HEADER LIGASE 19-JUN-13 3WDK TITLE CRYSTAL STRUCTURE OF 4-PHOSPHOPANTOATE-BETA-ALANINE LIGASE COMPLEXED TITLE 2 WITH REACTION INTERMEDIATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 4-PHOSPHOPANTOATE--BETA-ALANINE LIGASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: PHOSPHOPANTOTHENATE SYNTHETASE, PPS; COMPND 5 EC: 6.3.2.36; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARENSIS; SOURCE 3 ORGANISM_TAXID: 69014; SOURCE 4 STRAIN: KOD1; SOURCE 5 GENE: TK1686; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR A.KISHIMOTO,A.KITA,T.ISHIBASHI,H.TOMITA,Y.YOKOOJI,T.IMANAKA,H.ATOMI, AUTHOR 2 K.MIKI REVDAT 3 20-MAR-24 3WDK 1 REMARK REVDAT 2 22-FEB-17 3WDK 1 JRNL REVDAT 1 02-APR-14 3WDK 0 JRNL AUTH A.KISHIMOTO,A.KITA,T.ISHIBASHI,H.TOMITA,Y.YOKOOJI,T.IMANAKA, JRNL AUTH 2 H.ATOMI,K.MIKI JRNL TITL CRYSTAL STRUCTURE OF PHOSPHOPANTOTHENATE SYNTHETASE FROM JRNL TITL 2 THERMOCOCCUS KODAKARENSIS JRNL REF PROTEINS V. 82 1924 2014 JRNL REFN ISSN 0887-3585 JRNL PMID 24638914 JRNL DOI 10.1002/PROT.24546 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.49 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 4635031.030 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 60876 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3043 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 67.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6898 REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE : 0.2930 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 365 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7808 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 183 REMARK 3 SOLVENT ATOMS : 255 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.40000 REMARK 3 B22 (A**2) : 2.40000 REMARK 3 B33 (A**2) : -4.80000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.28 REMARK 3 ESD FROM SIGMAA (A) : 0.23 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.28 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.930 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.270 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.060 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.220 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.240 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 36.68 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : LIGAND4.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : LIGAND.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3WDK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JUN-13. REMARK 100 THE DEPOSITION ID IS D_1000096200. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NUMERICAL LINK TYPE SI(111) REMARK 200 DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64483 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 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 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50% TACSIMATE, 1% PEG 3350, 100MM REMARK 280 SODIUM ACETATE TRIHYDRATE, PH 4.5, VAPOR DIFFUSION, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 93.98050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 61.80450 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 61.80450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 46.99025 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 61.80450 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 61.80450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 140.97075 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 61.80450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 61.80450 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 46.99025 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 61.80450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 61.80450 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 140.97075 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 93.98050 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 VAL A 2 REMARK 465 ASN A 3 REMARK 465 ILE A 4 REMARK 465 PRO A 5 REMARK 465 LYS A 6 REMARK 465 SER A 7 REMARK 465 HIS A 8 REMARK 465 LEU A 139 REMARK 465 GLU A 140 REMARK 465 HIS A 141 REMARK 465 GLU A 261 REMARK 465 MET B 1 REMARK 465 VAL B 2 REMARK 465 ASN B 3 REMARK 465 ILE B 4 REMARK 465 PRO B 5 REMARK 465 LYS B 6 REMARK 465 SER B 7 REMARK 465 HIS B 8 REMARK 465 PRO B 9 REMARK 465 ARG B 257 REMARK 465 LYS B 258 REMARK 465 GLU B 259 REMARK 465 LEU B 260 REMARK 465 GLU B 261 REMARK 465 MET C 1 REMARK 465 VAL C 2 REMARK 465 ASN C 3 REMARK 465 ILE C 4 REMARK 465 PRO C 5 REMARK 465 LYS C 6 REMARK 465 SER C 7 REMARK 465 HIS C 8 REMARK 465 GLU C 140 REMARK 465 HIS C 141 REMARK 465 GLU C 142 REMARK 465 GLU C 259 REMARK 465 LEU C 260 REMARK 465 GLU C 261 REMARK 465 MET D 1 REMARK 465 VAL D 2 REMARK 465 ASN D 3 REMARK 465 ILE D 4 REMARK 465 PRO D 5 REMARK 465 LYS D 6 REMARK 465 SER D 7 REMARK 465 HIS D 8 REMARK 465 PRO D 9 REMARK 465 GLU D 142 REMARK 465 GLU D 261 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 PRO A 9 CG CD REMARK 470 GLU A 70 CG CD OE1 OE2 REMARK 470 GLU A 116 CG CD OE1 OE2 REMARK 470 LYS A 120 CG CD CE NZ REMARK 470 GLU A 124 CG CD OE1 OE2 REMARK 470 ILE A 136 CG1 CG2 CD1 REMARK 470 GLU A 142 CG CD OE1 OE2 REMARK 470 ARG A 143 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 145 CG CD CE NZ REMARK 470 LYS A 153 CG CD CE NZ REMARK 470 GLU A 259 CG CD OE1 OE2 REMARK 470 ARG B 10 CG CD NE CZ NH1 NH2 REMARK 470 LEU B 14 CG CD1 CD2 REMARK 470 GLU B 142 CG CD OE1 OE2 REMARK 470 TRP B 255 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP B 255 CZ3 CH2 REMARK 470 ARG C 10 CG CD NE CZ NH1 NH2 REMARK 470 LEU C 14 CG CD1 CD2 REMARK 470 GLU C 18 CG CD OE1 OE2 REMARK 470 LYS C 98 CG CD CE NZ REMARK 470 ARG C 112 CG CD NE CZ NH1 NH2 REMARK 470 ILE C 125 CG1 CG2 CD1 REMARK 470 ARG C 135 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 143 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 145 CG CD CE NZ REMARK 470 GLU C 148 CG CD OE1 OE2 REMARK 470 LYS C 258 CG CD CE NZ REMARK 470 ARG D 10 CG CD NE CZ NH1 NH2 REMARK 470 LEU D 14 CG CD1 CD2 REMARK 470 GLU D 126 CG CD OE1 OE2 REMARK 470 ARG D 135 CG CD NE CZ NH1 NH2 REMARK 470 ILE D 136 CG1 CG2 CD1 REMARK 470 GLU D 140 CG CD OE1 OE2 REMARK 470 HIS D 141 CG ND1 CD2 CE1 NE2 REMARK 470 ARG D 143 CG CD NE CZ NH1 NH2 REMARK 470 LYS D 145 CG CD CE NZ REMARK 470 GLU D 148 CG CD OE1 OE2 REMARK 470 LYS D 233 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 TYR A 105 62.57 -112.46 REMARK 500 PRO A 137 76.68 -64.08 REMARK 500 TYR B 105 64.39 -104.39 REMARK 500 HIS B 141 -135.14 50.00 REMARK 500 LEU B 161 58.20 37.78 REMARK 500 ILE B 254 170.71 -56.56 REMARK 500 TYR C 105 63.45 -101.08 REMARK 500 LEU C 161 55.60 39.76 REMARK 500 TYR D 105 64.16 -104.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PTJ A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FLC A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PTJ B 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PTJ C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FLC C 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PTJ D 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FLC D 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WDL RELATED DB: PDB REMARK 900 RELATED ID: 3WDM RELATED DB: PDB DBREF 3WDK A 1 261 UNP Q5JIZ8 PPS_PYRKO 1 261 DBREF 3WDK B 1 261 UNP Q5JIZ8 PPS_PYRKO 1 261 DBREF 3WDK C 1 261 UNP Q5JIZ8 PPS_PYRKO 1 261 DBREF 3WDK D 1 261 UNP Q5JIZ8 PPS_PYRKO 1 261 SEQRES 1 A 261 MET VAL ASN ILE PRO LYS SER HIS PRO ARG TYR TRP SER SEQRES 2 A 261 LEU TYR TYR ARG GLU LYS ILE ILE GLU GLY MET GLU LYS SEQRES 3 A 261 GLY MET THR ALA LYS ALA GLY LEU ILE ALA HIS GLY ARG SEQRES 4 A 261 GLY GLU ALA PHE ASP TYR LEU ILE GLY GLU ARG THR ILE SEQRES 5 A 261 GLU PRO ALA GLU ARG ALA MET ARG ALA ALA VAL ALA LYS SEQRES 6 A 261 PHE LEU LEU ALA GLU HIS PRO VAL ILE SER VAL ASN GLY SEQRES 7 A 261 ASN VAL ALA ALA LEU VAL PRO LYS GLU THR ILE GLU LEU SEQRES 8 A 261 ALA LYS ALA LEU ASN ALA LYS LEU GLU ILE ASN LEU PHE SEQRES 9 A 261 TYR ARG THR GLU GLU ARG VAL ARG THR ILE ALA GLU GLU SEQRES 10 A 261 LEU ARG LYS TYR ASP PRO GLU ILE GLU ILE LEU GLY ILE SEQRES 11 A 261 ASN PRO THR LYS ARG ILE PRO GLY LEU GLU HIS GLU ARG SEQRES 12 A 261 GLY LYS VAL ASP GLU ASN GLY ILE TRP LYS ALA ASP VAL SEQRES 13 A 261 VAL LEU VAL PRO LEU GLU ASP GLY ASP ARG THR GLU ALA SEQRES 14 A 261 LEU VAL ARG MET GLY LYS PHE VAL VAL THR VAL ASP LEU SEQRES 15 A 261 ASN PRO LEU SER ARG SER ALA ARG MET ALA ASP ILE THR SEQRES 16 A 261 ILE VAL ASP ASN ILE VAL ARG ALA TYR PRO ARG MET VAL SEQRES 17 A 261 GLU LEU ALA ARG GLU MET LYS ASP TYR SER ARG GLU GLU SEQRES 18 A 261 LEU LEU LYS ILE VAL GLY GLU TYR ASP ASN GLY LYS THR SEQRES 19 A 261 LEU SER ASP VAL LEU LEU HIS ILE ARG ASP ARG LEU THR SEQRES 20 A 261 ARG LEU ALA GLU GLU GLY ILE TRP ARG ARG LYS GLU LEU SEQRES 21 A 261 GLU SEQRES 1 B 261 MET VAL ASN ILE PRO LYS SER HIS PRO ARG TYR TRP SER SEQRES 2 B 261 LEU TYR TYR ARG GLU LYS ILE ILE GLU GLY MET GLU LYS SEQRES 3 B 261 GLY MET THR ALA LYS ALA GLY LEU ILE ALA HIS GLY ARG SEQRES 4 B 261 GLY GLU ALA PHE ASP TYR LEU ILE GLY GLU ARG THR ILE SEQRES 5 B 261 GLU PRO ALA GLU ARG ALA MET ARG ALA ALA VAL ALA LYS SEQRES 6 B 261 PHE LEU LEU ALA GLU HIS PRO VAL ILE SER VAL ASN GLY SEQRES 7 B 261 ASN VAL ALA ALA LEU VAL PRO LYS GLU THR ILE GLU LEU SEQRES 8 B 261 ALA LYS ALA LEU ASN ALA LYS LEU GLU ILE ASN LEU PHE SEQRES 9 B 261 TYR ARG THR GLU GLU ARG VAL ARG THR ILE ALA GLU GLU SEQRES 10 B 261 LEU ARG LYS TYR ASP PRO GLU ILE GLU ILE LEU GLY ILE SEQRES 11 B 261 ASN PRO THR LYS ARG ILE PRO GLY LEU GLU HIS GLU ARG SEQRES 12 B 261 GLY LYS VAL ASP GLU ASN GLY ILE TRP LYS ALA ASP VAL SEQRES 13 B 261 VAL LEU VAL PRO LEU GLU ASP GLY ASP ARG THR GLU ALA SEQRES 14 B 261 LEU VAL ARG MET GLY LYS PHE VAL VAL THR VAL ASP LEU SEQRES 15 B 261 ASN PRO LEU SER ARG SER ALA ARG MET ALA ASP ILE THR SEQRES 16 B 261 ILE VAL ASP ASN ILE VAL ARG ALA TYR PRO ARG MET VAL SEQRES 17 B 261 GLU LEU ALA ARG GLU MET LYS ASP TYR SER ARG GLU GLU SEQRES 18 B 261 LEU LEU LYS ILE VAL GLY GLU TYR ASP ASN GLY LYS THR SEQRES 19 B 261 LEU SER ASP VAL LEU LEU HIS ILE ARG ASP ARG LEU THR SEQRES 20 B 261 ARG LEU ALA GLU GLU GLY ILE TRP ARG ARG LYS GLU LEU SEQRES 21 B 261 GLU SEQRES 1 C 261 MET VAL ASN ILE PRO LYS SER HIS PRO ARG TYR TRP SER SEQRES 2 C 261 LEU TYR TYR ARG GLU LYS ILE ILE GLU GLY MET GLU LYS SEQRES 3 C 261 GLY MET THR ALA LYS ALA GLY LEU ILE ALA HIS GLY ARG SEQRES 4 C 261 GLY GLU ALA PHE ASP TYR LEU ILE GLY GLU ARG THR ILE SEQRES 5 C 261 GLU PRO ALA GLU ARG ALA MET ARG ALA ALA VAL ALA LYS SEQRES 6 C 261 PHE LEU LEU ALA GLU HIS PRO VAL ILE SER VAL ASN GLY SEQRES 7 C 261 ASN VAL ALA ALA LEU VAL PRO LYS GLU THR ILE GLU LEU SEQRES 8 C 261 ALA LYS ALA LEU ASN ALA LYS LEU GLU ILE ASN LEU PHE SEQRES 9 C 261 TYR ARG THR GLU GLU ARG VAL ARG THR ILE ALA GLU GLU SEQRES 10 C 261 LEU ARG LYS TYR ASP PRO GLU ILE GLU ILE LEU GLY ILE SEQRES 11 C 261 ASN PRO THR LYS ARG ILE PRO GLY LEU GLU HIS GLU ARG SEQRES 12 C 261 GLY LYS VAL ASP GLU ASN GLY ILE TRP LYS ALA ASP VAL SEQRES 13 C 261 VAL LEU VAL PRO LEU GLU ASP GLY ASP ARG THR GLU ALA SEQRES 14 C 261 LEU VAL ARG MET GLY LYS PHE VAL VAL THR VAL ASP LEU SEQRES 15 C 261 ASN PRO LEU SER ARG SER ALA ARG MET ALA ASP ILE THR SEQRES 16 C 261 ILE VAL ASP ASN ILE VAL ARG ALA TYR PRO ARG MET VAL SEQRES 17 C 261 GLU LEU ALA ARG GLU MET LYS ASP TYR SER ARG GLU GLU SEQRES 18 C 261 LEU LEU LYS ILE VAL GLY GLU TYR ASP ASN GLY LYS THR SEQRES 19 C 261 LEU SER ASP VAL LEU LEU HIS ILE ARG ASP ARG LEU THR SEQRES 20 C 261 ARG LEU ALA GLU GLU GLY ILE TRP ARG ARG LYS GLU LEU SEQRES 21 C 261 GLU SEQRES 1 D 261 MET VAL ASN ILE PRO LYS SER HIS PRO ARG TYR TRP SER SEQRES 2 D 261 LEU TYR TYR ARG GLU LYS ILE ILE GLU GLY MET GLU LYS SEQRES 3 D 261 GLY MET THR ALA LYS ALA GLY LEU ILE ALA HIS GLY ARG SEQRES 4 D 261 GLY GLU ALA PHE ASP TYR LEU ILE GLY GLU ARG THR ILE SEQRES 5 D 261 GLU PRO ALA GLU ARG ALA MET ARG ALA ALA VAL ALA LYS SEQRES 6 D 261 PHE LEU LEU ALA GLU HIS PRO VAL ILE SER VAL ASN GLY SEQRES 7 D 261 ASN VAL ALA ALA LEU VAL PRO LYS GLU THR ILE GLU LEU SEQRES 8 D 261 ALA LYS ALA LEU ASN ALA LYS LEU GLU ILE ASN LEU PHE SEQRES 9 D 261 TYR ARG THR GLU GLU ARG VAL ARG THR ILE ALA GLU GLU SEQRES 10 D 261 LEU ARG LYS TYR ASP PRO GLU ILE GLU ILE LEU GLY ILE SEQRES 11 D 261 ASN PRO THR LYS ARG ILE PRO GLY LEU GLU HIS GLU ARG SEQRES 12 D 261 GLY LYS VAL ASP GLU ASN GLY ILE TRP LYS ALA ASP VAL SEQRES 13 D 261 VAL LEU VAL PRO LEU GLU ASP GLY ASP ARG THR GLU ALA SEQRES 14 D 261 LEU VAL ARG MET GLY LYS PHE VAL VAL THR VAL ASP LEU SEQRES 15 D 261 ASN PRO LEU SER ARG SER ALA ARG MET ALA ASP ILE THR SEQRES 16 D 261 ILE VAL ASP ASN ILE VAL ARG ALA TYR PRO ARG MET VAL SEQRES 17 D 261 GLU LEU ALA ARG GLU MET LYS ASP TYR SER ARG GLU GLU SEQRES 18 D 261 LEU LEU LYS ILE VAL GLY GLU TYR ASP ASN GLY LYS THR SEQRES 19 D 261 LEU SER ASP VAL LEU LEU HIS ILE ARG ASP ARG LEU THR SEQRES 20 D 261 ARG LEU ALA GLU GLU GLY ILE TRP ARG ARG LYS GLU LEU SEQRES 21 D 261 GLU HET PTJ A 301 36 HET FLC A 302 13 HET PTJ B 901 36 HET PTJ C 301 36 HET FLC C 302 13 HET PTJ D 301 36 HET FLC D 302 13 HETNAM PTJ 5'-O-[(S)-HYDROXY{[(2R)-2-HYDROXY-3,3-DIMETHYL-4- HETNAM 2 PTJ (PHOSPHONOOXY)BUTANOYL]OXY}PHOSPHORYL]ADENOSINE HETNAM FLC CITRATE ANION FORMUL 5 PTJ 4(C16 H25 N5 O13 P2) FORMUL 6 FLC 3(C6 H5 O7 3-) FORMUL 12 HOH *255(H2 O) HELIX 1 1 PRO A 9 LYS A 26 1 18 HELIX 2 2 ALA A 30 ILE A 47 1 18 HELIX 3 3 ILE A 52 ALA A 69 1 18 HELIX 4 4 ASN A 77 VAL A 84 1 8 HELIX 5 5 VAL A 84 LEU A 95 1 12 HELIX 6 6 THR A 107 LYS A 120 1 14 HELIX 7 7 ASP A 163 MET A 173 1 11 HELIX 8 8 SER A 186 ALA A 192 1 7 HELIX 9 9 ASN A 199 MET A 214 1 16 HELIX 10 10 SER A 218 TYR A 229 1 12 HELIX 11 11 ASP A 230 GLY A 253 1 24 HELIX 12 12 TYR B 11 LYS B 26 1 16 HELIX 13 13 ALA B 30 GLY B 48 1 19 HELIX 14 14 ILE B 52 ALA B 69 1 18 HELIX 15 15 ASN B 77 VAL B 84 1 8 HELIX 16 16 VAL B 84 LEU B 95 1 12 HELIX 17 17 THR B 107 LYS B 120 1 14 HELIX 18 18 GLU B 140 ARG B 143 5 4 HELIX 19 19 ASP B 163 MET B 173 1 11 HELIX 20 20 SER B 186 ALA B 192 1 7 HELIX 21 21 ASN B 199 LYS B 215 1 17 HELIX 22 22 SER B 218 TYR B 229 1 12 HELIX 23 23 ASP B 230 ALA B 250 1 21 HELIX 24 24 ARG C 10 LYS C 26 1 17 HELIX 25 25 LYS C 31 GLY C 48 1 18 HELIX 26 26 ILE C 52 ALA C 69 1 18 HELIX 27 27 ASN C 77 VAL C 84 1 8 HELIX 28 28 VAL C 84 LEU C 95 1 12 HELIX 29 29 THR C 107 LYS C 120 1 14 HELIX 30 30 GLY C 150 ALA C 154 5 5 HELIX 31 31 ASP C 163 MET C 173 1 11 HELIX 32 32 SER C 186 ALA C 192 1 7 HELIX 33 33 ASN C 199 LYS C 215 1 17 HELIX 34 34 SER C 218 TYR C 229 1 12 HELIX 35 35 ASP C 230 GLY C 253 1 24 HELIX 36 36 TYR D 11 LYS D 26 1 16 HELIX 37 37 ALA D 30 GLY D 48 1 19 HELIX 38 38 ILE D 52 ALA D 69 1 18 HELIX 39 39 ASN D 77 VAL D 84 1 8 HELIX 40 40 VAL D 84 LEU D 95 1 12 HELIX 41 41 THR D 107 ASP D 122 1 16 HELIX 42 42 GLY D 150 ALA D 154 5 5 HELIX 43 43 ASP D 163 MET D 173 1 11 HELIX 44 44 SER D 186 ALA D 192 1 7 HELIX 45 45 ASN D 199 LYS D 215 1 17 HELIX 46 46 SER D 218 TYR D 229 1 12 HELIX 47 47 ASP D 230 GLU D 252 1 23 HELIX 48 48 ARG D 256 LEU D 260 5 5 SHEET 1 A 6 ILE A 127 LEU A 128 0 SHEET 2 A 6 LYS A 98 ILE A 101 1 N LEU A 99 O LEU A 128 SHEET 3 A 6 PRO A 72 VAL A 76 1 N ILE A 74 O LYS A 98 SHEET 4 A 6 VAL A 156 LEU A 158 1 O LEU A 158 N SER A 75 SHEET 5 A 6 PHE A 176 VAL A 180 1 O VAL A 178 N VAL A 157 SHEET 6 A 6 ILE A 194 ILE A 196 1 O ILE A 196 N THR A 179 SHEET 1 B 2 LYS A 134 ARG A 135 0 SHEET 2 B 2 LYS A 145 VAL A 146 -1 O VAL A 146 N LYS A 134 SHEET 1 C 6 ILE B 127 LEU B 128 0 SHEET 2 C 6 LYS B 98 ILE B 101 1 N LEU B 99 O LEU B 128 SHEET 3 C 6 PRO B 72 VAL B 76 1 N ILE B 74 O LYS B 98 SHEET 4 C 6 VAL B 156 LEU B 158 1 O LEU B 158 N SER B 75 SHEET 5 C 6 PHE B 176 VAL B 180 1 O VAL B 178 N VAL B 157 SHEET 6 C 6 ILE B 194 ILE B 196 1 O ILE B 196 N THR B 179 SHEET 1 D 2 LYS B 134 ARG B 135 0 SHEET 2 D 2 LYS B 145 VAL B 146 -1 O VAL B 146 N LYS B 134 SHEET 1 E 5 LYS C 98 ILE C 101 0 SHEET 2 E 5 VAL C 73 VAL C 76 1 N ILE C 74 O LYS C 98 SHEET 3 E 5 VAL C 156 LEU C 158 1 O LEU C 158 N SER C 75 SHEET 4 E 5 PHE C 176 VAL C 180 1 O VAL C 178 N VAL C 157 SHEET 5 E 5 ILE C 194 ILE C 196 1 O ILE C 196 N THR C 179 SHEET 1 F 2 LYS C 134 ARG C 135 0 SHEET 2 F 2 LYS C 145 VAL C 146 -1 O VAL C 146 N LYS C 134 SHEET 1 G 6 ILE D 127 LEU D 128 0 SHEET 2 G 6 LYS D 98 ILE D 101 1 N ILE D 101 O LEU D 128 SHEET 3 G 6 VAL D 73 VAL D 76 1 N ILE D 74 O LYS D 98 SHEET 4 G 6 VAL D 156 LEU D 158 1 O LEU D 158 N SER D 75 SHEET 5 G 6 PHE D 176 VAL D 180 1 O VAL D 178 N VAL D 157 SHEET 6 G 6 ILE D 194 ILE D 196 1 O ILE D 196 N THR D 179 SHEET 1 H 2 LYS D 134 ARG D 135 0 SHEET 2 H 2 LYS D 145 VAL D 146 -1 O VAL D 146 N LYS D 134 SITE 1 AC1 23 ALA A 36 GLY A 40 ASN A 77 GLY A 78 SITE 2 AC1 23 LEU A 103 PHE A 104 TYR A 105 ARG A 110 SITE 3 AC1 23 LEU A 161 GLU A 162 ASP A 163 ASP A 181 SITE 4 AC1 23 LEU A 182 ASN A 183 ASP A 198 ASN A 199 SITE 5 AC1 23 ILE A 200 HOH A 403 HOH A 408 HOH A 411 SITE 6 AC1 23 HOH A 419 HOH A 432 HOH A 440 SITE 1 AC2 11 GLU A 53 PRO A 54 ARG A 57 ASP A 237 SITE 2 AC2 11 LEU A 240 HIS A 241 ASP A 244 HOH A 449 SITE 3 AC2 11 GLU B 220 GLU B 221 LYS B 224 SITE 1 AC3 24 ALA B 36 ARG B 39 GLY B 40 ASN B 77 SITE 2 AC3 24 GLY B 78 LEU B 103 PHE B 104 TYR B 105 SITE 3 AC3 24 ARG B 110 LEU B 161 GLU B 162 ASP B 163 SITE 4 AC3 24 ASP B 181 LEU B 182 ASN B 183 ASP B 198 SITE 5 AC3 24 ASN B 199 ILE B 200 HOH B1003 HOH B1007 SITE 6 AC3 24 HOH B1008 HOH B1023 HOH B1033 HOH B1058 SITE 1 AC4 23 ALA C 36 ARG C 39 GLY C 40 ASN C 77 SITE 2 AC4 23 GLY C 78 LEU C 103 PHE C 104 TYR C 105 SITE 3 AC4 23 ARG C 110 LEU C 161 GLU C 162 ASP C 163 SITE 4 AC4 23 ASP C 181 LEU C 182 ASN C 183 ASP C 198 SITE 5 AC4 23 ASN C 199 ILE C 200 HOH C 407 HOH C 411 SITE 6 AC4 23 HOH C 417 HOH C 418 HOH C 459 SITE 1 AC5 9 GLU A 251 GLU C 220 GLU C 221 LYS C 224 SITE 2 AC5 9 GLU D 53 PRO D 54 ASP D 237 HIS D 241 SITE 3 AC5 9 ASP D 244 SITE 1 AC6 23 HOH C 426 ALA D 36 ARG D 39 GLY D 40 SITE 2 AC6 23 ASN D 77 GLY D 78 ASN D 79 LEU D 103 SITE 3 AC6 23 PHE D 104 TYR D 105 ARG D 110 LEU D 161 SITE 4 AC6 23 GLU D 162 ASP D 163 ASP D 181 LEU D 182 SITE 5 AC6 23 ASN D 183 ASP D 198 ASN D 199 ILE D 200 SITE 6 AC6 23 HOH D 405 HOH D 408 HOH D 437 SITE 1 AC7 9 GLU C 53 PRO C 54 ASP C 237 LEU C 240 SITE 2 AC7 9 HIS C 241 ASP C 244 GLU D 220 GLU D 221 SITE 3 AC7 9 LYS D 224 CRYST1 123.609 123.609 187.961 90.00 90.00 90.00 P 41 21 2 32 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 0.008090 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008090 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005320 0.00000