20.73 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.82210 REMARK 3 B22 (A**2) : -5.76710 REMARK 3 B33 (A**2) : -3.05500 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 2588 REMARK 3 ANGLE : 1.042 3496 REMARK 3 CHIRALITY : 0.073 369 REMARK 3 PLANARITY : 0.004 451 REMARK 3 DIHEDRAL : 17.905 978 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3N4U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-MAY-10. REMARK 100 THE DEPOSITION ID IS D_1000059381. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16313 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 28.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.37600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 23.19000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.24500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.29500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.24500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.19000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.29500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 40 29.03 48.94 REMARK 500 ARG A 41 -4.68 69.14 REMARK 500 SER A 85 110.47 -169.41 REMARK 500 GLU A 86 -117.97 61.38 REMARK 500 ASN A 196 3.39 80.60 REMARK 500 ASP A 197 44.55 -150.73 REMARK 500 ASP A 217 79.83 60.31 REMARK 500 SER A 224 -161.20 -164.27 REMARK 500 GLU A 239 -156.64 -123.85 REMARK 500 LYS A 253 32.12 70.86 REMARK 500 ASP A 286 -71.69 -44.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3N4T RELATED DB: PDB REMARK 900 APO APH(2")-IVA FORM I REMARK 900 RELATED ID: 3N4V RELATED DB: PDB REMARK 900 APO APH(2")-IVA FORM III DBREF 3N4U A 1 301 UNP O68183 O68183_ENTCA 1 301 SEQRES 1 A 301 MET ARG THR TYR THR PHE ASP GLN VAL GLU LYS ALA ILE SEQRES 2 A 301 GLU GLN LEU TYR PRO ASP PHE THR ILE ASN THR ILE GLU SEQRES 3 A 301 ILE SER GLY GLU GLY ASN ASP CYS ILE ALA TYR GLU ILE SEQRES 4 A 301 ASN ARG ASP PHE ILE PHE LYS PHE PRO LYS HIS SER ARG SEQRES 5 A 301 GLY SER THR ASN LEU PHE ASN GLU VAL ASN ILE LEU LYS SEQRES 6 A 301 ARG ILE HIS ASN LYS LEU PRO LEU PRO ILE PRO GLU VAL SEQRES 7 A 301 VAL PHE THR GLY MET PRO SER GLU THR TYR GLN MET SER SEQRES 8 A 301 PHE ALA GLY PHE THR LYS ILE LYS GLY VAL PRO LEU THR SEQRES 9 A 301 PRO LEU LEU LEU ASN ASN LEU PRO LYS GLN SER GLN ASN SEQRES 10 A 301 GLN ALA ALA LYS ASP LEU ALA ARG PHE LEU SER GLU LEU SEQRES 11 A 301 HIS SER ILE ASN ILE SER GLY PHE LYS SER ASN LEU VAL SEQRES 12 A 301 LEU ASP PHE ARG GLU LYS ILE ASN GLU ASP ASN LYS LYS SEQRES 13 A 301 ILE LYS LYS LEU LEU SER ARG GLU LEU LYS GLY PRO GLN SEQRES 14 A 301 MET LYS LYS VAL ASP ASP PHE TYR ARG ASP ILE LEU GLU SEQRES 15 A 301 ASN GLU ILE TYR PHE LYS TYR TYR PRO CYS LEU ILE HIS SEQRES 16 A 301 ASN ASP PHE SER SER ASP HIS ILE LEU PHE ASP THR GLU SEQRES 17 A 301 LYS ASN THR ILE CYS GLY ILE ILE ASP PHE GLY ASP ALA SEQRES 18 A 301 ALA ILE SER ASP PRO ASP ASN ASP PHE ILE SER LEU MET SEQRES 19 A 301 GLU ASP ASP GLU GLU TYR GLY MET GLU PHE VAL SER LYS SEQRES 20 A 301 ILE LEU ASN HIS TYR LYS HIS LYS ASP ILE PRO THR VAL SEQRES 21 A 301 LEU GLU LYS TYR ARG MET LYS GLU LYS TYR TRP SER PHE SEQRES 22 A 301 GLU LYS ILE ILE TYR GLY LYS GLU TYR GLY TYR MET ASP SEQRES 23 A 301 TRP TYR GLU GLU GLY LEU ASN GLU ILE ARG SER ILE LYS SEQRES 24 A 301 ILE LYS FORMUL 2 HOH *232(H2 O) HELIX 1 1 THR A 5 TYR A 17 1 13 HELIX 2 2 HIS A 50 ILE A 67 1 18 HELIX 3 3 THR A 104 ASN A 110 1 7 HELIX 4 4 PRO A 112 HIS A 131 1 20 HELIX 5 5 LYS A 139 VAL A 143 5 5 HELIX 6 6 ASP A 145 LEU A 161 1 17 HELIX 7 7 LYS A 166 GLU A 182 1 17 HELIX 8 8 ASN A 183 PHE A 187 5 5 HELIX 9 9 SER A 199 ASP A 201 5 3 HELIX 10 10 ASP A 227 SER A 232 1 6 HELIX 11 11 GLY A 241 LYS A 253 1 13 HELIX 12 12 ASP A 256 GLY A 283 1 28 HELIX 13 13 TYR A 284 ILE A 298 1 15 SHEET 1 A 5 ILE A 25 GLU A 30 0 SHEET 2 A 5 CYS A 34 ILE A 39 -1 O GLU A 38 N GLU A 26 SHEET 3 A 5 PHE A 43 PRO A 48 -1 O PHE A 45 N TYR A 37 SHEET 4 A 5 ALA A 93 THR A 96 -1 O PHE A 95 N ILE A 44 SHEET 5 A 5 VAL A 78 THR A 81 -1 N PHE A 80 O GLY A 94 SHEET 1 B 3 VAL A 101 PRO A 102 0 SHEET 2 B 3 ILE A 203 ASP A 206 -1 O PHE A 205 N VAL A 101 SHEET 3 B 3 THR A 211 ILE A 215 -1 O THR A 211 N ASP A 206 SHEET 1 C 2 CYS A 192 ILE A 194 0 SHEET 2 C 2 ALA A 222 SER A 224 -1 O ALA A 222 N ILE A 194 CRYST1 46.380 62.590 96.490 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.021561 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015977 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010364 0.00000