HEADER TRANSFERASE 05-MAR-14 4CS6 TITLE CRYSTAL STRUCTURE OF AADA - AN AMINOGLYCOSIDE ADENYLTRANSFERASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMINOGLYCOSIDE ADENYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NUCLEOTIDYLTRANSFERASE DOMAIN AND ALPHA-HELICAL DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR SOURCE 3 TYPHIMURIUM STR. LT2; SOURCE 4 ORGANISM_TAXID: 99287; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: STAR KEYWDS TRANSFERASE, AMINOGLYCOSIDE ADENYLTRANSFERASE, ANT(3'') EXPDTA X-RAY DIFFRACTION AUTHOR Y.CHEN,J.NASVALL,D.I.ANDERSSON,M.SELMER REVDAT 2 11-NOV-15 4CS6 1 JRNL REVDAT 1 25-MAR-15 4CS6 0 JRNL AUTH Y.CHEN,J.NASVALL,S.WU,D.I.ANDERSSON,M.SELMER JRNL TITL STRUCTURE OF AADA FROM SALMONELLA ENTERICA: A MONOMERIC JRNL TITL 2 AMINOGLYCOSIDE (3'')(9) ADENYLTRANSFERASE. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 71 2267 2015 JRNL REFN ISSN 0907-4449 JRNL PMID 26527143 JRNL DOI 10.1107/S1399004715016429 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT 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) : 2.502 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.029 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.34 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.66 REMARK 3 NUMBER OF REFLECTIONS : 10816 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1962 REMARK 3 R VALUE (WORKING SET) : 0.1935 REMARK 3 FREE R VALUE : 0.2521 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.8 REMARK 3 FREE R VALUE TEST SET COUNT : 517 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 39.0340 - 3.9704 0.99 2685 128 0.1698 0.2001 REMARK 3 2 3.9704 - 3.1519 1.00 2571 120 0.1898 0.2684 REMARK 3 3 3.1519 - 2.7536 1.00 2543 126 0.2505 0.3378 REMARK 3 4 2.7536 - 2.5019 0.99 2500 143 0.2754 0.3924 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.40 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.26 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 61.76 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.3 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 2103 REMARK 3 ANGLE : 1.277 2876 REMARK 3 CHIRALITY : 0.084 333 REMARK 3 PLANARITY : 0.006 368 REMARK 3 DIHEDRAL : 16.128 769 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 5.0012 15.7438 128.4074 REMARK 3 T TENSOR REMARK 3 T11: 0.3167 T22: 0.3152 REMARK 3 T33: 0.3456 T12: 0.0093 REMARK 3 T13: -0.0735 T23: 0.0479 REMARK 3 L TENSOR REMARK 3 L11: 3.8162 L22: 2.5265 REMARK 3 L33: 4.6969 L12: 0.4463 REMARK 3 L13: -1.9422 L23: -1.2033 REMARK 3 S TENSOR REMARK 3 S11: 0.2259 S12: 0.2458 S13: 0.1288 REMARK 3 S21: 0.1132 S22: 0.1811 S23: 0.0898 REMARK 3 S31: 0.3438 S32: -0.2254 S33: -0.3659 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 4CS6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-MAR-14. REMARK 100 THE PDBE ID CODE IS EBI-57849. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 193 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0, 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD (QUANTUM 315R) REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10853 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.50 REMARK 200 RESOLUTION RANGE LOW (A) : 39.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.1 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.05 REMARK 200 R MERGE (I) : 0.08 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.00 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 7.14 REMARK 200 R MERGE FOR SHELL (I) : 0.95 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.10 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,-Y,-Z+1/2 REMARK 290 4555 -X+1/2,-Y,Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 24.32900 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.29350 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 24.32900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 52.29350 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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 LYS A 263 REMARK 465 GLY A 264 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ILE A 20 OG1 THR A 24 2.12 REMARK 500 REMARK 500 REMARK: NULL 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 ALA A 79 -64.17 -94.33 REMARK 500 GLU A 82 -4.18 67.01 REMARK 500 ALA A 157 75.27 63.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO A 156 ALA A 157 50.28 REMARK 500 REMARK 500 REMARK: NULL DBREF 4CS6 A 1 262 UNP Q8ZPX9 Q8ZPX9_SALTY 1 262 SEQADV 4CS6 LYS A 263 UNP Q8ZPX9 EXPRESSION TAG SEQADV 4CS6 GLY A 264 UNP Q8ZPX9 EXPRESSION TAG SEQRES 1 A 264 MET THR LEU SER ILE PRO PRO SER ILE GLN CYS GLN THR SEQRES 2 A 264 GLU ALA ALA CYS ARG LEU ILE THR ARG VAL THR GLY ASP SEQRES 3 A 264 THR LEU ARG ALA ILE HIS LEU TYR GLY SER ALA VAL ALA SEQRES 4 A 264 GLY GLY LEU LYS PRO ASN SER ASP ILE ASP LEU LEU VAL SEQRES 5 A 264 THR ILE CSS GLN PRO LEU THR GLU ALA GLN ARG ALA THR SEQRES 6 A 264 LEU MET GLN GLU LEU LEU ALA LEU SER SER PRO PRO GLY SEQRES 7 A 264 ALA SER ALA GLU LYS ARG ALA LEU GLU VAL THR VAL VAL SEQRES 8 A 264 LEU TYR SER GLN LEU VAL PRO TRP CYS PHE PRO PRO SER SEQRES 9 A 264 ARG GLU MET GLN PHE GLY GLU TRP LEU ARG GLU ASP ILE SEQRES 10 A 264 CYS GLN GLY ILE TYR GLU PRO ALA GLN GLN ASP TRP ASP SEQRES 11 A 264 MET VAL LEU LEU ILE THR GLN ILE LEU GLU THR SER ILE SEQRES 12 A 264 PRO LEU LYS GLY GLU ARG ALA GLU ARG LEU PHE THR PRO SEQRES 13 A 264 ALA PRO ALA ALA GLN LEU LEU LYS ALA LEU ARG TYR PRO SEQRES 14 A 264 LEU ASP LEU TRP GLN SER THR ALA ASP VAL GLN GLY ASP SEQRES 15 A 264 GLU TYR HIS ILE VAL LEU THR LEU ALA ARG ILE TRP TYR SEQRES 16 A 264 THR LEU SER THR GLY ARG PHE THR SER LYS ASP ALA ALA SEQRES 17 A 264 ALA ASP TRP LEU LEU PRO GLN LEU PRO GLU ASP TYR ALA SEQRES 18 A 264 ALA THR LEU ARG ALA ALA GLN ARG GLU TYR LEU GLY LEU SEQRES 19 A 264 GLU GLN GLN ASP TRP HIS ILE LEU LEU PRO ALA VAL VAL SEQRES 20 A 264 ARG PHE VAL ASP PHE ALA LYS ALA HIS ILE PRO THR GLN SEQRES 21 A 264 PHE THR LYS GLY MODRES 4CS6 CSS A 55 CYS S-MERCAPTOCYSTEINE HET CSS A 55 7 HETNAM CSS S-MERCAPTOCYSTEINE FORMUL 1 CSS C3 H7 N O2 S2 FORMUL 2 HOH *30(H2 O) HELIX 1 1 PRO A 6 GLY A 25 1 20 HELIX 2 2 THR A 59 LEU A 73 1 15 HELIX 3 3 TYR A 93 VAL A 97 1 5 HELIX 4 4 GLY A 110 TRP A 112 5 3 HELIX 5 5 LEU A 113 GLN A 119 1 7 HELIX 6 6 TRP A 129 THR A 141 1 13 HELIX 7 7 ARG A 149 PHE A 154 1 6 HELIX 8 8 PRO A 158 TYR A 168 1 11 HELIX 9 9 PRO A 169 TRP A 173 5 5 HELIX 10 10 SER A 175 GLN A 180 1 6 HELIX 11 11 ASP A 182 GLY A 200 1 19 HELIX 12 12 ALA A 207 LEU A 213 1 7 HELIX 13 13 PRO A 214 LEU A 216 5 3 HELIX 14 14 PRO A 217 LEU A 232 1 16 HELIX 15 15 LEU A 242 ILE A 257 1 16 SHEET 1 AA 5 MET A 107 PHE A 109 0 SHEET 2 AA 5 LEU A 86 LEU A 92 -1 O VAL A 88 N PHE A 109 SHEET 3 AA 5 ILE A 48 ILE A 54 1 O ILE A 48 N GLU A 87 SHEET 4 AA 5 LEU A 28 TYR A 34 -1 N ARG A 29 O THR A 53 SHEET 5 AA 5 ILE A 143 LYS A 146 -1 O ILE A 143 N LEU A 33 SHEET 1 AB 2 SER A 104 ARG A 105 0 SHEET 2 AB 2 GLN A 126 GLN A 127 -1 O GLN A 126 N ARG A 105 LINK C ILE A 54 N CSS A 55 1555 1555 1.33 LINK C CSS A 55 N GLN A 56 1555 1555 1.33 CISPEP 1 VAL A 97 PRO A 98 0 4.93 CISPEP 2 PHE A 101 PRO A 102 0 -5.48 CRYST1 48.658 58.642 104.587 90.00 90.00 90.00 P 21 2 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 0.020552 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017053 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009561 0.00000