HEADER TRANSFERASE 15-FEB-07 2JGU TITLE CRYSTAL STRUCTURE OF DNA-DIRECTED DNA POLYMERASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PFU POLYMERASE, DNA POLYMERASE PFU; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 2261; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(BE3) KEYWDS DNA-DIRECTED DNA POLYMERASE, PFU, NUCLEASE, HYDROLASE, TRANSFERASE, KEYWDS 2 DNA-BINDING, ENDONUCLEASE, DNA REPLICATION, NUCLEOTIDYLTRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.U.KIM,H.S.CHO REVDAT 3 13-DEC-23 2JGU 1 LINK REVDAT 2 24-FEB-09 2JGU 1 VERSN REVDAT 1 22-APR-08 2JGU 0 JRNL AUTH S.W.KIM,D.U.KIM,J.K.KIM,L.W.KANG,H.S.CHO JRNL TITL CRYSTAL STRUCTURE OF PFU, THE HIGH FIDELITY DNA POLYMERASE JRNL TITL 2 FROM PYROCOCCUS FURIOSUS. JRNL REF INT.J.BIOL.MACROMOL. V. 42 356 2008 JRNL REFN ISSN 0141-8130 JRNL PMID 18355915 JRNL DOI 10.1016/J.IJBIOMAC.2008.01.010 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 28166 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) : 0.275 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1403 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 : 5826 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 31 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) : 12.37200 REMARK 3 B22 (A**2) : 0.19300 REMARK 3 B33 (A**2) : -12.56400 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.63300 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) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 2.334 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 : 0.30 REMARK 3 BSOL : 30.20 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 : ION.PARAM REMARK 3 PARAMETER FILE 4 : 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 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2JGU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-FEB-07. REMARK 100 THE DEPOSITION ID IS D_1290031459. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 4A 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 CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 848408 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.26000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.720 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: PDB ENTRY 1QQC REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.5 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 46.08900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 63.96150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 46.08900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 63.96150 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 ILE A 611 REMARK 465 VAL A 612 REMARK 465 ARG A 613 REMARK 465 ARG A 614 REMARK 465 ASP A 615 REMARK 465 TRP A 616 REMARK 465 ILE A 663 REMARK 465 TYR A 664 REMARK 465 GLU A 665 REMARK 465 GLN A 666 REMARK 465 ILE A 667 REMARK 465 THR A 668 REMARK 465 ARG A 669 REMARK 465 PRO A 670 REMARK 465 LEU A 671 REMARK 465 HIS A 672 REMARK 465 GLU A 673 REMARK 465 TYR A 674 REMARK 465 LYS A 675 REMARK 465 ALA A 676 REMARK 465 ILE A 677 REMARK 465 GLY A 678 REMARK 465 LEU A 705 REMARK 465 ARG A 706 REMARK 465 GLY A 707 REMARK 465 ASP A 708 REMARK 465 GLY A 709 REMARK 465 PRO A 710 REMARK 465 ILE A 711 REMARK 465 SER A 712 REMARK 465 ASN A 713 REMARK 465 ARG A 714 REMARK 465 ALA A 715 REMARK 465 ILE A 716 REMARK 465 LEU A 717 REMARK 465 ALA A 718 REMARK 465 GLU A 719 REMARK 465 GLU A 720 REMARK 465 TYR A 721 REMARK 465 ASP A 722 REMARK 465 PRO A 723 REMARK 465 LYS A 724 REMARK 465 LYS A 725 REMARK 465 HIS A 726 REMARK 465 LYS A 727 REMARK 465 TYR A 728 REMARK 465 GLN A 759 REMARK 465 LYS A 760 REMARK 465 THR A 761 REMARK 465 ARG A 762 REMARK 465 GLN A 763 REMARK 465 VAL A 764 REMARK 465 GLY A 765 REMARK 465 LEU A 766 REMARK 465 THR A 767 REMARK 465 SER A 768 REMARK 465 TRP A 769 REMARK 465 LEU A 770 REMARK 465 ASN A 771 REMARK 465 ILE A 772 REMARK 465 LYS A 773 REMARK 465 LYS A 774 REMARK 465 SER A 775 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 47 CG CD CE NZ REMARK 470 TYR A 758 CA C O CB CG CD1 CD2 REMARK 470 TYR A 758 CE1 CE2 CZ OH 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 NZ LYS A 430 O HOH A 2021 0.61 REMARK 500 CE LYS A 430 O HOH A 2021 0.91 REMARK 500 O SER A 384 O TYR A 385 1.65 REMARK 500 OG SER A 617 NE2 GLN A 737 1.65 REMARK 500 OE2 GLU A 460 NH2 ARG A 483 1.98 REMARK 500 CE1 PHE A 389 CG ARG A 519 2.00 REMARK 500 OD1 ASP A 141 OD1 ASP A 315 2.00 REMARK 500 O GLU A 303 N LEU A 305 2.00 REMARK 500 O ASP A 315 OG1 THR A 319 2.02 REMARK 500 O ARG A 379 N ARG A 382 2.07 REMARK 500 O ALA A 298 O GLU A 300 2.08 REMARK 500 O ARG A 58 N GLY A 60 2.08 REMARK 500 O LYS A 47 N GLU A 49 2.11 REMARK 500 O HIS A 680 N ALA A 682 2.12 REMARK 500 O ILE A 295 O GLU A 300 2.12 REMARK 500 O TYR A 732 N GLU A 735 2.13 REMARK 500 O ASP A 45 CG2 ILE A 48 2.13 REMARK 500 OE2 GLU A 143 OD1 ASP A 315 2.14 REMARK 500 CD LYS A 430 O HOH A 2021 2.16 REMARK 500 OD2 ASP A 473 N ILE A 475 2.17 REMARK 500 O LYS A 47 N GLU A 50 2.18 REMARK 500 O GLU A 383 N TYR A 385 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 251 CB GLU A 251 CG 0.233 REMARK 500 GLU A 251 CG GLU A 251 CD 0.143 REMARK 500 LYS A 285 C PRO A 286 N -0.274 REMARK 500 GLU A 556 CB GLU A 556 CG -0.123 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLY A 60 N - CA - C ANGL. DEV. = -15.4 DEGREES REMARK 500 LEU A 145 CA - CB - CG ANGL. DEV. = 17.5 DEGREES REMARK 500 GLU A 150 N - CA - C ANGL. DEV. = 21.0 DEGREES REMARK 500 GLY A 245 N - CA - C ANGL. DEV. = -16.2 DEGREES REMARK 500 PRO A 286 C - N - CA ANGL. DEV. = 12.0 DEGREES REMARK 500 PRO A 286 C - N - CD ANGL. DEV. = -27.8 DEGREES REMARK 500 TYR A 291 N - CA - C ANGL. DEV. = 17.9 DEGREES REMARK 500 TRP A 299 N - CA - CB ANGL. DEV. = 11.7 DEGREES REMARK 500 LEU A 305 CA - CB - CG ANGL. DEV. = 18.5 DEGREES REMARK 500 ARG A 382 N - CA - CB ANGL. DEV. = 11.2 DEGREES REMARK 500 ARG A 382 CA - C - N ANGL. DEV. = -21.2 DEGREES REMARK 500 GLU A 383 CA - C - N ANGL. DEV. = -14.4 DEGREES REMARK 500 THR A 386 CA - C - N ANGL. DEV. = 12.6 DEGREES REMARK 500 GLY A 387 N - CA - C ANGL. DEV. = 19.2 DEGREES REMARK 500 PHE A 389 CB - CA - C ANGL. DEV. = -12.8 DEGREES REMARK 500 PRO A 393 C - N - CA ANGL. DEV. = 14.6 DEGREES REMARK 500 CYS A 443 CA - CB - SG ANGL. DEV. = 6.9 DEGREES REMARK 500 ASP A 543 CB - CA - C ANGL. DEV. = -12.8 DEGREES REMARK 500 SER A 554 N - CA - C ANGL. DEV. = 20.9 DEGREES REMARK 500 GLU A 556 N - CA - CB ANGL. DEV. = -11.8 DEGREES REMARK 500 LEU A 578 CA - CB - CG ANGL. DEV. = 14.6 DEGREES REMARK 500 LYS A 650 N - CA - C ANGL. DEV. = -16.6 DEGREES REMARK 500 LEU A 661 CA - CB - CG ANGL. DEV. = -14.5 DEGREES REMARK 500 VAL A 683 C - N - CA ANGL. DEV. = -17.7 DEGREES REMARK 500 ALA A 684 N - CA - C ANGL. DEV. = -28.4 DEGREES REMARK 500 LEU A 687 CA - CB - CG ANGL. DEV. = 18.5 DEGREES 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 GLU A 11 86.17 49.36 REMARK 500 ASP A 44 114.11 -166.95 REMARK 500 ILE A 48 -36.76 -11.86 REMARK 500 VAL A 51 33.38 -75.54 REMARK 500 ILE A 54 106.45 -44.30 REMARK 500 GLU A 57 97.69 -178.12 REMARK 500 ARG A 58 -143.58 -102.70 REMARK 500 HIS A 59 4.47 -15.21 REMARK 500 ASP A 67 140.85 9.42 REMARK 500 LYS A 73 -145.36 -120.89 REMARK 500 LEU A 76 18.82 36.79 REMARK 500 LEU A 87 -159.25 -140.22 REMARK 500 PRO A 90 6.64 -63.35 REMARK 500 GLU A 132 69.58 -150.10 REMARK 500 THR A 144 -166.98 -117.77 REMARK 500 HIS A 147 -168.99 -43.39 REMARK 500 GLU A 150 76.50 -108.35 REMARK 500 PHE A 152 95.78 85.16 REMARK 500 ASP A 164 -136.65 -174.56 REMARK 500 ALA A 168 109.49 -163.72 REMARK 500 ASP A 177 43.15 -58.62 REMARK 500 SER A 185 -41.71 -22.49 REMARK 500 THR A 208 -158.57 -134.23 REMARK 500 TYR A 209 84.57 -151.27 REMARK 500 PHE A 214 -71.64 -124.92 REMARK 500 ALA A 223 -31.19 -151.79 REMARK 500 GLU A 224 6.02 -65.50 REMARK 500 ILE A 244 -146.63 -152.26 REMARK 500 TYR A 261 -65.96 -29.92 REMARK 500 ARG A 265 33.60 -46.43 REMARK 500 THR A 266 -73.25 -142.97 REMARK 500 THR A 267 -113.98 -54.11 REMARK 500 ALA A 281 -33.77 -36.02 REMARK 500 LYS A 285 177.20 -19.30 REMARK 500 LYS A 287 -90.79 -132.63 REMARK 500 GLU A 288 109.72 146.13 REMARK 500 LYS A 289 148.42 -175.73 REMARK 500 VAL A 290 90.45 149.65 REMARK 500 ALA A 292 28.27 162.52 REMARK 500 GLU A 294 22.56 -74.59 REMARK 500 ALA A 296 -29.12 -38.77 REMARK 500 LYS A 297 -75.11 -96.63 REMARK 500 ALA A 298 152.71 -32.30 REMARK 500 TRP A 299 147.89 -30.25 REMARK 500 GLU A 300 74.84 79.56 REMARK 500 GLU A 303 -125.23 -28.83 REMARK 500 ASN A 304 -9.40 47.99 REMARK 500 ARG A 307 -70.88 -56.07 REMARK 500 ASP A 315 -39.73 -37.45 REMARK 500 GLU A 363 -37.01 -39.86 REMARK 500 REMARK 500 THIS ENTRY HAS 112 RAMACHANDRAN OUTLIERS. 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 PHE A 389 VAL A 390 143.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 162 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A1759 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 141 OD1 REMARK 620 2 GLU A 143 OE2 72.1 REMARK 620 3 ASP A 315 OD1 55.8 61.7 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A1758 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A1759 DBREF 2JGU A 1 775 UNP P61875 DPOL_PYRFU 1 775 SEQADV 2JGU LEU A 96 UNP P61875 ILE 96 CONFLICT SEQADV 2JGU ARG A 169 UNP P61875 LYS 169 CONFLICT SEQADV 2JGU SER A 183 UNP P61875 VAL 183 CONFLICT SEQADV 2JGU THR A 186 UNP P61875 SER 186 CONFLICT SEQADV 2JGU LYS A 188 UNP P61875 ARG 188 CONFLICT SEQADV 2JGU ARG A 265 UNP P61875 THR 265 CONFLICT SEQADV 2JGU THR A 266 UNP P61875 ARG 266 CONFLICT SEQADV 2JGU TYR A 406 UNP P61875 PHE 406 CONFLICT SEQADV 2JGU LYS A 407 UNP P61875 ARG 407 CONFLICT SEQADV 2JGU SER A 408 UNP P61875 ALA 408 CONFLICT SEQRES 1 A 775 MET ILE LEU ASP VAL ASP TYR ILE THR GLU GLU GLY LYS SEQRES 2 A 775 PRO VAL ILE ARG LEU PHE LYS LYS GLU ASN GLY LYS PHE SEQRES 3 A 775 LYS ILE GLU HIS ASP ARG THR PHE ARG PRO TYR ILE TYR SEQRES 4 A 775 ALA LEU LEU ARG ASP ASP SER LYS ILE GLU GLU VAL LYS SEQRES 5 A 775 LYS ILE THR GLY GLU ARG HIS GLY LYS ILE VAL ARG ILE SEQRES 6 A 775 VAL ASP VAL GLU LYS VAL GLU LYS LYS PHE LEU GLY LYS SEQRES 7 A 775 PRO ILE THR VAL TRP LYS LEU TYR LEU GLU HIS PRO GLN SEQRES 8 A 775 ASP VAL PRO THR LEU ARG GLU LYS VAL ARG GLU HIS PRO SEQRES 9 A 775 ALA VAL VAL ASP ILE PHE GLU TYR ASP ILE PRO PHE ALA SEQRES 10 A 775 LYS ARG TYR LEU ILE ASP LYS GLY LEU ILE PRO MET GLU SEQRES 11 A 775 GLY GLU GLU GLU LEU LYS ILE LEU ALA PHE ASP ILE GLU SEQRES 12 A 775 THR LEU TYR HIS GLU GLY GLU GLU PHE GLY LYS GLY PRO SEQRES 13 A 775 ILE ILE MET ILE SER TYR ALA ASP GLU ASN GLU ALA ARG SEQRES 14 A 775 VAL ILE THR TRP LYS ASN ILE ASP LEU PRO TYR VAL GLU SEQRES 15 A 775 SER VAL SER THR GLU LYS GLU MET ILE LYS ARG PHE LEU SEQRES 16 A 775 ARG ILE ILE ARG GLU LYS ASP PRO ASP ILE ILE VAL THR SEQRES 17 A 775 TYR ASN GLY ASP SER PHE ASP PHE PRO TYR LEU ALA LYS SEQRES 18 A 775 ARG ALA GLU LYS LEU GLY ILE LYS LEU THR ILE GLY ARG SEQRES 19 A 775 ASP GLY SER GLU PRO LYS MET GLN ARG ILE GLY ASP MET SEQRES 20 A 775 THR ALA VAL GLU VAL LYS GLY ARG ILE HIS PHE ASP LEU SEQRES 21 A 775 TYR HIS VAL ILE ARG THR THR ILE ASN LEU PRO THR TYR SEQRES 22 A 775 THR LEU GLU ALA VAL TYR GLU ALA ILE PHE GLY LYS PRO SEQRES 23 A 775 LYS GLU LYS VAL TYR ALA ASP GLU ILE ALA LYS ALA TRP SEQRES 24 A 775 GLU SER GLY GLU ASN LEU GLU ARG VAL ALA LYS TYR SER SEQRES 25 A 775 MET GLU ASP ALA LYS ALA THR TYR GLU LEU GLY LYS GLU SEQRES 26 A 775 PHE LEU PRO MET GLU ILE GLN LEU SER ARG LEU VAL GLY SEQRES 27 A 775 GLN PRO LEU TRP ASP VAL SER ARG SER SER THR GLY ASN SEQRES 28 A 775 LEU VAL GLU TRP PHE LEU LEU ARG LYS ALA TYR GLU ARG SEQRES 29 A 775 ASN GLU VAL ALA PRO ASN LYS PRO SER GLU GLU GLU TYR SEQRES 30 A 775 GLN ARG ARG LEU ARG GLU SER TYR THR GLY GLY PHE VAL SEQRES 31 A 775 LYS GLU PRO GLU LYS GLY LEU TRP GLU ASN ILE VAL TYR SEQRES 32 A 775 LEU ASP TYR LYS SER LEU TYR PRO SER ILE ILE ILE THR SEQRES 33 A 775 HIS ASN VAL SER PRO ASP THR LEU ASN LEU GLU GLY CYS SEQRES 34 A 775 LYS ASN TYR ASP ILE ALA PRO GLN VAL GLY HIS LYS PHE SEQRES 35 A 775 CYS LYS ASP ILE PRO GLY PHE ILE PRO SER LEU LEU GLY SEQRES 36 A 775 HIS LEU LEU GLU GLU ARG GLN LYS ILE LYS THR LYS MET SEQRES 37 A 775 LYS GLU THR GLN ASP PRO ILE GLU LYS ILE LEU LEU ASP SEQRES 38 A 775 TYR ARG GLN LYS ALA ILE LYS LEU LEU ALA ASN SER PHE SEQRES 39 A 775 TYR GLY TYR TYR GLY TYR ALA LYS ALA ARG TRP TYR CYS SEQRES 40 A 775 LYS GLU CYS ALA GLU SER VAL THR ALA TRP GLY ARG LYS SEQRES 41 A 775 TYR ILE GLU LEU VAL TRP LYS GLU LEU GLU GLU LYS PHE SEQRES 42 A 775 GLY PHE LYS VAL LEU TYR ILE ASP THR ASP GLY LEU TYR SEQRES 43 A 775 ALA THR ILE PRO GLY GLY GLU SER GLU GLU ILE LYS LYS SEQRES 44 A 775 LYS ALA LEU GLU PHE VAL LYS TYR ILE ASN SER LYS LEU SEQRES 45 A 775 PRO GLY LEU LEU GLU LEU GLU TYR GLU GLY PHE TYR LYS SEQRES 46 A 775 ARG GLY PHE PHE VAL THR LYS LYS ARG TYR ALA VAL ILE SEQRES 47 A 775 ASP GLU GLU GLY LYS VAL ILE THR ARG GLY LEU GLU ILE SEQRES 48 A 775 VAL ARG ARG ASP TRP SER GLU ILE ALA LYS GLU THR GLN SEQRES 49 A 775 ALA ARG VAL LEU GLU THR ILE LEU LYS HIS GLY ASP VAL SEQRES 50 A 775 GLU GLU ALA VAL ARG ILE VAL LYS GLU VAL ILE GLN LYS SEQRES 51 A 775 LEU ALA ASN TYR GLU ILE PRO PRO GLU LYS LEU ALA ILE SEQRES 52 A 775 TYR GLU GLN ILE THR ARG PRO LEU HIS GLU TYR LYS ALA SEQRES 53 A 775 ILE GLY PRO HIS VAL ALA VAL ALA LYS LYS LEU ALA ALA SEQRES 54 A 775 LYS GLY VAL LYS ILE LYS PRO GLY MET VAL ILE GLY TYR SEQRES 55 A 775 ILE VAL LEU ARG GLY ASP GLY PRO ILE SER ASN ARG ALA SEQRES 56 A 775 ILE LEU ALA GLU GLU TYR ASP PRO LYS LYS HIS LYS TYR SEQRES 57 A 775 ASP ALA GLU TYR TYR ILE GLU ASN GLN VAL LEU PRO ALA SEQRES 58 A 775 VAL LEU ARG ILE LEU GLU GLY PHE GLY TYR ARG LYS GLU SEQRES 59 A 775 ASP LEU ARG TYR GLN LYS THR ARG GLN VAL GLY LEU THR SEQRES 60 A 775 SER TRP LEU ASN ILE LYS LYS SER HET MN A1758 1 HET MN A1759 1 HETNAM MN MANGANESE (II) ION FORMUL 2 MN 2(MN 2+) FORMUL 4 HOH *31(H2 O) HELIX 1 1 ASP A 44 GLU A 50 5 7 HELIX 2 2 LEU A 96 GLU A 102 1 7 HELIX 3 3 PRO A 115 LYS A 124 1 10 HELIX 4 4 THR A 186 ASP A 202 1 17 HELIX 5 5 PHE A 214 ARG A 222 1 9 HELIX 6 6 LEU A 260 ARG A 265 1 6 HELIX 7 7 THR A 274 GLY A 284 1 11 HELIX 8 8 ASP A 293 LYS A 297 5 5 HELIX 9 9 ASN A 304 GLY A 338 1 35 HELIX 10 10 PRO A 340 SER A 345 1 6 HELIX 11 11 SER A 348 ARG A 364 1 17 HELIX 12 12 SER A 373 LEU A 381 1 9 HELIX 13 13 SER A 408 HIS A 417 1 10 HELIX 14 14 SER A 420 THR A 423 5 4 HELIX 15 15 GLY A 448 LYS A 469 1 22 HELIX 16 16 ASP A 473 SER A 493 1 21 HELIX 17 17 SER A 493 GLY A 499 1 7 HELIX 18 18 CYS A 507 GLU A 531 1 25 HELIX 19 19 GLU A 556 SER A 570 1 15 HELIX 20 20 SER A 617 LYS A 633 1 17 HELIX 21 21 ASP A 636 GLN A 649 1 14 HELIX 22 22 MET A 1 ASN A 736 1 690 HELIX 23 23 GLN A 737 GLY A 748 1 12 HELIX 24 24 ARG A 752 ARG A 757 1 6 SHEET 1 AA 3 ILE A 2 THR A 9 0 SHEET 2 AA 3 PRO A 14 LYS A 21 -1 O VAL A 15 N ILE A 8 SHEET 3 AA 3 PHE A 26 ASP A 31 -1 O LYS A 27 N LYS A 20 SHEET 1 AB 4 LYS A 70 PHE A 75 0 SHEET 2 AB 4 LYS A 78 TYR A 86 -1 O LYS A 78 N PHE A 75 SHEET 3 AB 4 TYR A 37 LEU A 42 -1 O ILE A 38 N LEU A 85 SHEET 4 AB 4 VAL A 106 PHE A 110 -1 N VAL A 107 O LEU A 41 SHEET 1 AC 6 VAL A 181 SER A 183 0 SHEET 2 AC 6 ALA A 168 THR A 172 1 O VAL A 170 N GLU A 182 SHEET 3 AC 6 MET A 159 ALA A 163 -1 O ILE A 160 N ILE A 171 SHEET 4 AC 6 ILE A 137 GLU A 143 -1 O ALA A 139 N ALA A 163 SHEET 5 AC 6 ILE A 205 THR A 208 1 O ILE A 205 N LEU A 138 SHEET 6 AC 6 ILE A 256 ASP A 259 1 O ILE A 256 N ILE A 206 SHEET 1 AD 2 LYS A 240 ARG A 243 0 SHEET 2 AD 2 THR A 248 GLU A 251 -1 O ALA A 249 N GLN A 242 SHEET 1 AE 6 LYS A 536 ASP A 541 0 SHEET 2 AE 6 GLY A 544 THR A 548 -1 O GLY A 544 N ASP A 541 SHEET 3 AE 6 TRP A 398 TYR A 406 -1 O VAL A 402 N ALA A 547 SHEET 4 AE 6 LEU A 578 THR A 591 -1 O GLU A 579 N ASP A 405 SHEET 5 AE 6 ARG A 594 ASP A 599 -1 O ARG A 594 N THR A 591 SHEET 6 AE 6 VAL A 604 ARG A 607 -1 O ILE A 605 N VAL A 597 SHEET 1 AF 2 TYR A 432 ILE A 434 0 SHEET 2 AF 2 LYS A 441 CYS A 443 -1 O PHE A 442 N ASP A 433 SSBOND 1 CYS A 429 CYS A 443 1555 1555 2.02 SSBOND 2 CYS A 507 CYS A 510 1555 1555 2.01 LINK OD1 ASP A 141 MN MN A1759 1555 1555 2.23 LINK OE2 GLU A 143 MN MN A1759 1555 1555 2.14 LINK OE2 GLU A 251 MN MN A1758 1555 1555 2.36 LINK OD1 ASP A 315 MN MN A1759 1555 1555 2.03 SITE 1 AC1 4 ASP A 4 VAL A 5 GLU A 251 ASP A 343 SITE 1 AC2 4 ASP A 141 ILE A 142 GLU A 143 ASP A 315 CRYST1 92.178 127.923 89.210 90.00 109.11 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 0.010849 0.000000 0.003759 0.00000 SCALE2 0.000000 0.007817 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011863 0.00000