HEADER TOXIN 30-MAR-20 6YHN TITLE CRYSTAL STRUCTURE OF DOMAINS 4-5 OF CNFY FROM YERSINIA TITLE 2 PSEUDOTUBERCULOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOTOXIC NECROTIZING FACTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CNFY RESIDUES 526-1014; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: FRAGMENT OF CNFY COMPRISING RESIDUES 526-1014. CYS 866 COMPND 7 HAS FOUND TO BE OXIDIZED IN THE STRUCTURE. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA PSEUDOTUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 633; SOURCE 4 GENE: CNF; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PCOLA-DUET-1 KEYWDS TOXIN, CNF, CYTOTOXIC NECROTIZING FACTOR, DEAMIDASE, RHOA KEYWDS 2 MODIFICATION, RHOA ACTIVATION, PUTATIVE ADP-RIBOSYLTRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR P.LUKAT,E.M.GAZDAG,T.V.HEIDLER,W.BLANKENFELDT REVDAT 4 01-MAY-24 6YHN 1 REMARK REVDAT 3 24-FEB-21 6YHN 1 JRNL REVDAT 2 20-JAN-21 6YHN 1 JRNL REVDAT 1 30-DEC-20 6YHN 0 JRNL AUTH P.CHAOPRASID,P.LUKAT,S.MUHLEN,T.HEIDLER,E.M.GAZDAG,S.DONG, JRNL AUTH 2 W.BI,C.RUTER,M.KIRCHENWITZ,A.STEFFEN,L.JANSCH,T.E.B.STRADAL, JRNL AUTH 3 P.DERSCH,W.BLANKENFELDT JRNL TITL CRYSTAL STRUCTURE OF BACTERIAL CYTOTOXIC NECROTIZING FACTOR JRNL TITL 2 CNF Y REVEALS MOLECULAR BUILDING BLOCKS FOR INTOXICATION. JRNL REF EMBO J. V. 40 05202 2021 JRNL REFN ESSN 1460-2075 JRNL PMID 33410511 JRNL DOI 10.15252/EMBJ.2020105202 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14RC1_3177 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 49821 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.840 REMARK 3 FREE R VALUE TEST SET COUNT : 2410 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 45.2650 - 4.6268 1.00 3007 154 0.1666 0.2004 REMARK 3 2 4.6268 - 3.6729 1.00 2843 148 0.1243 0.1481 REMARK 3 3 3.6729 - 3.2088 1.00 2835 148 0.1363 0.1592 REMARK 3 4 3.2088 - 2.9155 1.00 2809 165 0.1586 0.1887 REMARK 3 5 2.9155 - 2.7065 1.00 2791 131 0.1638 0.2212 REMARK 3 6 2.7065 - 2.5470 1.00 2761 162 0.1524 0.2071 REMARK 3 7 2.5470 - 2.4194 1.00 2795 130 0.1555 0.1868 REMARK 3 8 2.4194 - 2.3141 1.00 2757 160 0.1499 0.1913 REMARK 3 9 2.3141 - 2.2250 1.00 2773 138 0.1496 0.1785 REMARK 3 10 2.2250 - 2.1483 1.00 2767 139 0.1561 0.2220 REMARK 3 11 2.1483 - 2.0811 1.00 2769 137 0.1615 0.1986 REMARK 3 12 2.0811 - 2.0216 1.00 2766 136 0.1697 0.1924 REMARK 3 13 2.0216 - 1.9684 1.00 2733 133 0.1725 0.1935 REMARK 3 14 1.9684 - 1.9204 1.00 2786 117 0.1890 0.1848 REMARK 3 15 1.9204 - 1.8767 1.00 2783 131 0.2240 0.2544 REMARK 3 16 1.8767 - 1.8368 1.00 2696 144 0.2550 0.3153 REMARK 3 17 1.8368 - 1.8000 1.00 2740 137 0.3034 0.3546 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.20 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 524 THROUGH 562 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.9551 -8.8951 7.4390 REMARK 3 T TENSOR REMARK 3 T11: 0.2886 T22: 0.3053 REMARK 3 T33: 0.2648 T12: 0.0509 REMARK 3 T13: 0.0386 T23: 0.0315 REMARK 3 L TENSOR REMARK 3 L11: 0.7809 L22: 1.0179 REMARK 3 L33: 0.8444 L12: -0.2094 REMARK 3 L13: 0.3774 L23: -0.2506 REMARK 3 S TENSOR REMARK 3 S11: 0.0495 S12: 0.1619 S13: -0.1493 REMARK 3 S21: -0.0932 S22: -0.1535 S23: -0.0915 REMARK 3 S31: 0.4387 S32: 0.6143 S33: 0.0045 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 563 THROUGH 621 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.4596 -4.7042 12.6971 REMARK 3 T TENSOR REMARK 3 T11: 0.2213 T22: 0.3359 REMARK 3 T33: 0.2526 T12: -0.0590 REMARK 3 T13: 0.0463 T23: -0.0329 REMARK 3 L TENSOR REMARK 3 L11: 1.0334 L22: 1.4330 REMARK 3 L33: 0.9754 L12: -0.7952 REMARK 3 L13: -0.2878 L23: -0.4805 REMARK 3 S TENSOR REMARK 3 S11: -0.1203 S12: 0.1090 S13: -0.2610 REMARK 3 S21: 0.0965 S22: -0.0168 S23: 0.2840 REMARK 3 S31: 0.1688 S32: -0.4688 S33: -0.0071 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 622 THROUGH 654 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.7467 2.5270 13.6959 REMARK 3 T TENSOR REMARK 3 T11: 0.2334 T22: 0.3180 REMARK 3 T33: 0.2248 T12: 0.0150 REMARK 3 T13: 0.0134 T23: -0.0162 REMARK 3 L TENSOR REMARK 3 L11: 0.5852 L22: 0.7708 REMARK 3 L33: 0.3399 L12: -0.4584 REMARK 3 L13: 0.4266 L23: -0.4121 REMARK 3 S TENSOR REMARK 3 S11: -0.0782 S12: -0.1464 S13: 0.1171 REMARK 3 S21: 0.0882 S22: 0.0078 S23: 0.1087 REMARK 3 S31: -0.2934 S32: -0.2061 S33: 0.0017 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 655 THROUGH 733 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.2059 -1.4623 4.0200 REMARK 3 T TENSOR REMARK 3 T11: 0.1961 T22: 0.2493 REMARK 3 T33: 0.2074 T12: 0.0083 REMARK 3 T13: 0.0087 T23: -0.0110 REMARK 3 L TENSOR REMARK 3 L11: 0.0923 L22: 0.4987 REMARK 3 L33: 2.1389 L12: 0.1043 REMARK 3 L13: 0.0187 L23: -0.5615 REMARK 3 S TENSOR REMARK 3 S11: 0.0224 S12: 0.0040 S13: -0.1159 REMARK 3 S21: 0.0396 S22: -0.0876 S23: 0.0229 REMARK 3 S31: 0.1444 S32: 0.0532 S33: -0.0066 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 734 THROUGH 908 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.1157 11.6676 -11.5869 REMARK 3 T TENSOR REMARK 3 T11: 0.1507 T22: 0.1236 REMARK 3 T33: 0.1790 T12: -0.0153 REMARK 3 T13: -0.0056 T23: -0.0301 REMARK 3 L TENSOR REMARK 3 L11: 1.6713 L22: 1.4588 REMARK 3 L33: 3.4250 L12: -0.3669 REMARK 3 L13: 0.3302 L23: 0.3020 REMARK 3 S TENSOR REMARK 3 S11: -0.0259 S12: -0.1383 S13: 0.0768 REMARK 3 S21: 0.0271 S22: -0.0419 S23: 0.0887 REMARK 3 S31: -0.1391 S32: 0.0342 S33: -0.0198 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 909 THROUGH 1016 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.2409 17.3919 -25.5740 REMARK 3 T TENSOR REMARK 3 T11: 0.2813 T22: 0.1487 REMARK 3 T33: 0.2090 T12: 0.0108 REMARK 3 T13: -0.0582 T23: -0.0081 REMARK 3 L TENSOR REMARK 3 L11: 2.3835 L22: 2.5800 REMARK 3 L33: 3.4672 L12: -0.8949 REMARK 3 L13: 0.0347 L23: -0.0289 REMARK 3 S TENSOR REMARK 3 S11: -0.0828 S12: 0.0931 S13: 0.1975 REMARK 3 S21: -0.2333 S22: -0.0913 S23: 0.1943 REMARK 3 S31: -0.5613 S32: -0.1243 S33: -0.1169 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6YHN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1292107630. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-APR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.6.3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49960 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 48.270 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 32.70 REMARK 200 R MERGE (I) : 0.25700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 19.80 REMARK 200 R MERGE FOR SHELL (I) : 3.56000 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: PHASER REMARK 200 STARTING MODEL: CORRESPONDING FRAGMENT FROM THE FULL-LENGTH TOXIN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.24 M MAGNESIUM CHLORIDE, 22.5 % REMARK 280 (W/V) PEG 2000 MME, 1 MM ATP, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 24.13550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.35850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.26550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.35850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.13550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.26550 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -66.0 KCAL/MOL 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 GLY A 522 REMARK 465 GLY A 523 REMARK 465 ALA A 548 REMARK 465 SER A 549 REMARK 465 SER A 550 REMARK 465 VAL A 551 REMARK 465 GLU A 628 REMARK 465 ALA A 629 REMARK 465 GLY A 630 REMARK 465 PRO A 631 REMARK 465 GLN A 632 REMARK 465 PHE A 633 REMARK 465 ASN A 634 REMARK 465 VAL A 702 REMARK 465 LYS A 703 REMARK 465 PRO A 704 REMARK 465 LYS A 705 REMARK 465 LEU A 706 REMARK 465 SER A 707 REMARK 465 PHE A 708 REMARK 465 ILE A 709 REMARK 465 GLN A 710 REMARK 465 LYS A 711 REMARK 465 ILE A 712 REMARK 465 ALA A 713 REMARK 465 ASN A 714 REMARK 465 ARG A 715 REMARK 465 PHE A 716 REMARK 465 LEU A 717 REMARK 465 THR A 718 REMARK 465 ASN A 998 REMARK 465 SER A 999 REMARK 465 ASN A 1000 REMARK 465 SER A 1001 REMARK 465 SER A 1002 REMARK 465 GLY A 1017 REMARK 465 GLY A 1018 REMARK 465 ASP A 1019 REMARK 465 TYR A 1020 REMARK 465 LYS A 1021 REMARK 465 ASP A 1022 REMARK 465 HIS A 1023 REMARK 465 ASP A 1024 REMARK 465 GLY A 1025 REMARK 465 ASP A 1026 REMARK 465 TYR A 1027 REMARK 465 LYS A 1028 REMARK 465 ASP A 1029 REMARK 465 HIS A 1030 REMARK 465 ASP A 1031 REMARK 465 ILE A 1032 REMARK 465 ASP A 1033 REMARK 465 TYR A 1034 REMARK 465 LYS A 1035 REMARK 465 ASP A 1036 REMARK 465 ASP A 1037 REMARK 465 ASP A 1038 REMARK 465 ASP A 1039 REMARK 465 LYS A 1040 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 ARG A 525 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 552 CG CD OE1 OE2 REMARK 470 GLN A 814 CG CD OE1 NE2 REMARK 470 GLU A 911 CG CD OE1 OE2 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 HD21 ASN A 670 O HOH A 1307 1.52 REMARK 500 H GLY A 769 O HOH A 1309 1.53 REMARK 500 O HOH A 1548 O HOH A 1638 2.07 REMARK 500 O HOH A 1627 O HOH A 1656 2.10 REMARK 500 O HOH A 1380 O HOH A 1425 2.17 REMARK 500 OH TYR A 807 O HOH A 1301 2.17 REMARK 500 O HOH A 1538 O HOH A 1643 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 1312 O HOH A 1314 1455 2.08 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 ASN A 586 59.27 -119.09 REMARK 500 HIS A 654 -135.11 -139.96 REMARK 500 ASP A 779 -165.47 -125.09 REMARK 500 PHE A 787 42.17 -108.19 REMARK 500 ILE A 794 -61.70 -104.85 REMARK 500 THR A 817 -83.60 -134.90 REMARK 500 THR A 825 160.61 68.36 REMARK 500 THR A 894 -80.55 -131.80 REMARK 500 ASP A 984 12.06 80.76 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 NA A1207 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 545 OG REMARK 620 2 GLU A 546 OE2 120.6 REMARK 620 3 HOH A1549 O 101.7 117.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1206 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 611 OD1 REMARK 620 2 HOH A1474 O 127.9 REMARK 620 3 HOH A1475 O 126.2 87.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1205 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1336 O REMARK 620 2 HOH A1561 O 78.8 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BU3 A 1201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 1202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 1203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 1204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 1205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 1206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 1207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 1208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1209 DBREF1 6YHN A 526 1014 UNP A0A0N9JNY6_YERPU DBREF2 6YHN A A0A0N9JNY6 526 1014 SEQADV 6YHN GLY A 522 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHN GLY A 523 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHN GLY A 524 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHN ARG A 525 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHN SER A 1015 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHN ALA A 1016 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHN GLY A 1017 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHN GLY A 1018 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHN ASP A 1019 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHN TYR A 1020 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHN LYS A 1021 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHN ASP A 1022 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHN HIS A 1023 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHN ASP A 1024 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHN GLY A 1025 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHN ASP A 1026 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHN TYR A 1027 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHN LYS A 1028 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHN ASP A 1029 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHN HIS A 1030 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHN ASP A 1031 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHN ILE A 1032 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHN ASP A 1033 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHN TYR A 1034 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHN LYS A 1035 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHN ASP A 1036 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHN ASP A 1037 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHN ASP A 1038 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHN ASP A 1039 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHN LYS A 1040 UNP A0A0N9JNY EXPRESSION TAG SEQRES 1 A 519 GLY GLY GLY ARG GLN PRO PHE ASN PHE GLU GLY LEU ASP SEQRES 2 A 519 ILE PRO VAL TYR PHE ILE ASP LYS PRO TYR SER GLU LEU SEQRES 3 A 519 ALA SER SER VAL GLU LEU SER PHE VAL ASN ASP ASP SER SEQRES 4 A 519 PRO LEU LEU PHE PRO GLU MET ASP SER ARG LEU PRO LYS SEQRES 5 A 519 PRO THR PRO GLU LEU ASP ILE LYS TYR TYR SER SER ASN SEQRES 6 A 519 LEU SER SER PHE LYS GLU ASP THR VAL ILE LEU MET ARG SEQRES 7 A 519 GLY THR THR GLU GLU GLU ALA TRP ASN ILE ALA ASN TYR SEQRES 8 A 519 LYS THR ALA GLY GLY SER ASN LYS ASP LEU GLU GLU ASN SEQRES 9 A 519 PHE ILE GLU ALA GLY PRO GLN PHE ASN LEU SER PHE SER SEQRES 10 A 519 GLU TYR THR SER SER ILE ASN SER ALA ASP THR ALA SER SEQRES 11 A 519 ARG LYS HIS PHE LEU VAL ILE ILE LYS VAL GLN VAL LYS SEQRES 12 A 519 TYR ILE SER ASN ASP ASN VAL LEU TYR ALA ASN HIS TRP SEQRES 13 A 519 ALA ILE PRO ASP GLU ALA PRO VAL GLU VAL LEU ALA VAL SEQRES 14 A 519 VAL ASP ARG ARG PHE ILE PHE PRO GLU PRO PRO VAL LYS SEQRES 15 A 519 PRO LYS LEU SER PHE ILE GLN LYS ILE ALA ASN ARG PHE SEQRES 16 A 519 LEU THR GLU ASN VAL ALA GLU ILE SER SER ILE ASN PHE SEQRES 17 A 519 ARG ARG LEU ASN SER GLY ASN ILE ASN VAL LEU LYS GLY SEQRES 18 A 519 ARG GLY VAL PHE SER SER ARG ARG LEU ARG GLU ILE TYR SEQRES 19 A 519 LEU ARG PHE ASP ALA ALA ASN ALA ASP GLU LEU ARG PRO SEQRES 20 A 519 GLY ASP VAL TYR VAL LYS LYS THR LYS PHE ASP SER MET SEQRES 21 A 519 GLY TYR ASP SER HIS PHE TYR ASN GLU GLY ILE GLY ILE SEQRES 22 A 519 ASN GLY ALA PRO THR LEU ASN THR TYR THR GLY GLU TYR SEQRES 23 A 519 VAL ALA ASP SER SER SER GLN GLY ALA THR TYR TRP LEU SEQRES 24 A 519 LYS TYR ASN LEU THR ASN GLU THR SER ILE ILE LYS VAL SEQRES 25 A 519 SER ASN SER ALA ARG GLY ALA ASN GLY ILE LYS ILE ALA SEQRES 26 A 519 LEU GLU GLU ILE GLU GLU ASN LYS PRO VAL VAL ILE THR SEQRES 27 A 519 SER GLY THR LEU THR GLY CSO THR VAL VAL PHE ALA ARG SEQRES 28 A 519 LYS GLY GLU TYR PHE TYR ALA VAL HIS THR GLY ASN SER SEQRES 29 A 519 GLU SER LEU ILE GLY PHE THR SER THR SER GLY VAL ALA SEQRES 30 A 519 LYS ALA ILE GLU VAL LEU SER SER LEU SER GLU LEU GLU SEQRES 31 A 519 VAL PRO ALA LEU PRO ASP VAL ILE ASN ASN ASN THR LEU SEQRES 32 A 519 VAL GLU TYR LEU SER ASP ASN PHE ASP SER ALA LEU ILE SEQRES 33 A 519 SER TYR SER SER SER SER LEU LYS PRO ASN SER MET ILE SEQRES 34 A 519 ASN ILE SER ARG GLU ASN VAL SER THR PHE SER TYR TYR SEQRES 35 A 519 THR ASP ASP ILE GLN LEU PRO SER PHE GLY THR SER VAL SEQRES 36 A 519 THR ILE LEU VAL ARG THR ASN ASP ASN THR VAL VAL ARG SEQRES 37 A 519 SER LEU SER GLU SER TYR THR MET ASN SER ASN SER SER SEQRES 38 A 519 LYS MET VAL VAL PHE ASN VAL LEU GLN LYS ASP PHE SER SEQRES 39 A 519 ALA GLY GLY ASP TYR LYS ASP HIS ASP GLY ASP TYR LYS SEQRES 40 A 519 ASP HIS ASP ILE ASP TYR LYS ASP ASP ASP ASP LYS MODRES 6YHN CSO A 866 CYS MODIFIED RESIDUE HET CSO A 866 12 HET BU3 A1201 16 HET MG A1202 1 HET MG A1203 1 HET MG A1204 1 HET MG A1205 1 HET NA A1206 1 HET NA A1207 1 HET CL A1208 1 HET SO4 A1209 5 HETNAM CSO S-HYDROXYCYSTEINE HETNAM BU3 (R,R)-2,3-BUTANEDIOL HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM SO4 SULFATE ION FORMUL 1 CSO C3 H7 N O3 S FORMUL 2 BU3 C4 H10 O2 FORMUL 3 MG 4(MG 2+) FORMUL 7 NA 2(NA 1+) FORMUL 9 CL CL 1- FORMUL 10 SO4 O4 S 2- FORMUL 11 HOH *367(H2 O) HELIX 1 AA1 PRO A 543 LEU A 547 5 5 HELIX 2 AA2 PRO A 576 ASN A 586 1 11 HELIX 3 AA3 ASN A 586 LYS A 591 1 6 HELIX 4 AA4 THR A 602 LYS A 613 1 12 HELIX 5 AA5 ASP A 621 ILE A 627 5 7 HELIX 6 AA6 SER A 643 ARG A 652 1 10 HELIX 7 AA7 LYS A 664 ILE A 666 5 3 HELIX 8 AA8 ASN A 720 SER A 734 1 15 HELIX 9 AA9 ASN A 736 LYS A 741 5 6 HELIX 10 AB1 ASP A 784 HIS A 786 5 3 HELIX 11 AB2 THR A 817 TYR A 822 1 6 HELIX 12 AB3 GLU A 848 ILE A 850 5 3 HELIX 13 AB4 THR A 894 SER A 908 1 15 HELIX 14 AB5 ASN A 920 PHE A 932 1 13 HELIX 15 AB6 LYS A 945 MET A 949 5 5 SHEET 1 AA1 4 VAL A 537 ILE A 540 0 SHEET 2 AA1 4 GLU A 686 ASP A 692 1 O VAL A 690 N VAL A 537 SHEET 3 AA1 4 PHE A 655 GLN A 662 -1 N LEU A 656 O VAL A 691 SHEET 4 AA1 4 THR A 594 THR A 601 -1 N ARG A 599 O VAL A 657 SHEET 1 AA2 2 PHE A 637 THR A 641 0 SHEET 2 AA2 2 HIS A 676 PRO A 680 -1 O ILE A 679 N SER A 638 SHEET 1 AA3 7 TYR A 772 LYS A 774 0 SHEET 2 AA3 7 ASP A 759 ASP A 764 -1 N ALA A 760 O LYS A 774 SHEET 3 AA3 7 ARG A 838 ALA A 846 -1 O GLY A 842 N ALA A 761 SHEET 4 AA3 7 TYR A 876 ASN A 884 -1 O PHE A 877 N ILE A 845 SHEET 5 AA3 7 THR A 867 LYS A 873 -1 N VAL A 869 O VAL A 880 SHEET 6 AA3 7 SER A 934 SER A 940 -1 O LEU A 936 N PHE A 870 SHEET 7 AA3 7 VAL A 957 TYR A 963 1 O PHE A 960 N ILE A 937 SHEET 1 AA4 2 TYR A 788 ASN A 789 0 SHEET 2 AA4 2 ALA A 797 PRO A 798 -1 O ALA A 797 N ASN A 789 SHEET 1 AA5 6 LEU A 800 GLY A 805 0 SHEET 2 AA5 6 THR A 825 VAL A 833 -1 O ILE A 830 N TYR A 803 SHEET 3 AA5 6 VAL A 856 THR A 859 1 O VAL A 857 N ILE A 831 SHEET 4 AA5 6 PHE A 972 THR A 982 -1 O THR A 977 N ILE A 858 SHEET 5 AA5 6 ASN A 985 THR A 996 -1 O VAL A 987 N VAL A 980 SHEET 6 AA5 6 VAL A1005 ASP A1013 -1 O LYS A1012 N SER A 990 LINK C GLY A 865 N CSO A 866 1555 1555 1.33 LINK C CSO A 866 N THR A 867 1555 1555 1.33 LINK OG SER A 545 NA NA A1207 1555 1555 2.89 LINK OE2 GLU A 546 NA NA A1207 1555 1555 2.39 LINK OD1 ASN A 611 NA NA A1206 1555 1555 2.39 LINK MG MG A1202 O HOH A1634 1555 1555 2.97 LINK MG MG A1204 O HOH A1585 1555 1555 2.80 LINK MG MG A1205 O HOH A1336 1555 1555 2.91 LINK MG MG A1205 O HOH A1561 1555 1555 2.90 LINK NA NA A1206 O HOH A1474 1555 1555 2.82 LINK NA NA A1206 O HOH A1475 1555 1555 2.86 LINK NA NA A1207 O HOH A1549 1555 1555 2.97 CISPEP 1 PHE A 564 PRO A 565 0 1.04 CISPEP 2 LEU A 969 PRO A 970 0 3.81 SITE 1 AC1 6 TYR A 673 LYS A 774 THR A 776 ASP A 784 SITE 2 AC1 6 HOH A1393 HOH A1422 SITE 1 AC2 4 THR A 602 GLU A 603 HIS A 654 HOH A1634 SITE 1 AC3 2 ARG A 743 HOH A1538 SITE 1 AC4 5 ARG A 599 GLY A 600 ALA A 650 HOH A1313 SITE 2 AC4 5 HOH A1585 SITE 1 AC5 5 LYS A 832 GLY A 861 THR A 862 HOH A1336 SITE 2 AC5 5 HOH A1561 SITE 1 AC6 5 LEU A 533 ASN A 611 LYS A 741 HOH A1474 SITE 2 AC6 5 HOH A1475 SITE 1 AC7 4 SER A 545 GLU A 546 PRO A 698 HOH A1549 SITE 1 AC8 3 ARG A 652 GLU A 753 HOH A1419 SITE 1 AC9 2 GLU A 753 ASP A 779 CRYST1 48.271 90.531 120.717 90.00 90.00 90.00 P 21 21 21 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 0.020716 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011046 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008284 0.00000