HEADER TRANSFERASE 03-NOV-17 5YPV TITLE CRYSTAL STRUCTURE OF FABD FROM ACINETOBACTER BAUMANNII COMPND MOL_ID: 1; COMPND 2 MOLECULE: MALONYL COA-ACYL CARRIER PROTEIN TRANSACYLASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FABD; COMPND 5 EC: 2.3.1.39; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACINETOBACTER BAUMANNII; SOURCE 3 ORGANISM_TAXID: 470; SOURCE 4 GENE: FABD; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS TRANSACYLASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR W.C.LEE,Y.KIM REVDAT 3 27-MAR-24 5YPV 1 REMARK REVDAT 2 22-MAY-19 5YPV 1 JRNL REVDAT 1 07-NOV-18 5YPV 0 JRNL AUTH W.C.LEE,J.PARK,P.K.BALASUBRAMANIAN,Y.KIM JRNL TITL ELUCIDATION OF THE CRYSTAL STRUCTURE OF FABD FROM THE JRNL TITL 2 MULTIDRUG-RESISTANT BACTERIUM ACINETOBACTER BAUMANNII. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 505 208 2018 JRNL REFN ESSN 1090-2104 JRNL PMID 30243724 JRNL DOI 10.1016/J.BBRC.2018.09.079 REMARK 2 REMARK 2 RESOLUTION. 1.67 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.67 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 34650 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.750 REMARK 3 FREE R VALUE TEST SET COUNT : 1993 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 29.2151 - 4.0075 0.99 2495 152 0.1825 0.2281 REMARK 3 2 4.0075 - 3.1821 1.00 2382 144 0.1981 0.2079 REMARK 3 3 3.1821 - 2.7802 1.00 2356 140 0.2167 0.2468 REMARK 3 4 2.7802 - 2.5262 1.00 2351 143 0.2315 0.2750 REMARK 3 5 2.5262 - 2.3452 1.00 2323 143 0.2350 0.2862 REMARK 3 6 2.3452 - 2.2070 1.00 2322 144 0.2314 0.2848 REMARK 3 7 2.2070 - 2.0965 1.00 2319 136 0.2315 0.2616 REMARK 3 8 2.0965 - 2.0053 1.00 2326 143 0.2373 0.3015 REMARK 3 9 2.0053 - 1.9281 1.00 2292 142 0.2587 0.3271 REMARK 3 10 1.9281 - 1.8616 1.00 2330 143 0.2543 0.3397 REMARK 3 11 1.8616 - 1.8034 1.00 2288 141 0.2555 0.3819 REMARK 3 12 1.8034 - 1.7518 1.00 2312 145 0.2729 0.3234 REMARK 3 13 1.7518 - 1.7057 1.00 2303 140 0.2722 0.3291 REMARK 3 14 1.7057 - 1.6641 0.99 2258 137 0.2828 0.3544 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.660 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.58 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.98 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 : 0.010 2331 REMARK 3 ANGLE : 1.083 3168 REMARK 3 CHIRALITY : 0.063 379 REMARK 3 PLANARITY : 0.008 412 REMARK 3 DIHEDRAL : 3.003 1411 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 5YPV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1300005699. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34750 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.670 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 11.30 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.67 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.10 REMARK 200 R MERGE FOR SHELL (I) : 0.57200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4M AMMONIUM TARTRATE DIBASIC, 0.1M REMARK 280 TRIS PH 8.5, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.76533 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 73.53067 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 73.53067 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 36.76533 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 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 252 CG CD OE1 NE2 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 HOH A 408 O HOH A 521 2.07 REMARK 500 O THR A 229 NH2 ARG A 254 2.14 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 SER A 101 -99.23 63.93 REMARK 500 ARG A 297 -6.04 129.18 REMARK 500 REMARK 500 REMARK: NULL DBREF 5YPV A 12 323 UNP V5VFX0 V5VFX0_ACIBA 12 323 SEQADV 5YPV ALA A 11 UNP V5VFX0 EXPRESSION TAG SEQADV 5YPV ALA A 324 UNP V5VFX0 EXPRESSION TAG SEQRES 1 A 314 ALA ALA THR LYS THR ALA PHE VAL PHE PRO GLY GLN GLY SEQRES 2 A 314 SER GLN LYS VAL GLY MET LEU ALA GLU LEU ALA GLU GLN SEQRES 3 A 314 PHE SER GLY VAL GLY GLN THR PHE ALA GLU ALA SER ASP SEQRES 4 A 314 ALA LEU GLY PHE ASP LEU TRP HIS ILE ALA GLN SER GLY SEQRES 5 A 314 GLU GLY LEU ASP GLN THR GLU ASN THR GLN PRO VAL LEU SEQRES 6 A 314 LEU THR ALA SER ILE ALA LEU TRP ARG LEU TRP LEU ASP SEQRES 7 A 314 LEU GLY GLY LEU ALA PRO LYS TYR LEU ALA GLY HIS SER SEQRES 8 A 314 LEU GLY GLU TYR SER ALA LEU VAL ALA ALA GLY SER MET SEQRES 9 A 314 SER LEU ALA ASP ALA VAL LYS LEU VAL ASN LEU ARG GLY SEQRES 10 A 314 LYS LEU MET GLN ASN ALA VAL PRO GLN GLY GLU GLY ALA SEQRES 11 A 314 MET ALA ALA ILE LEU GLY LEU ALA ASP ASP LYS VAL VAL SEQRES 12 A 314 GLU LEU CYS GLN SER VAL SER ALA LEU GLY GLN GLY SER SEQRES 13 A 314 VAL GLU ALA ALA ASN TYR ASN SER GLN GLY GLN VAL VAL SEQRES 14 A 314 ILE ALA GLY SER THR ALA SER VAL GLN GLN VAL MET ALA SEQRES 15 A 314 LEU ALA LYS GLU GLN SER ALA LYS ALA ILE ALA LEU PRO SEQRES 16 A 314 VAL SER VAL PRO SER HIS CYS SER LEU MET LYS PRO ALA SEQRES 17 A 314 ALA GLU LYS PHE ALA GLU ALA LEU GLU GLN THR ALA ILE SEQRES 18 A 314 GLU LEU PRO THR ILE PRO VAL ILE GLN ASN VAL ASN ALA SEQRES 19 A 314 GLY ILE ALA THR ASP VAL ALA GLN LEU ARG GLN ALA LEU SEQRES 20 A 314 THR ALA GLN LEU TYR GLN SER VAL GLN TRP THR ARG THR SEQRES 21 A 314 MET GLN SER LEU GLN ASP GLN GLY ILE GLN TYR ILE VAL SEQRES 22 A 314 GLU CYS GLY PRO GLY THR VAL LEU SER ASN LEU ALA LYS SEQRES 23 A 314 ARG LEU PRO ASN ILE GLU LYS ALA PHE SER ILE ASP SER SEQRES 24 A 314 LYS SER LYS MET GLU ASP ALA LEU ASN ALA VAL LEU VAL SEQRES 25 A 314 ALA ALA FORMUL 2 HOH *127(H2 O) HELIX 1 AA1 LEU A 30 PHE A 37 1 8 HELIX 2 AA2 PHE A 37 GLY A 52 1 16 HELIX 3 AA3 ASP A 54 GLY A 62 1 9 HELIX 4 AA4 GLN A 67 LEU A 89 1 23 HELIX 5 AA5 SER A 101 ALA A 111 1 11 HELIX 6 AA6 SER A 115 ASN A 132 1 18 HELIX 7 AA7 ALA A 148 LEU A 162 1 15 HELIX 8 AA8 THR A 184 GLN A 197 1 14 HELIX 9 AA9 CYS A 212 LEU A 214 5 3 HELIX 10 AB1 MET A 215 GLN A 228 1 14 HELIX 11 AB2 ASP A 249 LEU A 261 1 13 HELIX 12 AB3 TRP A 267 ASP A 276 1 10 HELIX 13 AB4 THR A 289 LEU A 294 1 6 HELIX 14 AB5 SER A 309 ALA A 324 1 16 SHEET 1 AA1 5 VAL A 238 ILE A 239 0 SHEET 2 AA1 5 TYR A 96 GLY A 99 1 N LEU A 97 O ILE A 239 SHEET 3 AA1 5 THR A 15 PHE A 19 1 N PHE A 17 O TYR A 96 SHEET 4 AA1 5 TYR A 281 GLU A 284 1 O VAL A 283 N VAL A 18 SHEET 5 AA1 5 LYS A 303 SER A 306 1 O PHE A 305 N GLU A 284 SHEET 1 AA2 5 LYS A 200 ALA A 203 0 SHEET 2 AA2 5 GLY A 139 LEU A 145 -1 N LEU A 145 O LYS A 200 SHEET 3 AA2 5 GLN A 177 SER A 183 -1 O VAL A 178 N ILE A 144 SHEET 4 AA2 5 VAL A 167 SER A 174 -1 N ALA A 170 O VAL A 179 SHEET 5 AA2 5 VAL A 265 GLN A 266 1 O VAL A 265 N TYR A 172 CRYST1 67.459 67.459 110.296 90.00 90.00 120.00 P 31 2 1 6 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 0.014824 0.008559 0.000000 0.00000 SCALE2 0.000000 0.017117 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009067 0.00000