PDB Short entry for 1U7U HEADER LIGASE 04-AUG-04 1U7U TITLE PHOSPHOPANTOTHENOYLCYSTEINE SYNTHETASE FROM E. COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: COENZYME A BIOSYNTHESIS BIFUNCTIONAL PROTEIN COABC; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PHOSPHOPANTOTHENOYLCYSTEINE SYNTHETASE(RESIDUES 181-406); COMPND 5 EC: 6.3.2.5; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COENZYME A BIOSYNTHESIS, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR S.STANITZEK,M.A.AUGUSTIN,R.HUBER,T.KUPKE,S.STEINBACHER REVDAT 3 10-NOV-21 1U7U 1 SEQADV REVDAT 2 24-FEB-09 1U7U 1 VERSN REVDAT 1 30-NOV-04 1U7U 0 JRNL AUTH S.STANITZEK,M.A.AUGUSTIN,R.HUBER,T.KUPKE,S.STEINBACHER JRNL TITL STRUCTURAL BASIS OF CTP-DEPENDENT PEPTIDE BOND FORMATION IN JRNL TITL 2 COENZYME A BIOSYNTHESIS CATALYZED BY ESCHERICHIA COLI PPC JRNL TITL 3 SYNTHETASE JRNL REF STRUCTURE V. 12 1977 2004 JRNL REFN ISSN 0969-2126 JRNL PMID 15530362 JRNL DOI 10.1016/J.STR.2004.08.007 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 8804 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 698 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1528 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 77 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) : 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.730 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1U7U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-AUG-04. REMARK 100 THE DEPOSITION ID IS D_1000023354. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-AUG-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MPG/DESY, HAMBURG REMARK 200 BEAMLINE : BW6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8804 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, PH 8, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Z 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 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 26.46500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.62750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 26.46500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 28.62750 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: DIMERIC 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -25.45842 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 74.52769 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 SER A 181 REMARK 465 THR A 284 REMARK 465 VAL A 285 REMARK 465 ALA A 286 REMARK 465 PRO A 287 REMARK 465 GLU A 288 REMARK 465 LYS A 289 REMARK 465 ILE A 290 REMARK 465 LYS A 291 REMARK 465 LYS A 292 REMARK 465 GLN A 293 REMARK 465 ALA A 294 REMARK 465 THR A 295 REMARK 465 GLN A 296 REMARK 465 GLY A 297 REMARK 465 ASP A 298 REMARK 465 GLU A 299 REMARK 465 ASP A 354 REMARK 465 VAL A 355 REMARK 465 SER A 356 REMARK 465 GLN A 357 REMARK 465 PRO A 358 REMARK 465 THR A 359 REMARK 465 GLN A 360 REMARK 465 GLY A 361 REMARK 465 PHE A 362 REMARK 465 ASN A 363 REMARK 465 ARG A 406 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 PRO A 204 REMARK 475 VAL A 205 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 303 CG CD CE NZ 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 184 12.62 -143.39 REMARK 500 ASP A 203 -171.70 174.70 REMARK 500 ARG A 206 138.53 171.19 REMARK 500 TYR A 207 148.09 -174.91 REMARK 500 SER A 209 -159.23 -128.45 REMARK 500 PRO A 237 96.98 -50.35 REMARK 500 ARG A 281 -148.26 -118.58 REMARK 500 THR A 331 -79.73 -91.02 REMARK 500 ASN A 333 65.77 61.58 REMARK 500 VAL A 334 -60.73 -94.29 REMARK 500 LYS A 345 1.02 -69.38 REMARK 500 ASP A 375 66.00 -103.35 REMARK 500 PRO A 381 156.31 -46.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1U7W RELATED DB: PDB REMARK 900 THE SAME PROTEIN, CTP-COMPLEX REMARK 900 RELATED ID: 1U7Z RELATED DB: PDB REMARK 900 THE SAME PROTEIN, 4'-PHOSPHOPANTOTHENOYL-CMP COMPLEX REMARK 900 RELATED ID: 1U80 RELATED DB: PDB REMARK 900 THE SAME PROTEIN, CMP COMPLEX DBREF 1U7U A 181 406 UNP P0ABQ0 COABC_ECOLI 180 405 SEQADV 1U7U ASP A 210 UNP P0ABQ0 ASN 209 ENGINEERED MUTATION SEQRES 1 A 226 SER PRO VAL ASN ASP LEU LYS HIS LEU ASN ILE MET ILE SEQRES 2 A 226 THR ALA GLY PRO THR ARG GLU PRO LEU ASP PRO VAL ARG SEQRES 3 A 226 TYR ILE SER ASP HIS SER SER GLY LYS MET GLY PHE ALA SEQRES 4 A 226 ILE ALA ALA ALA ALA ALA ARG ARG GLY ALA ASN VAL THR SEQRES 5 A 226 LEU VAL SER GLY PRO VAL SER LEU PRO THR PRO PRO PHE SEQRES 6 A 226 VAL LYS ARG VAL ASP VAL MET THR ALA LEU GLU MET GLU SEQRES 7 A 226 ALA ALA VAL ASN ALA SER VAL GLN GLN GLN ASN ILE PHE SEQRES 8 A 226 ILE GLY CYS ALA ALA VAL ALA ASP TYR ARG ALA ALA THR SEQRES 9 A 226 VAL ALA PRO GLU LYS ILE LYS LYS GLN ALA THR GLN GLY SEQRES 10 A 226 ASP GLU LEU THR ILE LYS MET VAL LYS ASN PRO ASP ILE SEQRES 11 A 226 VAL ALA GLY VAL ALA ALA LEU LYS ASP HIS ARG PRO TYR SEQRES 12 A 226 VAL VAL GLY PHE ALA ALA GLU THR ASN ASN VAL GLU GLU SEQRES 13 A 226 TYR ALA ARG GLN LYS ARG ILE ARG LYS ASN LEU ASP LEU SEQRES 14 A 226 ILE CYS ALA ASN ASP VAL SER GLN PRO THR GLN GLY PHE SEQRES 15 A 226 ASN SER ASP ASN ASN ALA LEU HIS LEU PHE TRP GLN ASP SEQRES 16 A 226 GLY ASP LYS VAL LEU PRO LEU GLU ARG LYS GLU LEU LEU SEQRES 17 A 226 GLY GLN LEU LEU LEU ASP GLU ILE VAL THR ARG TYR ASP SEQRES 18 A 226 GLU LYS ASN ARG ARG FORMUL 2 HOH *77(H2 O) HELIX 1 1 GLY A 214 ARG A 226 1 13 HELIX 2 2 THR A 253 VAL A 265 1 13 HELIX 3 3 GLN A 266 GLN A 268 5 3 HELIX 4 4 ASP A 309 ALA A 316 1 8 HELIX 5 5 ASN A 333 LYS A 345 1 13 HELIX 6 6 LYS A 385 ARG A 405 1 21 SHEET 1 A 8 LYS A 247 ASP A 250 0 SHEET 2 A 8 ASN A 230 SER A 235 1 N LEU A 233 O LYS A 247 SHEET 3 A 8 ASN A 190 ALA A 195 1 N ILE A 193 O THR A 232 SHEET 4 A 8 ILE A 270 GLY A 273 1 O ILE A 270 N MET A 192 SHEET 5 A 8 TYR A 323 ALA A 328 1 O VAL A 325 N GLY A 273 SHEET 6 A 8 LEU A 349 ALA A 352 1 O CYS A 351 N ALA A 328 SHEET 7 A 8 ASN A 366 TRP A 373 -1 O HIS A 370 N ALA A 352 SHEET 8 A 8 GLY A 376 ARG A 384 -1 O LYS A 378 N LEU A 371 SHEET 1 B 2 GLU A 200 ASP A 203 0 SHEET 2 B 2 ARG A 206 ILE A 208 -1 O ILE A 208 N GLU A 200 CRYST1 52.930 57.255 78.756 90.00 108.86 90.00 C 1 2 1 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 0.018893 0.000000 0.006454 0.00000 SCALE2 0.000000 0.017466 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013418 0.00000