HEADER HYDROLASE/DNA 10-JUL-15 5CHI TITLE CRYSTAL STRUCTURE OF PF2046 IN COMPLEX WITH SSDNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: PF2046; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(P*TP*TP*TP*T)-3'); COMPND 8 CHAIN: D, E, F; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS (STRAIN ATCC 43587 / DSM SOURCE 3 3638 / JCM 8422 / VC1); SOURCE 4 ORGANISM_TAXID: 186497; SOURCE 5 STRAIN: ATCC 43587 / DSM 3638 / JCM 8422 / VC1; SOURCE 6 GENE: PF2046; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET21A; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630 KEYWDS RNASEH, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.S.KIM,K.Y.HWANG,W.C.LEE REVDAT 3 08-NOV-23 5CHI 1 LINK REVDAT 2 27-SEP-17 5CHI 1 REMARK REVDAT 1 10-AUG-16 5CHI 0 JRNL AUTH J.S.KIM,G.D.SAMBALKHUNDEV,S.H.KIM,A.HAN,S.M.KO,K.Y.HWANG, JRNL AUTH 2 W.C.LEE JRNL TITL STRUCTURAL BASIS OF TWO-NUCLEOTIDE REMOVAL OF SSDNA BY A JRNL TITL 2 CRYPTIC RNASE H FOLD 3'-5' EXONUCLEASE PF2046 FROM JRNL TITL 3 PYROCOCCUS FURIOSUS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.880 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 24745 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.940 REMARK 3 FREE R VALUE TEST SET COUNT : 3832 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 34.5911 - 7.3917 1.00 1704 137 0.1365 0.1375 REMARK 3 2 7.3917 - 5.8764 1.00 1711 145 0.1577 0.1758 REMARK 3 3 5.8764 - 5.1363 1.00 1718 139 0.1633 0.2189 REMARK 3 4 5.1363 - 4.6679 1.00 1687 148 0.1356 0.1733 REMARK 3 5 4.6679 - 4.3340 1.00 1721 138 0.1418 0.2021 REMARK 3 6 4.3340 - 4.0789 1.00 1651 163 0.1543 0.1870 REMARK 3 7 4.0789 - 3.8749 1.00 1735 164 0.1566 0.1986 REMARK 3 8 3.8749 - 3.7064 1.00 1660 156 0.1632 0.2199 REMARK 3 9 3.7064 - 3.5639 1.00 1711 140 0.1677 0.1983 REMARK 3 10 3.5639 - 3.4410 1.00 1690 156 0.1826 0.2151 REMARK 3 11 3.4410 - 3.3335 1.00 1708 164 0.1876 0.2475 REMARK 3 12 3.3335 - 3.2383 1.00 1685 148 0.1976 0.2576 REMARK 3 13 3.2383 - 3.1531 1.00 1703 158 0.2144 0.2867 REMARK 3 14 3.1531 - 3.0762 1.00 1720 136 0.2161 0.2306 REMARK 3 15 3.0762 - 3.0064 1.00 1693 167 0.2133 0.3205 REMARK 3 16 3.0064 - 2.9424 1.00 1722 125 0.2206 0.2739 REMARK 3 17 2.9424 - 2.8836 1.00 1690 165 0.2254 0.2929 REMARK 3 18 2.8836 - 2.8292 1.00 1731 116 0.2189 0.2836 REMARK 3 19 2.8292 - 2.7787 1.00 1721 141 0.2259 0.2678 REMARK 3 20 2.7787 - 2.7316 1.00 1730 150 0.2381 0.2951 REMARK 3 21 2.7316 - 2.6876 1.00 1652 168 0.2556 0.2831 REMARK 3 22 2.6876 - 2.6462 1.00 1716 114 0.2477 0.3481 REMARK 3 23 2.6462 - 2.6073 1.00 1715 136 0.2572 0.3143 REMARK 3 24 2.6073 - 2.5706 1.00 1688 151 0.2616 0.3486 REMARK 3 25 2.5706 - 2.5359 1.00 1714 133 0.2666 0.3091 REMARK 3 26 2.5359 - 2.5030 0.90 1537 156 0.3178 0.3871 REMARK 3 27 2.5030 - 2.4717 0.17 300 18 0.5997 0.3830 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.720 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.92 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 5774 REMARK 3 ANGLE : 1.358 7854 REMARK 3 CHIRALITY : 0.052 888 REMARK 3 PLANARITY : 0.007 961 REMARK 3 DIHEDRAL : 15.500 2212 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE ENTRY CONTAINS FRIEDEL PAIRS IN REMARK 3 F_PLUS/MINUS COLUMNS REMARK 4 REMARK 4 5CHI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211640. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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-1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24745 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.470 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 6.570 REMARK 200 R MERGE (I) : 0.13300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.5400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.70900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 4O8U REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM MALONATE, 0.1M TRIS PH REMARK 280 8.0, 30% (W/V) PEG 1000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 42.95150 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: 1610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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: 1620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, E 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: 3 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: 1320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, F 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 ARG B 229 REMARK 465 LYS C 228 REMARK 465 ARG C 229 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 OD1 ASP C 92 OG1 THR C 95 1.86 REMARK 500 O LEU C 91 OG SER C 113 2.09 REMARK 500 OD1 ASP B 97 NZ LYS B 110 2.15 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 DT D 5 O3' DT D 5 C3' -0.047 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 DT D 6 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT F 8 O4' - C1' - N1 ANGL. DEV. = 2.4 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 ASP A 49 64.57 80.57 REMARK 500 TYR A 173 70.35 20.04 REMARK 500 ARG A 219 4.44 82.40 REMARK 500 LYS A 228 76.40 -45.02 REMARK 500 MET B 1 112.51 -36.95 REMARK 500 GLU B 15 2.38 -66.56 REMARK 500 LYS B 73 78.87 29.23 REMARK 500 TYR B 173 70.03 15.45 REMARK 500 ARG B 219 -8.22 82.55 REMARK 500 ASP C 49 59.82 -160.17 REMARK 500 GLN C 56 -79.02 -57.15 REMARK 500 PRO C 74 -172.91 -66.69 REMARK 500 ASP C 80 78.38 -69.67 REMARK 500 LEU C 91 75.70 -64.21 REMARK 500 ASP C 92 -156.63 -81.89 REMARK 500 THR C 95 -58.37 -140.73 REMARK 500 SER C 102 164.52 -49.83 REMARK 500 ASP C 115 -56.88 -121.87 REMARK 500 GLU C 158 1.22 -59.12 REMARK 500 TYR C 173 60.57 24.12 REMARK 500 ARG C 219 3.97 88.42 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 THR C 95 ILE C 96 -147.02 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 MG A 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 7 OD1 REMARK 620 2 ASP A 7 OD2 56.6 REMARK 620 3 GLU A 145 OE2 176.3 122.8 REMARK 620 4 HOH A 608 O 114.7 156.9 64.3 REMARK 620 5 DT D 7 OP1 81.2 119.7 101.8 75.9 REMARK 620 6 HOH D 102 O 105.1 78.8 78.0 123.8 72.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 7 OD1 REMARK 620 2 ASP A 80 OD2 96.0 REMARK 620 3 HOH A 605 O 85.5 178.5 REMARK 620 4 HOH A 612 O 134.1 91.8 87.5 REMARK 620 5 DT D 6 O3' 141.9 87.2 91.4 83.6 REMARK 620 6 DT D 7 OP1 83.1 89.4 90.3 142.3 58.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 7 OD1 REMARK 620 2 ASP B 80 OD2 81.3 REMARK 620 3 HOH B 415 O 113.1 165.1 REMARK 620 4 HOH B 417 O 124.6 79.4 88.8 REMARK 620 5 DT E 6 O3' 142.2 76.3 92.9 80.7 REMARK 620 6 DT E 7 OP1 90.4 78.4 104.2 134.4 55.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 7 OD2 REMARK 620 2 GLU B 145 OE2 94.0 REMARK 620 3 DT E 7 OP1 97.7 100.0 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 MG A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 302 DBREF 5CHI A 1 229 UNP Q8TZE9 Q8TZE9_PYRFU 1 229 DBREF 5CHI B 1 229 UNP Q8TZE9 Q8TZE9_PYRFU 1 229 DBREF 5CHI C 1 229 UNP Q8TZE9 Q8TZE9_PYRFU 1 229 DBREF 5CHI D 5 8 PDB 5CHI 5CHI 5 8 DBREF 5CHI E 5 8 PDB 5CHI 5CHI 5 8 DBREF 5CHI F 5 8 PDB 5CHI 5CHI 5 8 SEQADV 5CHI MET A 0 UNP Q8TZE9 INITIATING METHIONINE SEQADV 5CHI MET B 0 UNP Q8TZE9 INITIATING METHIONINE SEQADV 5CHI MET C 0 UNP Q8TZE9 INITIATING METHIONINE SEQRES 1 A 230 MET MET ARG ILE VAL ALA ALA ASP THR GLY GLY ALA VAL SEQRES 2 A 230 LEU ASP GLU THR PHE GLU PRO ILE GLY LEU ILE ALA THR SEQRES 3 A 230 VAL ALA VAL LEU VAL GLU LYS PRO TYR ARG SER ALA LYS SEQRES 4 A 230 GLU VAL MET VAL LYS TYR ALA ASN PRO TYR ASP TYR ASP SEQRES 5 A 230 LEU THR GLY ARG GLN ALA ILE ARG ASP GLU VAL LEU LEU SEQRES 6 A 230 ALA ILE GLU LEU ALA ARG LYS VAL LYS PRO ASP VAL ILE SEQRES 7 A 230 HIS LEU ASP SER THR LEU GLY GLY ILE GLU LEU ARG LYS SEQRES 8 A 230 LEU ASP GLU PRO THR ILE ASP ALA LEU GLY ILE SER ASP SEQRES 9 A 230 LYS GLY LYS GLU VAL TRP LYS GLU LEU SER LYS ASP LEU SEQRES 10 A 230 GLN PRO LEU ALA ARG LYS PHE TRP GLU GLU THR ASN ILE SEQRES 11 A 230 GLU ILE VAL ALA ILE GLY LYS SER SER VAL PRO VAL ARG SEQRES 12 A 230 ILE ALA GLU ILE TYR ALA GLY ILE TYR SER ALA LYS TRP SEQRES 13 A 230 GLY ILE GLU ASN VAL GLU LYS GLU GLY HIS LEU ILE ILE SEQRES 14 A 230 GLY LEU PRO ARG TYR MET GLU VAL ASN ILE LYS ASP GLY SEQRES 15 A 230 LYS ILE ILE GLY ARG SER LEU ASP PRO ARG GLU GLY GLY SEQRES 16 A 230 LEU TYR GLY SER ALA GLU VAL SER VAL PRO GLU GLY VAL SEQRES 17 A 230 LYS TRP GLU ILE TYR PRO ASN PRO VAL ALA ARG ARG PHE SEQRES 18 A 230 MET ILE PHE GLU ILE PHE SER LYS ARG SEQRES 1 B 230 MET MET ARG ILE VAL ALA ALA ASP THR GLY GLY ALA VAL SEQRES 2 B 230 LEU ASP GLU THR PHE GLU PRO ILE GLY LEU ILE ALA THR SEQRES 3 B 230 VAL ALA VAL LEU VAL GLU LYS PRO TYR ARG SER ALA LYS SEQRES 4 B 230 GLU VAL MET VAL LYS TYR ALA ASN PRO TYR ASP TYR ASP SEQRES 5 B 230 LEU THR GLY ARG GLN ALA ILE ARG ASP GLU VAL LEU LEU SEQRES 6 B 230 ALA ILE GLU LEU ALA ARG LYS VAL LYS PRO ASP VAL ILE SEQRES 7 B 230 HIS LEU ASP SER THR LEU GLY GLY ILE GLU LEU ARG LYS SEQRES 8 B 230 LEU ASP GLU PRO THR ILE ASP ALA LEU GLY ILE SER ASP SEQRES 9 B 230 LYS GLY LYS GLU VAL TRP LYS GLU LEU SER LYS ASP LEU SEQRES 10 B 230 GLN PRO LEU ALA ARG LYS PHE TRP GLU GLU THR ASN ILE SEQRES 11 B 230 GLU ILE VAL ALA ILE GLY LYS SER SER VAL PRO VAL ARG SEQRES 12 B 230 ILE ALA GLU ILE TYR ALA GLY ILE TYR SER ALA LYS TRP SEQRES 13 B 230 GLY ILE GLU ASN VAL GLU LYS GLU GLY HIS LEU ILE ILE SEQRES 14 B 230 GLY LEU PRO ARG TYR MET GLU VAL ASN ILE LYS ASP GLY SEQRES 15 B 230 LYS ILE ILE GLY ARG SER LEU ASP PRO ARG GLU GLY GLY SEQRES 16 B 230 LEU TYR GLY SER ALA GLU VAL SER VAL PRO GLU GLY VAL SEQRES 17 B 230 LYS TRP GLU ILE TYR PRO ASN PRO VAL ALA ARG ARG PHE SEQRES 18 B 230 MET ILE PHE GLU ILE PHE SER LYS ARG SEQRES 1 C 230 MET MET ARG ILE VAL ALA ALA ASP THR GLY GLY ALA VAL SEQRES 2 C 230 LEU ASP GLU THR PHE GLU PRO ILE GLY LEU ILE ALA THR SEQRES 3 C 230 VAL ALA VAL LEU VAL GLU LYS PRO TYR ARG SER ALA LYS SEQRES 4 C 230 GLU VAL MET VAL LYS TYR ALA ASN PRO TYR ASP TYR ASP SEQRES 5 C 230 LEU THR GLY ARG GLN ALA ILE ARG ASP GLU VAL LEU LEU SEQRES 6 C 230 ALA ILE GLU LEU ALA ARG LYS VAL LYS PRO ASP VAL ILE SEQRES 7 C 230 HIS LEU ASP SER THR LEU GLY GLY ILE GLU LEU ARG LYS SEQRES 8 C 230 LEU ASP GLU PRO THR ILE ASP ALA LEU GLY ILE SER ASP SEQRES 9 C 230 LYS GLY LYS GLU VAL TRP LYS GLU LEU SER LYS ASP LEU SEQRES 10 C 230 GLN PRO LEU ALA ARG LYS PHE TRP GLU GLU THR ASN ILE SEQRES 11 C 230 GLU ILE VAL ALA ILE GLY LYS SER SER VAL PRO VAL ARG SEQRES 12 C 230 ILE ALA GLU ILE TYR ALA GLY ILE TYR SER ALA LYS TRP SEQRES 13 C 230 GLY ILE GLU ASN VAL GLU LYS GLU GLY HIS LEU ILE ILE SEQRES 14 C 230 GLY LEU PRO ARG TYR MET GLU VAL ASN ILE LYS ASP GLY SEQRES 15 C 230 LYS ILE ILE GLY ARG SER LEU ASP PRO ARG GLU GLY GLY SEQRES 16 C 230 LEU TYR GLY SER ALA GLU VAL SER VAL PRO GLU GLY VAL SEQRES 17 C 230 LYS TRP GLU ILE TYR PRO ASN PRO VAL ALA ARG ARG PHE SEQRES 18 C 230 MET ILE PHE GLU ILE PHE SER LYS ARG SEQRES 1 D 4 DT DT DT DT SEQRES 1 E 4 DT DT DT DT SEQRES 1 F 4 DT DT DT DT HET MG A 501 1 HET MG A 502 1 HET MG B 301 1 HET MG B 302 1 HETNAM MG MAGNESIUM ION FORMUL 7 MG 4(MG 2+) FORMUL 11 HOH *103(H2 O) HELIX 1 AA1 GLY A 54 LYS A 73 1 20 HELIX 2 AA2 GLU A 87 LEU A 91 5 5 HELIX 3 AA3 ASP A 92 ALA A 98 1 7 HELIX 4 AA4 SER A 102 ASN A 128 1 27 HELIX 5 AA5 ILE A 134 SER A 137 5 4 HELIX 6 AA6 SER A 138 GLU A 158 1 21 HELIX 7 AA7 ASP A 189 GLY A 193 5 5 HELIX 8 AA8 ASN B 46 TYR B 50 5 5 HELIX 9 AA9 GLY B 54 LYS B 73 1 20 HELIX 10 AB1 GLU B 87 LEU B 91 5 5 HELIX 11 AB2 ASP B 92 ASP B 97 1 6 HELIX 12 AB3 LYS B 104 ASN B 128 1 25 HELIX 13 AB4 ILE B 134 SER B 137 5 4 HELIX 14 AB5 SER B 138 GLU B 158 1 21 HELIX 15 AB6 ASN B 159 GLY B 164 1 6 HELIX 16 AB7 ASP B 189 GLY B 193 5 5 HELIX 17 AB8 ASN C 46 TYR C 50 5 5 HELIX 18 AB9 GLY C 54 LYS C 73 1 20 HELIX 19 AC1 ASP C 92 ASP C 97 1 6 HELIX 20 AC2 LYS C 104 TRP C 109 1 6 HELIX 21 AC3 LEU C 112 ASN C 128 1 17 HELIX 22 AC4 ILE C 134 SER C 137 5 4 HELIX 23 AC5 SER C 138 GLU C 158 1 21 HELIX 24 AC6 ASP C 189 GLY C 193 5 5 SHEET 1 AA1 5 GLU A 39 TYR A 44 0 SHEET 2 AA1 5 ALA A 24 VAL A 30 -1 N THR A 25 O LYS A 43 SHEET 3 AA1 5 ILE A 3 THR A 8 -1 N ALA A 5 O VAL A 28 SHEET 4 AA1 5 VAL A 76 HIS A 78 1 O HIS A 78 N VAL A 4 SHEET 5 AA1 5 ILE A 131 VAL A 132 1 O VAL A 132 N ILE A 77 SHEET 1 AA2 5 PRO A 19 LEU A 22 0 SHEET 2 AA2 5 ALA A 11 LEU A 13 -1 N VAL A 12 O ILE A 20 SHEET 3 AA2 5 HIS A 165 GLY A 169 -1 O GLY A 169 N ALA A 11 SHEET 4 AA2 5 MET A 221 PHE A 226 -1 O PHE A 223 N ILE A 168 SHEET 5 AA2 5 LYS A 208 PRO A 213 -1 N TYR A 212 O ILE A 222 SHEET 1 AA3 3 MET A 174 LYS A 179 0 SHEET 2 AA3 3 LYS A 182 SER A 187 -1 O ILE A 184 N ASN A 177 SHEET 3 AA3 3 TYR A 196 GLU A 200 -1 O ALA A 199 N ILE A 183 SHEET 1 AA4 5 GLU B 39 TYR B 44 0 SHEET 2 AA4 5 PRO B 19 VAL B 30 -1 N THR B 25 O LYS B 43 SHEET 3 AA4 5 ILE B 3 LEU B 13 -1 N ASP B 7 O VAL B 26 SHEET 4 AA4 5 VAL B 76 HIS B 78 1 O HIS B 78 N VAL B 4 SHEET 5 AA4 5 ILE B 131 VAL B 132 1 O VAL B 132 N ILE B 77 SHEET 1 AA5 6 GLU B 39 TYR B 44 0 SHEET 2 AA5 6 PRO B 19 VAL B 30 -1 N THR B 25 O LYS B 43 SHEET 3 AA5 6 ILE B 3 LEU B 13 -1 N ASP B 7 O VAL B 26 SHEET 4 AA5 6 HIS B 165 ARG B 172 -1 O ILE B 167 N LEU B 13 SHEET 5 AA5 6 PHE B 220 PHE B 226 -1 O PHE B 223 N ILE B 168 SHEET 6 AA5 6 LYS B 208 PRO B 213 -1 N LYS B 208 O PHE B 226 SHEET 1 AA6 3 MET B 174 ILE B 178 0 SHEET 2 AA6 3 LYS B 182 SER B 187 -1 O ILE B 184 N ASN B 177 SHEET 3 AA6 3 TYR B 196 GLU B 200 -1 O ALA B 199 N ILE B 183 SHEET 1 AA7 5 GLU C 39 TYR C 44 0 SHEET 2 AA7 5 ALA C 24 VAL C 30 -1 N THR C 25 O LYS C 43 SHEET 3 AA7 5 ILE C 3 THR C 8 -1 N ILE C 3 O VAL C 30 SHEET 4 AA7 5 VAL C 76 LEU C 79 1 O HIS C 78 N VAL C 4 SHEET 5 AA7 5 ILE C 131 VAL C 132 1 O VAL C 132 N LEU C 79 SHEET 1 AA8 2 ALA C 11 LEU C 13 0 SHEET 2 AA8 2 PRO C 19 LEU C 22 -1 O ILE C 20 N VAL C 12 SHEET 1 AA9 3 LEU C 166 GLY C 169 0 SHEET 2 AA9 3 MET C 221 ILE C 225 -1 O PHE C 223 N ILE C 168 SHEET 3 AA9 3 TRP C 209 PRO C 213 -1 N TYR C 212 O ILE C 222 SHEET 1 AB1 3 MET C 174 LYS C 179 0 SHEET 2 AB1 3 LYS C 182 SER C 187 -1 O ARG C 186 N GLU C 175 SHEET 3 AB1 3 TYR C 196 GLU C 200 -1 O ALA C 199 N ILE C 183 LINK OD1 ASP A 7 MG MG A 501 1555 1555 2.26 LINK OD2 ASP A 7 MG MG A 501 1555 1555 2.38 LINK OD1 ASP A 7 MG MG A 502 1555 1555 2.30 LINK OD2 ASP A 80 MG MG A 502 1555 1555 2.12 LINK OE2 GLU A 145 MG MG A 501 1555 1555 2.44 LINK MG MG A 501 O HOH A 608 1555 1555 2.23 LINK MG MG A 501 OP1 DT D 7 1555 1555 2.56 LINK MG MG A 501 O HOH D 102 1555 1555 2.28 LINK MG MG A 502 O HOH A 605 1555 1555 2.87 LINK MG MG A 502 O HOH A 612 1555 1555 2.44 LINK MG MG A 502 O3' DT D 6 1555 1555 2.63 LINK MG MG A 502 OP1 DT D 7 1555 1555 2.44 LINK OD1 ASP B 7 MG MG B 301 1555 1555 2.34 LINK OD2 ASP B 7 MG MG B 302 1555 1555 2.86 LINK OD2 ASP B 80 MG MG B 301 1555 1555 2.27 LINK OE2 GLU B 145 MG MG B 302 1555 1555 2.18 LINK MG MG B 301 O HOH B 415 1555 1555 2.33 LINK MG MG B 301 O HOH B 417 1555 1555 2.46 LINK MG MG B 301 O3' DT E 6 1555 1555 2.69 LINK MG MG B 301 OP1 DT E 7 1555 1555 2.54 LINK MG MG B 302 OP1 DT E 7 1555 1555 2.59 CISPEP 1 LYS A 32 PRO A 33 0 8.73 CISPEP 2 LYS B 32 PRO B 33 0 4.99 CISPEP 3 LYS C 32 PRO C 33 0 5.95 SITE 1 AC1 7 ASP A 7 ASP A 80 GLU A 145 MG A 502 SITE 2 AC1 7 HOH A 608 DT D 7 HOH D 102 SITE 1 AC2 7 ASP A 7 ASP A 80 MG A 501 HOH A 605 SITE 2 AC2 7 HOH A 612 DT D 6 DT D 7 SITE 1 AC3 8 ASP B 7 THR B 8 GLU B 61 ASP B 80 SITE 2 AC3 8 HOH B 415 HOH B 417 DT E 6 DT E 7 SITE 1 AC4 5 ASP B 7 THR B 8 GLU B 145 DT E 7 SITE 2 AC4 5 DT E 8 CRYST1 69.010 85.903 69.204 90.00 118.44 90.00 P 1 21 1 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.014491 0.000000 0.007847 0.00000 SCALE2 0.000000 0.011641 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016433 0.00000