HEADER TRANSFERASE 25-JUL-12 4GA6 TITLE CRYSTAL STRUCTURE OF AMP PHOSPHORYLASE C-TERMINAL DELETION MUTANT IN TITLE 2 COMPLEX WITH SUBSTRATES COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE THYMIDINE PHOSPHORYLASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 1-493; COMPND 5 SYNONYM: TDRPASE; COMPND 6 EC: 2.4.2.4; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARENSIS; SOURCE 3 ORGANISM_TAXID: 69014; SOURCE 4 STRAIN: KOD1; SOURCE 5 GENE: DEOA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-21A(+) KEYWDS PHOSPHOROLYSIS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.NISHITANI,R.AONO,A.NAKAMURA,T.SATO,H.ATOMI,T.IMANAKA,K.MIKI REVDAT 3 08-NOV-23 4GA6 1 REMARK SEQADV REVDAT 2 12-MAR-14 4GA6 1 JRNL REVDAT 1 15-MAY-13 4GA6 0 JRNL AUTH Y.NISHITANI,R.AONO,A.NAKAMURA,T.SATO,H.ATOMI,T.IMANAKA, JRNL AUTH 2 K.MIKI JRNL TITL STRUCTURE ANALYSIS OF ARCHAEAL AMP PHOSPHORYLASE REVEALS TWO JRNL TITL 2 UNIQUE MODES OF DIMERIZATION JRNL REF J.MOL.BIOL. V. 425 2709 2013 JRNL REFN ISSN 0022-2836 JRNL PMID 23659790 JRNL DOI 10.1016/J.JMB.2013.04.026 REMARK 2 REMARK 2 RESOLUTION. 2.21 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) : 2.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 45875 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) : 0.214 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2310 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 : 7007 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 373 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.28500 REMARK 3 B22 (A**2) : -5.52400 REMARK 3 B33 (A**2) : -2.76100 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -4.29900 REMARK 3 B23 (A**2) : 0.00000 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) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.300 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) : 1.725 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.566 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.971 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.099 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 66.21 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 : AMP_XPLOR_PAR.TXT REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4GA6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000073931. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46007 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.210 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 (%) : 98.9 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) : 2.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.39600 REMARK 200 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 4GA5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M PHOSPHATE-CITRATE, 20% (W/V) PEG REMARK 280 1000, 50MM LI2SO4, 0.2M GUANIDINE-HCL, PH 4.2, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 43.95750 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -103.0 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 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 GLY A 494 REMARK 465 ASN A 495 REMARK 465 SER A 496 REMARK 465 SER A 497 REMARK 465 SER A 498 REMARK 465 VAL A 499 REMARK 465 ASP A 500 REMARK 465 LYS A 501 REMARK 465 LEU A 502 REMARK 465 ALA A 503 REMARK 465 ALA A 504 REMARK 465 ALA A 505 REMARK 465 LEU A 506 REMARK 465 GLU A 507 REMARK 465 HIS A 508 REMARK 465 HIS A 509 REMARK 465 HIS A 510 REMARK 465 HIS A 511 REMARK 465 HIS A 512 REMARK 465 HIS A 513 REMARK 465 GLY B 494 REMARK 465 ASN B 495 REMARK 465 SER B 496 REMARK 465 SER B 497 REMARK 465 SER B 498 REMARK 465 VAL B 499 REMARK 465 ASP B 500 REMARK 465 LYS B 501 REMARK 465 LEU B 502 REMARK 465 ALA B 503 REMARK 465 ALA B 504 REMARK 465 ALA B 505 REMARK 465 LEU B 506 REMARK 465 GLU B 507 REMARK 465 HIS B 508 REMARK 465 HIS B 509 REMARK 465 HIS B 510 REMARK 465 HIS B 511 REMARK 465 HIS B 512 REMARK 465 HIS B 513 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 LYS A 2 CG CD CE NZ REMARK 470 LYS A 4 CG CD CE NZ REMARK 470 ARG A 6 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 9 CG OD1 OD2 REMARK 470 ILE A 19 CG1 CG2 CD1 REMARK 470 GLU A 22 CG CD OE1 OE2 REMARK 470 LYS A 28 CG CD CE NZ REMARK 470 LYS A 36 CG CD CE NZ REMARK 470 ILE A 37 CG1 CG2 CD1 REMARK 470 GLU A 38 CG CD OE1 OE2 REMARK 470 LYS A 42 CG CD CE NZ REMARK 470 ASN A 52 CG OD1 ND2 REMARK 470 LYS A 56 CG CD CE NZ REMARK 470 GLU A 58 CG CD OE1 OE2 REMARK 470 ARG A 63 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 67 CG OD1 OD2 REMARK 470 LEU A 68 CG CD1 CD2 REMARK 470 SER A 72 OG REMARK 470 GLU A 73 CG CD OE1 OE2 REMARK 470 SER A 78 OG REMARK 470 ILE A 80 CG1 CG2 CD1 REMARK 470 ARG A 110 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 111 CG OD1 OD2 REMARK 470 LYS A 116 CG CD CE NZ REMARK 470 ASP A 154 CG OD1 OD2 REMARK 470 ILE A 155 CG1 CG2 CD1 REMARK 470 ASP A 218 CG OD1 OD2 REMARK 470 LYS A 221 CG CD CE NZ REMARK 470 ARG A 222 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 238 CG OD1 ND2 REMARK 470 LYS A 268 CG CD CE NZ REMARK 470 LYS A 285 CG CD CE NZ REMARK 470 GLU A 290 CG CD OE1 OE2 REMARK 470 GLU A 293 CG CD OE1 OE2 REMARK 470 GLU A 304 CG CD OE1 OE2 REMARK 470 LYS A 307 CG CD CE NZ REMARK 470 LYS A 345 CG CD CE NZ REMARK 470 LYS A 375 CG CD CE NZ REMARK 470 LYS A 378 CG CD CE NZ REMARK 470 LYS A 385 CG CD CE NZ REMARK 470 GLU A 388 CG CD OE1 OE2 REMARK 470 LYS A 404 CG CD CE NZ REMARK 470 ILE A 408 CG1 CG2 CD1 REMARK 470 TYR A 424 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 444 CG CD OE1 OE2 REMARK 470 LYS A 455 CG CD CE NZ REMARK 470 LYS A 459 CG CD CE NZ REMARK 470 LYS A 461 CG CD CE NZ REMARK 470 GLN A 479 CG CD OE1 NE2 REMARK 470 ARG A 486 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 488 CG CD OE1 OE2 REMARK 470 ARG A 491 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 493 CG CD OE1 OE2 REMARK 470 LYS B 2 CG CD CE NZ REMARK 470 ILE B 7 CG1 CG2 CD1 REMARK 470 PHE B 11 CG CD1 CD2 CE1 CE2 CZ REMARK 470 SER B 12 OG REMARK 470 GLU B 22 CG CD OE1 OE2 REMARK 470 LYS B 25 CG CD CE NZ REMARK 470 GLU B 26 CG CD OE1 OE2 REMARK 470 ASP B 32 CG OD1 OD2 REMARK 470 ARG B 63 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 67 CG OD1 OD2 REMARK 470 ILE B 80 CG1 CG2 CD1 REMARK 470 GLU B 86 CG CD OE1 OE2 REMARK 470 LYS B 93 CG CD CE NZ REMARK 470 GLU B 148 CG CD OE1 OE2 REMARK 470 THR B 149 OG1 CG2 REMARK 470 ASP B 218 CG OD1 OD2 REMARK 470 LYS B 226 CG CD CE NZ REMARK 470 ASN B 238 CG OD1 ND2 REMARK 470 ASP B 243 CG OD1 OD2 REMARK 470 LYS B 285 CG CD CE NZ REMARK 470 GLU B 290 CG CD OE1 OE2 REMARK 470 GLU B 293 CG CD OE1 OE2 REMARK 470 GLU B 294 CG CD OE1 OE2 REMARK 470 ARG B 300 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 304 CG CD OE1 OE2 REMARK 470 LYS B 307 CG CD CE NZ REMARK 470 LYS B 345 CG CD CE NZ REMARK 470 GLU B 352 CG CD OE1 OE2 REMARK 470 LYS B 375 CG CD CE NZ REMARK 470 LYS B 378 CG CD CE NZ REMARK 470 LYS B 385 CG CD CE NZ REMARK 470 GLU B 407 CG CD OE1 OE2 REMARK 470 ILE B 408 CG1 CG2 CD1 REMARK 470 GLU B 444 CG CD OE1 OE2 REMARK 470 LYS B 461 CG CD CE NZ REMARK 470 ARG B 476 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 485 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 486 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 488 CG CD OE1 OE2 REMARK 470 GLU B 493 CG CD OE1 OE2 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 39 -79.00 -114.66 REMARK 500 ARG A 118 -164.03 -117.45 REMARK 500 ALA B 39 -92.20 -116.13 REMARK 500 ARG B 118 -160.42 -104.66 REMARK 500 ILE B 197 -75.46 -112.69 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 AMP A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AMP B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 603 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GA4 RELATED DB: PDB REMARK 900 RELATED ID: 4GA5 RELATED DB: PDB DBREF 4GA6 A 1 493 UNP Q5JCX3 TYPH_PYRKO 1 493 DBREF 4GA6 B 1 493 UNP Q5JCX3 TYPH_PYRKO 1 493 SEQADV 4GA6 GLY A 494 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 ASN A 495 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 SER A 496 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 SER A 497 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 SER A 498 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 VAL A 499 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 ASP A 500 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 LYS A 501 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 LEU A 502 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 ALA A 503 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 ALA A 504 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 ALA A 505 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 LEU A 506 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 GLU A 507 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 HIS A 508 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 HIS A 509 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 HIS A 510 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 HIS A 511 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 HIS A 512 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 HIS A 513 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 GLY B 494 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 ASN B 495 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 SER B 496 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 SER B 497 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 SER B 498 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 VAL B 499 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 ASP B 500 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 LYS B 501 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 LEU B 502 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 ALA B 503 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 ALA B 504 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 ALA B 505 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 LEU B 506 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 GLU B 507 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 HIS B 508 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 HIS B 509 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 HIS B 510 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 HIS B 511 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 HIS B 512 UNP Q5JCX3 EXPRESSION TAG SEQADV 4GA6 HIS B 513 UNP Q5JCX3 EXPRESSION TAG SEQRES 1 A 513 MET LYS ALA LYS ILE ARG ILE LEU ASP MET PHE SER GLY SEQRES 2 A 513 ARG TYR THR VAL LEU ILE ASN GLU GLU ASP ALA LYS GLU SEQRES 3 A 513 ALA LYS LEU HIS PRO ASP ASP LEU VAL LYS ILE GLU ALA SEQRES 4 A 513 GLY LYS LYS ALA VAL TYR GLY SER VAL ALA LEU SER ASN SEQRES 5 A 513 LEU VAL GLY LYS GLY GLU VAL GLY ILE SER ARG ASP VAL SEQRES 6 A 513 LEU ASP LEU HIS ASN PHE SER GLU GLY GLU THR VAL SER SEQRES 7 A 513 VAL ILE PRO ALA GLY THR PRO GLU SER VAL ARG TYR ILE SEQRES 8 A 513 LYS LYS LYS MET HIS GLY GLU LYS LEU ARG LYS VAL GLU SEQRES 9 A 513 ILE GLU ALA ILE VAL ARG ASP ILE VAL ASP ARG LYS LEU SEQRES 10 A 513 ARG ASP ILE GLU ILE SER SER PHE VAL THR ALA LEU GLU SEQRES 11 A 513 ILE ASN GLY LEU ASP MET ASP GLU ILE ALA ALA LEU THR SEQRES 12 A 513 ILE ALA MET ALA GLU THR GLY ASP MET LEU ASP ILE ASP SEQRES 13 A 513 ARG LYS PRO ILE MET ASP VAL HIS SER ILE GLY GLY VAL SEQRES 14 A 513 PRO GLY ASN LYS THR ASN ILE LEU VAL VAL PRO ILE VAL SEQRES 15 A 513 ALA ALA ALA GLY LEU THR ILE PRO LYS THR SER SER ARG SEQRES 16 A 513 ALA ILE THR SER ALA ALA GLY THR ALA ASP VAL VAL GLU SEQRES 17 A 513 VAL PHE ALA ASP VAL SER PHE SER LEU ASP GLU ILE LYS SEQRES 18 A 513 ARG ILE VAL GLU LYS VAL GLY ALA CYS LEU VAL TRP GLY SEQRES 19 A 513 GLY ALA LEU ASN LEU ALA PRO ALA ASP ASP ILE THR ILE SEQRES 20 A 513 LYS ALA GLU ARG ALA LEU SER ILE ASP PRO THR GLY LEU SEQRES 21 A 513 MET LEU ALA SER ILE MET SER LYS LYS TYR ALA MET GLY SEQRES 22 A 513 SER GLN TYR VAL LEU ILE ASP ILE PRO THR GLY LYS GLY SEQRES 23 A 513 VAL LYS VAL GLU THR VAL GLU GLU ALA ARG SER LEU ALA SEQRES 24 A 513 ARG ASP PHE ILE GLU LEU GLY LYS ARG LEU GLY GLN TYR SEQRES 25 A 513 VAL GLU VAL ALA ILE THR TYR GLY GLY GLN PRO ILE GLY SEQRES 26 A 513 HIS THR VAL GLY PRO ALA LEU GLU ALA ARG GLU ALA LEU SEQRES 27 A 513 SER ALA LEU MET THR GLY LYS GLY PRO GLY SER LEU ILE SEQRES 28 A 513 GLU LYS ALA THR GLY LEU ALA GLY ILE LEU LEU GLU MET SEQRES 29 A 513 GLY GLY VAL ALA PRO ALA GLY THR GLY LYS LYS MET ALA SEQRES 30 A 513 LYS GLU ILE LEU GLU SER GLY LYS ALA TRP GLU LYS MET SEQRES 31 A 513 LYS GLU ILE ILE GLU ALA GLN GLY GLY ASP PRO ASN ILE SEQRES 32 A 513 LYS PRO GLU GLU ILE PRO ILE GLY ASP LYS THR TYR THR SEQRES 33 A 513 PHE THR ALA ALA THR SER GLY TYR VAL THR ALA ILE ASP SEQRES 34 A 513 ASN ARG ALA ILE THR ALA ILE ALA ARG ALA ALA GLY ALA SEQRES 35 A 513 PRO GLU ASP LYS GLY ALA GLY ILE GLU LEU TYR VAL LYS SEQRES 36 A 513 VAL GLY GLU LYS VAL LYS GLU GLY ASP PRO LEU PHE THR SEQRES 37 A 513 ILE HIS ALA GLU HIS GLU ALA ARG LEU ASP GLN ALA ILE SEQRES 38 A 513 VAL LEU ALA ARG ARG THR GLU PRO ILE ARG ILE GLU GLY SEQRES 39 A 513 ASN SER SER SER VAL ASP LYS LEU ALA ALA ALA LEU GLU SEQRES 40 A 513 HIS HIS HIS HIS HIS HIS SEQRES 1 B 513 MET LYS ALA LYS ILE ARG ILE LEU ASP MET PHE SER GLY SEQRES 2 B 513 ARG TYR THR VAL LEU ILE ASN GLU GLU ASP ALA LYS GLU SEQRES 3 B 513 ALA LYS LEU HIS PRO ASP ASP LEU VAL LYS ILE GLU ALA SEQRES 4 B 513 GLY LYS LYS ALA VAL TYR GLY SER VAL ALA LEU SER ASN SEQRES 5 B 513 LEU VAL GLY LYS GLY GLU VAL GLY ILE SER ARG ASP VAL SEQRES 6 B 513 LEU ASP LEU HIS ASN PHE SER GLU GLY GLU THR VAL SER SEQRES 7 B 513 VAL ILE PRO ALA GLY THR PRO GLU SER VAL ARG TYR ILE SEQRES 8 B 513 LYS LYS LYS MET HIS GLY GLU LYS LEU ARG LYS VAL GLU SEQRES 9 B 513 ILE GLU ALA ILE VAL ARG ASP ILE VAL ASP ARG LYS LEU SEQRES 10 B 513 ARG ASP ILE GLU ILE SER SER PHE VAL THR ALA LEU GLU SEQRES 11 B 513 ILE ASN GLY LEU ASP MET ASP GLU ILE ALA ALA LEU THR SEQRES 12 B 513 ILE ALA MET ALA GLU THR GLY ASP MET LEU ASP ILE ASP SEQRES 13 B 513 ARG LYS PRO ILE MET ASP VAL HIS SER ILE GLY GLY VAL SEQRES 14 B 513 PRO GLY ASN LYS THR ASN ILE LEU VAL VAL PRO ILE VAL SEQRES 15 B 513 ALA ALA ALA GLY LEU THR ILE PRO LYS THR SER SER ARG SEQRES 16 B 513 ALA ILE THR SER ALA ALA GLY THR ALA ASP VAL VAL GLU SEQRES 17 B 513 VAL PHE ALA ASP VAL SER PHE SER LEU ASP GLU ILE LYS SEQRES 18 B 513 ARG ILE VAL GLU LYS VAL GLY ALA CYS LEU VAL TRP GLY SEQRES 19 B 513 GLY ALA LEU ASN LEU ALA PRO ALA ASP ASP ILE THR ILE SEQRES 20 B 513 LYS ALA GLU ARG ALA LEU SER ILE ASP PRO THR GLY LEU SEQRES 21 B 513 MET LEU ALA SER ILE MET SER LYS LYS TYR ALA MET GLY SEQRES 22 B 513 SER GLN TYR VAL LEU ILE ASP ILE PRO THR GLY LYS GLY SEQRES 23 B 513 VAL LYS VAL GLU THR VAL GLU GLU ALA ARG SER LEU ALA SEQRES 24 B 513 ARG ASP PHE ILE GLU LEU GLY LYS ARG LEU GLY GLN TYR SEQRES 25 B 513 VAL GLU VAL ALA ILE THR TYR GLY GLY GLN PRO ILE GLY SEQRES 26 B 513 HIS THR VAL GLY PRO ALA LEU GLU ALA ARG GLU ALA LEU SEQRES 27 B 513 SER ALA LEU MET THR GLY LYS GLY PRO GLY SER LEU ILE SEQRES 28 B 513 GLU LYS ALA THR GLY LEU ALA GLY ILE LEU LEU GLU MET SEQRES 29 B 513 GLY GLY VAL ALA PRO ALA GLY THR GLY LYS LYS MET ALA SEQRES 30 B 513 LYS GLU ILE LEU GLU SER GLY LYS ALA TRP GLU LYS MET SEQRES 31 B 513 LYS GLU ILE ILE GLU ALA GLN GLY GLY ASP PRO ASN ILE SEQRES 32 B 513 LYS PRO GLU GLU ILE PRO ILE GLY ASP LYS THR TYR THR SEQRES 33 B 513 PHE THR ALA ALA THR SER GLY TYR VAL THR ALA ILE ASP SEQRES 34 B 513 ASN ARG ALA ILE THR ALA ILE ALA ARG ALA ALA GLY ALA SEQRES 35 B 513 PRO GLU ASP LYS GLY ALA GLY ILE GLU LEU TYR VAL LYS SEQRES 36 B 513 VAL GLY GLU LYS VAL LYS GLU GLY ASP PRO LEU PHE THR SEQRES 37 B 513 ILE HIS ALA GLU HIS GLU ALA ARG LEU ASP GLN ALA ILE SEQRES 38 B 513 VAL LEU ALA ARG ARG THR GLU PRO ILE ARG ILE GLU GLY SEQRES 39 B 513 ASN SER SER SER VAL ASP LYS LEU ALA ALA ALA LEU GLU SEQRES 40 B 513 HIS HIS HIS HIS HIS HIS HET AMP A 601 23 HET SO4 A 602 5 HET SO4 A 603 5 HET AMP B 601 23 HET SO4 B 602 5 HET SO4 B 603 5 HETNAM AMP ADENOSINE MONOPHOSPHATE HETNAM SO4 SULFATE ION FORMUL 3 AMP 2(C10 H14 N5 O7 P) FORMUL 4 SO4 4(O4 S 2-) FORMUL 9 HOH *373(H2 O) HELIX 1 1 ASN A 20 LYS A 28 1 9 HELIX 2 2 ASP A 64 ASP A 67 5 4 HELIX 3 3 GLU A 86 HIS A 96 1 11 HELIX 4 4 ARG A 101 ASP A 114 1 14 HELIX 5 5 ARG A 118 GLY A 133 1 16 HELIX 6 6 ASP A 135 THR A 149 1 15 HELIX 7 7 LYS A 173 ALA A 185 1 13 HELIX 8 8 GLY A 202 GLU A 208 1 7 HELIX 9 9 SER A 216 GLY A 228 1 13 HELIX 10 10 ALA A 240 SER A 254 1 15 HELIX 11 11 PRO A 257 GLY A 273 1 17 HELIX 12 12 THR A 291 LEU A 309 1 19 HELIX 13 13 GLY A 329 GLY A 344 1 16 HELIX 14 14 PRO A 347 GLY A 365 1 19 HELIX 15 15 THR A 372 SER A 383 1 12 HELIX 16 16 GLY A 384 GLN A 397 1 14 HELIX 17 17 LYS A 404 ILE A 408 5 5 HELIX 18 18 ASP A 429 ALA A 440 1 12 HELIX 19 19 HIS A 473 GLU A 488 1 16 HELIX 20 20 GLU B 21 LYS B 28 1 8 HELIX 21 21 ASP B 64 LEU B 68 5 5 HELIX 22 22 GLU B 86 HIS B 96 1 11 HELIX 23 23 ARG B 101 ASP B 114 1 14 HELIX 24 24 ARG B 118 GLY B 133 1 16 HELIX 25 25 ASP B 135 THR B 149 1 15 HELIX 26 26 LYS B 173 ALA B 185 1 13 HELIX 27 27 GLY B 202 ALA B 211 1 10 HELIX 28 28 SER B 216 GLY B 228 1 13 HELIX 29 29 GLY B 235 LEU B 237 5 3 HELIX 30 30 ALA B 240 SER B 254 1 15 HELIX 31 31 PRO B 257 GLY B 273 1 17 HELIX 32 32 THR B 291 LEU B 309 1 19 HELIX 33 33 GLY B 329 GLY B 344 1 16 HELIX 34 34 PRO B 347 GLY B 365 1 19 HELIX 35 35 THR B 372 SER B 383 1 12 HELIX 36 36 GLY B 384 GLN B 397 1 14 HELIX 37 37 LYS B 404 ILE B 408 5 5 HELIX 38 38 ASP B 429 ALA B 440 1 12 HELIX 39 39 HIS B 473 GLU B 488 1 16 SHEET 1 A 8 MET B 10 PHE B 11 0 SHEET 2 A 8 ALA A 43 SER A 51 -1 N LEU A 50 O PHE B 11 SHEET 3 A 8 LEU A 34 GLU A 38 -1 N ILE A 37 O VAL A 44 SHEET 4 A 8 THR A 76 PRO A 81 -1 O SER A 78 N GLU A 38 SHEET 5 A 8 LYS A 2 LEU A 8 -1 N ALA A 3 O VAL A 77 SHEET 6 A 8 GLU A 58 SER A 62 1 O VAL A 59 N ARG A 6 SHEET 7 A 8 THR A 16 ILE A 19 -1 N LEU A 18 O GLY A 60 SHEET 8 A 8 ALA A 43 SER A 51 1 O ALA A 49 N ILE A 19 SHEET 1 B 8 MET A 10 PHE A 11 0 SHEET 2 B 8 ALA B 43 SER B 51 -1 O LEU B 50 N PHE A 11 SHEET 3 B 8 LEU B 34 GLU B 38 -1 N ILE B 37 O VAL B 44 SHEET 4 B 8 THR B 76 PRO B 81 -1 O SER B 78 N GLU B 38 SHEET 5 B 8 LYS B 2 LEU B 8 -1 N ALA B 3 O VAL B 77 SHEET 6 B 8 GLU B 58 SER B 62 1 O ILE B 61 N ARG B 6 SHEET 7 B 8 THR B 16 ASN B 20 -1 N LEU B 18 O GLY B 60 SHEET 8 B 8 ALA B 43 SER B 51 1 O ALA B 49 N ILE B 19 SHEET 1 C 3 MET A 161 SER A 165 0 SHEET 2 C 3 TYR A 276 THR A 283 1 O LEU A 278 N ASP A 162 SHEET 3 C 3 TYR A 312 TYR A 319 1 O THR A 318 N THR A 283 SHEET 1 D 2 ILE A 189 SER A 193 0 SHEET 2 D 2 ALA A 229 TRP A 233 1 O VAL A 232 N SER A 193 SHEET 1 E 4 THR A 327 VAL A 328 0 SHEET 2 E 4 GLY A 449 LEU A 452 -1 O ILE A 450 N VAL A 328 SHEET 3 E 4 PRO A 465 ALA A 471 -1 O HIS A 470 N GLY A 449 SHEET 4 E 4 LYS A 413 THR A 418 -1 N LYS A 413 O ALA A 471 SHEET 1 F 3 LYS A 459 VAL A 460 0 SHEET 2 F 3 GLY A 423 ILE A 428 -1 N GLY A 423 O VAL A 460 SHEET 3 F 3 ILE A 490 GLU A 493 -1 O ARG A 491 N ALA A 427 SHEET 1 G 3 MET B 161 SER B 165 0 SHEET 2 G 3 TYR B 276 THR B 283 1 O LEU B 278 N ASP B 162 SHEET 3 G 3 TYR B 312 TYR B 319 1 O THR B 318 N THR B 283 SHEET 1 H 2 ILE B 189 SER B 193 0 SHEET 2 H 2 ALA B 229 TRP B 233 1 O VAL B 232 N SER B 193 SHEET 1 I 4 THR B 327 VAL B 328 0 SHEET 2 I 4 GLY B 449 LEU B 452 -1 O ILE B 450 N VAL B 328 SHEET 3 I 4 PRO B 465 ALA B 471 -1 O HIS B 470 N GLY B 449 SHEET 4 I 4 LYS B 413 THR B 418 -1 N PHE B 417 O LEU B 466 SHEET 1 J 3 LYS B 459 VAL B 460 0 SHEET 2 J 3 GLY B 423 ILE B 428 -1 N GLY B 423 O VAL B 460 SHEET 3 J 3 ILE B 490 ILE B 492 -1 O ARG B 491 N THR B 426 CISPEP 1 LYS A 158 PRO A 159 0 -5.51 CISPEP 2 ALA A 442 PRO A 443 0 1.34 CISPEP 3 LYS B 158 PRO B 159 0 -7.45 CISPEP 4 ALA B 442 PRO B 443 0 3.01 SITE 1 AC1 16 HIS A 164 SER A 165 ILE A 166 GLY A 168 SITE 2 AC1 16 SER A 194 ALA A 196 ILE A 197 THR A 198 SITE 3 AC1 16 SER A 199 THR A 203 ASP A 256 MET A 261 SITE 4 AC1 16 SER A 264 LYS A 288 SO4 A 602 HOH A 839 SITE 1 AC2 9 HIS A 164 SER A 165 ASN A 175 LYS A 191 SITE 2 AC2 9 SER A 193 THR A 203 AMP A 601 HOH A 708 SITE 3 AC2 9 HOH A 742 SITE 1 AC3 6 HIS A 326 PRO A 347 GLY A 348 SER A 349 SITE 2 AC3 6 LYS A 455 HOH A 820 SITE 1 AC4 18 HIS B 164 SER B 165 ILE B 166 GLY B 167 SITE 2 AC4 18 GLY B 168 SER B 193 SER B 194 ALA B 196 SITE 3 AC4 18 ILE B 197 THR B 198 SER B 199 THR B 203 SITE 4 AC4 18 ASP B 256 MET B 261 SER B 264 LYS B 288 SITE 5 AC4 18 SO4 B 602 HOH B 795 SITE 1 AC5 9 HIS B 164 SER B 165 ASN B 175 LYS B 191 SITE 2 AC5 9 SER B 193 THR B 203 AMP B 601 HOH B 728 SITE 3 AC5 9 HOH B 785 SITE 1 AC6 5 HIS B 326 GLY B 348 SER B 349 LYS B 455 SITE 2 AC6 5 HOH B 798 CRYST1 51.177 87.915 105.549 90.00 98.77 90.00 P 1 21 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 0.019540 0.000000 0.003014 0.00000 SCALE2 0.000000 0.011375 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009586 0.00000