HEADER TOXIN 30-MAR-20 6YHK TITLE CRYSTAL STRUCTURE OF FULL-LENGTH CNFY (C866S) FROM YERSINIA TITLE 2 PSEUDOTUBERCULOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOTOXIC NECROTIZING FACTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FULL-LENGTH CNFY; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: C866S VARIANT OF FULL-LENGTH CNFY FROM Y. COMPND 8 PSEUDOTUBERCULOSIS 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 6YHK 1 REMARK REVDAT 3 24-FEB-21 6YHK 1 JRNL REVDAT 2 20-JAN-21 6YHK 1 JRNL REVDAT 1 30-DEC-20 6YHK 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. 2.70 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 38988 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 1991 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 47.0780 - 6.5021 1.00 2818 153 0.1921 0.2125 REMARK 3 2 6.5021 - 5.1630 1.00 2719 134 0.1964 0.2182 REMARK 3 3 5.1630 - 4.5110 1.00 2683 124 0.1610 0.1879 REMARK 3 4 4.5110 - 4.0988 1.00 2653 129 0.1594 0.1902 REMARK 3 5 4.0988 - 3.8051 1.00 2658 146 0.1890 0.2682 REMARK 3 6 3.8051 - 3.5809 1.00 2599 153 0.2124 0.2407 REMARK 3 7 3.5809 - 3.4016 1.00 2609 152 0.2207 0.2583 REMARK 3 8 3.4016 - 3.2536 1.00 2658 132 0.2425 0.3323 REMARK 3 9 3.2536 - 3.1283 1.00 2605 130 0.2584 0.3194 REMARK 3 10 3.1283 - 3.0204 1.00 2604 165 0.2715 0.2801 REMARK 3 11 3.0204 - 2.9260 1.00 2602 142 0.2789 0.3335 REMARK 3 12 2.9260 - 2.8424 1.00 2616 148 0.2868 0.3134 REMARK 3 13 2.8424 - 2.7675 1.00 2573 147 0.2973 0.3262 REMARK 3 14 2.7675 - 2.7000 1.00 2600 136 0.3113 0.3651 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) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.840 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 85.66 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 : 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 : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 686 THROUGH 774 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.8479 -15.3738 24.9445 REMARK 3 T TENSOR REMARK 3 T11: 0.8618 T22: 1.2685 REMARK 3 T33: 0.8184 T12: 0.0043 REMARK 3 T13: 0.0696 T23: 0.0719 REMARK 3 L TENSOR REMARK 3 L11: 0.3933 L22: 2.9399 REMARK 3 L33: 0.2151 L12: 0.3017 REMARK 3 L13: 0.2727 L23: 0.4951 REMARK 3 S TENSOR REMARK 3 S11: -0.1632 S12: 0.2567 S13: 0.0802 REMARK 3 S21: -0.1912 S22: 0.1591 S23: -0.5605 REMARK 3 S31: 0.1752 S32: 0.6784 S33: 0.0001 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 775 THROUGH 1014 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.1665 -22.9580 15.2794 REMARK 3 T TENSOR REMARK 3 T11: 0.9748 T22: 1.2679 REMARK 3 T33: 0.6625 T12: 0.1029 REMARK 3 T13: 0.0662 T23: 0.0036 REMARK 3 L TENSOR REMARK 3 L11: 3.0002 L22: 3.1007 REMARK 3 L33: 3.1134 L12: -0.0145 REMARK 3 L13: 0.0996 L23: 0.3494 REMARK 3 S TENSOR REMARK 3 S11: 0.0546 S12: 0.1075 S13: 0.0265 REMARK 3 S21: -0.5367 S22: -0.1499 S23: -0.2711 REMARK 3 S31: 0.0544 S32: 0.8191 S33: 0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -2 THROUGH 302 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.7266 28.1181 41.1323 REMARK 3 T TENSOR REMARK 3 T11: 0.5330 T22: 0.5103 REMARK 3 T33: 0.7693 T12: -0.0324 REMARK 3 T13: -0.0894 T23: -0.0138 REMARK 3 L TENSOR REMARK 3 L11: 0.9987 L22: 1.5040 REMARK 3 L33: 3.1930 L12: -0.1035 REMARK 3 L13: -0.5564 L23: -0.1341 REMARK 3 S TENSOR REMARK 3 S11: -0.0835 S12: -0.0044 S13: 0.0566 REMARK 3 S21: -0.0349 S22: 0.0370 S23: 0.1971 REMARK 3 S31: -0.0304 S32: 0.0018 S33: 0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 303 THROUGH 685 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.1354 14.3476 31.9438 REMARK 3 T TENSOR REMARK 3 T11: 0.7015 T22: 0.5183 REMARK 3 T33: 0.6964 T12: -0.0742 REMARK 3 T13: -0.0557 T23: 0.0096 REMARK 3 L TENSOR REMARK 3 L11: 1.5232 L22: 1.9079 REMARK 3 L33: 1.4006 L12: -0.1072 REMARK 3 L13: 0.2797 L23: 0.2689 REMARK 3 S TENSOR REMARK 3 S11: 0.0130 S12: 0.0977 S13: -0.1246 REMARK 3 S21: -0.0962 S22: 0.0294 S23: 0.1387 REMARK 3 S31: 0.2063 S32: -0.0791 S33: 0.0000 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 6YHK 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_1292107621. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-APR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.1 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 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38996 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 47.080 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 21.40 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 22.00 REMARK 200 R MERGE FOR SHELL (I) : 1.80500 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: MODELS OF N-TERMINAL AND C-TERMINAL DOMAINS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4 M AMMONIUM SULFATE, 0.13 M LITHIUM REMARK 280 ACETATE, 0.1 M HEPES/NAOH PH 7.1, VAPOR DIFFUSION, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y,-Z REMARK 290 8555 X,-Y,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 35.07650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 110.38050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 90.20800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 110.38050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.07650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 90.20800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 35.07650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 90.20800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 110.38050 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 90.20800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 35.07650 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 110.38050 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: 1760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -128.0 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 -3 REMARK 465 ASN A 430 REMARK 465 LYS A 431 REMARK 465 SER A 550 REMARK 465 VAL A 551 REMARK 465 GLU A 552 REMARK 465 LEU A 553 REMARK 465 PRO A 701 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 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 73 CG CD CE NZ REMARK 470 LYS A 192 CG CD CE NZ REMARK 470 LYS A 194 CG CD CE NZ REMARK 470 ASP A 425 CG OD1 OD2 REMARK 470 GLU A 439 CG CD OE1 OE2 REMARK 470 LYS A 440 CG CD CE NZ REMARK 470 ILE A 443 CG1 CG2 CD1 REMARK 470 LYS A 459 CG CD CE NZ REMARK 470 LYS A 469 CG CD CE NZ REMARK 470 GLU A 495 CG CD OE1 OE2 REMARK 470 GLU A 512 CG CD OE1 OE2 REMARK 470 PHE A 555 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 566 CG CD OE1 OE2 REMARK 470 ASP A 621 CG OD1 OD2 REMARK 470 GLU A 624 CG CD OE1 OE2 REMARK 470 ASN A 625 CG OD1 ND2 REMARK 470 GLU A 723 CG CD OE1 OE2 REMARK 470 ARG A 767 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 777 CG CD CE NZ REMARK 470 MET A 781 CG SD CE REMARK 470 LYS A 844 CG CD CE NZ REMARK 470 ARG A 872 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 875 CG CD OE1 OE2 REMARK 470 GLU A 886 CG CD OE1 OE2 REMARK 470 GLU A 911 CG CD OE1 OE2 REMARK 470 ASP A 984 CG OD1 OD2 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 HH11 ARG A 132 O3 SO4 A 1108 1.47 REMARK 500 HD21 ASN A 336 O HOH A 1203 1.51 REMARK 500 H GLY A 890 O2 SO4 A 1107 1.59 REMARK 500 OG SER A 893 O4 SO4 A 1107 2.00 REMARK 500 OG SER A 453 O2 SO4 A 1101 2.12 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 115 -155.37 -162.97 REMARK 500 ASP A 209 15.76 -145.54 REMARK 500 PHE A 402 -63.57 -103.24 REMARK 500 ILE A 428 107.02 -53.79 REMARK 500 ASN A 451 75.74 73.87 REMARK 500 ASN A 460 -72.73 -70.21 REMARK 500 TYR A 510 145.75 -170.59 REMARK 500 PHE A 528 74.64 -110.71 REMARK 500 PHE A 555 44.28 76.04 REMARK 500 PRO A 561 34.42 -96.80 REMARK 500 ASN A 586 60.32 -109.02 REMARK 500 LEU A 622 -75.25 -118.64 REMARK 500 ALA A 629 28.27 -165.69 REMARK 500 HIS A 654 -135.27 -146.66 REMARK 500 ASN A 738 -9.03 -57.53 REMARK 500 ASP A 770 153.15 73.28 REMARK 500 PHE A 787 46.87 -98.08 REMARK 500 ASN A 795 33.28 -144.03 REMARK 500 ASP A 810 -167.61 -115.41 REMARK 500 THR A 817 -58.47 -138.72 REMARK 500 THR A 825 164.68 66.26 REMARK 500 ARG A 838 58.01 -149.14 REMARK 500 GLU A 875 35.47 -81.58 REMARK 500 THR A 894 -72.84 -135.74 REMARK 500 GLU A 909 73.64 43.47 REMARK 500 ASP A 984 19.95 55.41 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 LEU A 622 GLU A 623 -146.92 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 SO4 A 1101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1107 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1108 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1109 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 1110 DBREF1 6YHK A 1 1014 UNP A0A0N9JNY6_YERPU DBREF2 6YHK A A0A0N9JNY6 1 1014 SEQADV 6YHK GLY A -3 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHK GLY A -2 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHK GLY A -1 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHK ARG A 0 UNP A0A0N9JNY EXPRESSION TAG SEQADV 6YHK SER A 866 UNP A0A0N9JNY CYS 866 ENGINEERED MUTATION SEQRES 1 A 1018 GLY GLY GLY ARG MET LYS ASN GLN TRP GLN HIS GLN TYR SEQRES 2 A 1018 PHE LEU SER TYR SER GLU LEU VAL ALA ASN PHE PRO SER SEQRES 3 A 1018 PRO GLU LYS VAL VAL SER ASP TYR ILE LYS HIS LYS PHE SEQRES 4 A 1018 SER THR THR LEU PRO TRP PHE GLY TRP ALA ASP PRO ASP SEQRES 5 A 1018 ASN LEU TYR PHE ILE ARG PHE THR GLN SER ARG SER ASN SEQRES 6 A 1018 ASN LYS SER TYR THR GLY TRP ASP HIS LEU GLY LYS TYR SEQRES 7 A 1018 ALA ILE GLU THR LEU THR LEU THR GLN ALA ALA ILE VAL SEQRES 8 A 1018 ASN ILE GLY SER ARG PHE ASP ILE PHE ASP GLU ALA ASN SEQRES 9 A 1018 SER THR ALA GLY ILE TYR LYS THR ASN ASN ALA ASP SER SEQRES 10 A 1018 PHE ASP GLU THR ASN GLU ALA LYS MET LEU PRO SER GLU SEQRES 11 A 1018 TYR LEU TYR PHE LEU ARG ASP CYS ASP PHE SER ASN LEU SEQRES 12 A 1018 TYR ASN LYS ALA LEU SER ASP TYR TRP ALA GLU ASN TYR SEQRES 13 A 1018 GLU LYS PHE SER THR LEU LEU GLN ASN TYR TYR ILE SER SEQRES 14 A 1018 SER ALA TYR TYR LEU TYR LYS ASP SER ALA ILE SER LYS SEQRES 15 A 1018 ASP GLU TYR GLU PHE SER ILE ASP ALA ILE PHE ASN LYS SEQRES 16 A 1018 LYS ASN LYS ILE LEU ARG TYR TYR PHE ASP VAL TYR GLY SEQRES 17 A 1018 TYR TYR SER SER ASP MET PHE VAL ALA MET ASN ASP ASN SEQRES 18 A 1018 LYS THR MET LEU PHE ILE PRO GLY ALA THR ASN PRO PHE SEQRES 19 A 1018 ILE PHE ALA ASP ASN ILE THR ASP LEU ARG ASP LYS ILE SEQRES 20 A 1018 LYS ALA LEU ILE SER ASP LYS ASN THR ARG GLU LEU PHE SEQRES 21 A 1018 SER LYS HIS PHE SER LEU TYR ASP ARG GLN ASP GLY ASN SEQRES 22 A 1018 THR TYR LEU GLY VAL ASN SER MET LEU GLU GLN ILE VAL SEQRES 23 A 1018 SER GLY VAL VAL ASP THR ASN TYR ILE MET TYR SER ASN SEQRES 24 A 1018 LYS ASN ILE ARG GLU ARG ASN VAL PHE GLU SER MET ALA SEQRES 25 A 1018 PHE SER THR ARG GLU ARG SER PHE ASN ASP GLY ASP VAL SEQRES 26 A 1018 ILE ILE LYS SER ASN ALA GLU VAL GLN ARG ASP TYR ALA SEQRES 27 A 1018 LEU ASN VAL LEU GLN THR ILE LEU SER LEU SER PRO ILE SEQRES 28 A 1018 PHE ASP ILE VAL LEU PRO GLU VAL SER ILE PRO ILE SER SEQRES 29 A 1018 LEU GLY ILE THR ALA SER SER VAL GLY ILE SER PHE ASP SEQRES 30 A 1018 GLU LEU ILE ASN GLY ASP THR TYR GLU GLU ARG ARG SER SEQRES 31 A 1018 ALA ILE PRO GLY LEU ALA THR ASN ALA VAL LEU LEU GLY SEQRES 32 A 1018 ILE SER PHE ALA ILE PRO PHE LEU ILE SER LYS ALA GLU SEQRES 33 A 1018 GLU ASN LYS LEU ILE ILE ASN ASN LEU VAL GLY SER ASP SEQRES 34 A 1018 GLU ASN ILE LEU ASN LYS ASN ASN LEU GLY ASP PHE LEU SEQRES 35 A 1018 GLU LYS TYR ASN ILE SER GLU SER ASP ILE PRO GLU ASN SEQRES 36 A 1018 GLY SER LEU VAL ILE ASN LEU LYS ASN THR ASN VAL PRO SEQRES 37 A 1018 VAL ARG LEU VAL LYS LEU ASN ASP GLU GLU GLY GLU ILE SEQRES 38 A 1018 VAL ALA ILE LYS GLY SER THR LEU SER GLY ILE TYR TYR SEQRES 39 A 1018 GLU VAL ASP THR GLU THR GLY TYR GLU ILE LEU SER ARG SEQRES 40 A 1018 ARG VAL PHE ARG THR GLU TYR ASN GLU LYS ILE TYR TRP SEQRES 41 A 1018 THR ARG GLY GLY GLY LEU LYS GLY GLY GLN PRO PHE ASN SEQRES 42 A 1018 PHE GLU GLY LEU ASP ILE PRO VAL TYR PHE ILE ASP LYS SEQRES 43 A 1018 PRO TYR SER GLU LEU ALA SER SER VAL GLU LEU SER PHE SEQRES 44 A 1018 VAL ASN ASP ASP SER PRO LEU LEU PHE PRO GLU MET ASP SEQRES 45 A 1018 SER ARG LEU PRO LYS PRO THR PRO GLU LEU ASP ILE LYS SEQRES 46 A 1018 TYR TYR SER SER ASN LEU SER SER PHE LYS GLU ASP THR SEQRES 47 A 1018 VAL ILE LEU MET ARG GLY THR THR GLU GLU GLU ALA TRP SEQRES 48 A 1018 ASN ILE ALA ASN TYR LYS THR ALA GLY GLY SER ASN LYS SEQRES 49 A 1018 ASP LEU GLU GLU ASN PHE ILE GLU ALA GLY PRO GLN PHE SEQRES 50 A 1018 ASN LEU SER PHE SER GLU TYR THR SER SER ILE ASN SER SEQRES 51 A 1018 ALA ASP THR ALA SER ARG LYS HIS PHE LEU VAL ILE ILE SEQRES 52 A 1018 LYS VAL GLN VAL LYS TYR ILE SER ASN ASP ASN VAL LEU SEQRES 53 A 1018 TYR ALA ASN HIS TRP ALA ILE PRO ASP GLU ALA PRO VAL SEQRES 54 A 1018 GLU VAL LEU ALA VAL VAL ASP ARG ARG PHE ILE PHE PRO SEQRES 55 A 1018 GLU PRO PRO VAL LYS PRO LYS LEU SER PHE ILE GLN LYS SEQRES 56 A 1018 ILE ALA ASN ARG PHE LEU THR GLU ASN VAL ALA GLU ILE SEQRES 57 A 1018 SER SER ILE ASN PHE ARG ARG LEU ASN SER GLY ASN ILE SEQRES 58 A 1018 ASN VAL LEU LYS GLY ARG GLY VAL PHE SER SER ARG ARG SEQRES 59 A 1018 LEU ARG GLU ILE TYR LEU ARG PHE ASP ALA ALA ASN ALA SEQRES 60 A 1018 ASP GLU LEU ARG PRO GLY ASP VAL TYR VAL LYS LYS THR SEQRES 61 A 1018 LYS PHE ASP SER MET GLY TYR ASP SER HIS PHE TYR ASN SEQRES 62 A 1018 GLU GLY ILE GLY ILE ASN GLY ALA PRO THR LEU ASN THR SEQRES 63 A 1018 TYR THR GLY GLU TYR VAL ALA ASP SER SER SER GLN GLY SEQRES 64 A 1018 ALA THR TYR TRP LEU LYS TYR ASN LEU THR ASN GLU THR SEQRES 65 A 1018 SER ILE ILE LYS VAL SER ASN SER ALA ARG GLY ALA ASN SEQRES 66 A 1018 GLY ILE LYS ILE ALA LEU GLU GLU ILE GLU GLU ASN LYS SEQRES 67 A 1018 PRO VAL VAL ILE THR SER GLY THR LEU THR GLY SER THR SEQRES 68 A 1018 VAL VAL PHE ALA ARG LYS GLY GLU TYR PHE TYR ALA VAL SEQRES 69 A 1018 HIS THR GLY ASN SER GLU SER LEU ILE GLY PHE THR SER SEQRES 70 A 1018 THR SER GLY VAL ALA LYS ALA ILE GLU VAL LEU SER SER SEQRES 71 A 1018 LEU SER GLU LEU GLU VAL PRO ALA LEU PRO ASP VAL ILE SEQRES 72 A 1018 ASN ASN ASN THR LEU VAL GLU TYR LEU SER ASP ASN PHE SEQRES 73 A 1018 ASP SER ALA LEU ILE SER TYR SER SER SER SER LEU LYS SEQRES 74 A 1018 PRO ASN SER MET ILE ASN ILE SER ARG GLU ASN VAL SER SEQRES 75 A 1018 THR PHE SER TYR TYR THR ASP ASP ILE GLN LEU PRO SER SEQRES 76 A 1018 PHE GLY THR SER VAL THR ILE LEU VAL ARG THR ASN ASP SEQRES 77 A 1018 ASN THR VAL VAL ARG SER LEU SER GLU SER TYR THR MET SEQRES 78 A 1018 ASN SER ASN SER SER LYS MET VAL VAL PHE ASN VAL LEU SEQRES 79 A 1018 GLN LYS ASP PHE HET SO4 A1101 5 HET SO4 A1102 5 HET SO4 A1103 5 HET SO4 A1104 5 HET SO4 A1105 5 HET SO4 A1106 5 HET SO4 A1107 5 HET SO4 A1108 5 HET SO4 A1109 5 HET CL A1110 1 HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION FORMUL 2 SO4 9(O4 S 2-) FORMUL 11 CL CL 1- FORMUL 12 HOH *56(H2 O) HELIX 1 AA1 GLN A 4 ASN A 19 1 16 HELIX 2 AA2 SER A 22 SER A 36 1 15 HELIX 3 AA3 LEU A 81 VAL A 87 1 7 HELIX 4 AA4 ASN A 88 PHE A 93 5 6 HELIX 5 AA5 ILE A 95 ASP A 97 5 3 HELIX 6 AA6 GLU A 98 THR A 102 1 5 HELIX 7 AA7 LEU A 123 ASP A 133 1 11 HELIX 8 AA8 ASP A 135 ASP A 173 1 39 HELIX 9 AA9 SER A 177 ALA A 187 1 11 HELIX 10 AB1 ASN A 235 SER A 248 1 14 HELIX 11 AB2 ASP A 249 LYS A 258 1 10 HELIX 12 AB3 SER A 261 GLN A 266 1 6 HELIX 13 AB4 GLY A 273 SER A 283 1 11 HELIX 14 AB5 ASP A 287 ILE A 291 5 5 HELIX 15 AB6 ASN A 302 SER A 325 1 24 HELIX 16 AB7 ASP A 332 VAL A 337 5 6 HELIX 17 AB8 LEU A 338 SER A 343 1 6 HELIX 18 AB9 ILE A 357 GLY A 362 5 6 HELIX 19 AC1 PHE A 372 GLY A 378 1 7 HELIX 20 AC2 TYR A 381 ILE A 388 1 8 HELIX 21 AC3 VAL A 396 SER A 401 1 6 HELIX 22 AC4 PHE A 402 GLY A 423 1 22 HELIX 23 AC5 ASN A 433 TYR A 441 1 9 HELIX 24 AC6 SER A 444 ILE A 448 5 5 HELIX 25 AC7 PRO A 543 LEU A 547 5 5 HELIX 26 AC8 PRO A 576 ASN A 586 1 11 HELIX 27 AC9 ASN A 586 LYS A 591 1 6 HELIX 28 AD1 THR A 602 LYS A 613 1 12 HELIX 29 AD2 SER A 643 ARG A 652 1 10 HELIX 30 AD3 LYS A 664 ILE A 666 5 3 HELIX 31 AD4 GLU A 719 SER A 734 1 16 HELIX 32 AD5 ASN A 736 LYS A 741 5 6 HELIX 33 AD6 ASP A 784 HIS A 786 5 3 HELIX 34 AD7 GLU A 848 ILE A 850 5 3 HELIX 35 AD8 THR A 894 SER A 908 1 15 HELIX 36 AD9 ASN A 920 PHE A 932 1 13 HELIX 37 AE1 LYS A 945 MET A 949 5 5 SHEET 1 AA1 3 ALA A 75 THR A 80 0 SHEET 2 AA1 3 TYR A 51 PHE A 55 -1 N ARG A 54 O GLU A 77 SHEET 3 AA1 3 ALA A 103 TYR A 106 -1 O TYR A 106 N TYR A 51 SHEET 1 AA2 3 ARG A 59 SER A 60 0 SHEET 2 AA2 3 TRP A 68 LEU A 71 -1 O ASP A 69 N ARG A 59 SHEET 3 AA2 3 SER A 113 PHE A 114 -1 O PHE A 114 N HIS A 70 SHEET 1 AA3 4 LEU A 196 VAL A 202 0 SHEET 2 AA3 4 TYR A 205 MET A 214 -1 O SER A 207 N PHE A 200 SHEET 3 AA3 4 THR A 219 PHE A 222 -1 O PHE A 222 N PHE A 211 SHEET 4 AA3 4 PHE A 230 ALA A 233 -1 O ILE A 231 N LEU A 221 SHEET 1 AA4 2 THR A 364 SER A 366 0 SHEET 2 AA4 2 GLY A 369 SER A 371 -1 O SER A 371 N THR A 364 SHEET 1 AA5 6 LEU A 454 ASN A 457 0 SHEET 2 AA5 6 PRO A 464 LYS A 469 -1 O LEU A 467 N LEU A 454 SHEET 3 AA5 6 ILE A 477 GLY A 482 -1 O ILE A 480 N ARG A 466 SHEET 4 AA5 6 ILE A 488 VAL A 492 -1 O TYR A 490 N LYS A 481 SHEET 5 AA5 6 GLU A 499 TYR A 510 -1 O ILE A 500 N GLU A 491 SHEET 6 AA5 6 LYS A 513 THR A 517 -1 O THR A 517 N PHE A 506 SHEET 1 AA6 4 TYR A 538 ILE A 540 0 SHEET 2 AA6 4 GLU A 686 ASP A 692 1 O ASP A 692 N PHE A 539 SHEET 3 AA6 4 PHE A 655 GLN A 662 -1 N LYS A 660 O GLU A 686 SHEET 4 AA6 4 THR A 594 THR A 601 -1 N ARG A 599 O VAL A 657 SHEET 1 AA7 2 PHE A 637 THR A 641 0 SHEET 2 AA7 2 HIS A 676 PRO A 680 -1 O ILE A 679 N SER A 638 SHEET 1 AA8 7 TYR A 772 LYS A 774 0 SHEET 2 AA8 7 ASP A 759 ASP A 764 -1 N ALA A 760 O LYS A 774 SHEET 3 AA8 7 ARG A 838 ALA A 846 -1 O ALA A 840 N ALA A 763 SHEET 4 AA8 7 TYR A 876 ASN A 884 -1 O HIS A 881 N ASN A 841 SHEET 5 AA8 7 THR A 867 LYS A 873 -1 N THR A 867 O THR A 882 SHEET 6 AA8 7 SER A 934 SER A 940 -1 O SER A 938 N VAL A 868 SHEET 7 AA8 7 VAL A 957 TYR A 963 1 O SER A 958 N ALA A 935 SHEET 1 AA9 2 TYR A 788 ASN A 789 0 SHEET 2 AA9 2 ALA A 797 PRO A 798 -1 O ALA A 797 N ASN A 789 SHEET 1 AB1 6 LEU A 800 THR A 804 0 SHEET 2 AB1 6 SER A 829 VAL A 833 -1 O ILE A 830 N TYR A 803 SHEET 3 AB1 6 VAL A 856 THR A 859 1 O THR A 859 N VAL A 833 SHEET 4 AB1 6 SER A 971 THR A 982 -1 O LEU A 979 N VAL A 856 SHEET 5 AB1 6 ASN A 985 MET A 997 -1 O ASN A 985 N THR A 982 SHEET 6 AB1 6 MET A1004 ASP A1013 -1 O PHE A1007 N SER A 994 CISPEP 1 LEU A 39 PRO A 40 0 0.46 CISPEP 2 PHE A 564 PRO A 565 0 2.11 SITE 1 AC1 3 SER A 453 ARG A 507 ILE A 514 SITE 1 AC2 4 SER A 643 ASN A 645 ASN A 675 HOH A1201 SITE 1 AC3 4 GLN A 330 ARG A 331 ASP A 332 ASN A 377 SITE 1 AC4 4 TYR A 13 SER A 14 SER A 356 ASN A 414 SITE 1 AC5 3 TRP A 68 ASN A 736 ARG A 989 SITE 1 AC6 5 SER A 747 SER A 812 LYS A 832 GLY A 861 SITE 2 AC6 5 THR A 862 SITE 1 AC7 7 ILE A 889 GLY A 890 PHE A 891 THR A 892 SITE 2 AC7 7 SER A 893 LYS A 945 HOH A1211 SITE 1 AC8 4 TYR A 129 ARG A 132 ARG A 730 HOH A1230 SITE 1 AC9 2 ILE A 792 GLY A 793 SITE 1 AD1 3 ARG A 466 LYS A 481 GLY A 482 CRYST1 70.153 180.416 220.761 90.00 90.00 90.00 I 21 21 21 8 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 0.014255 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005543 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004530 0.00000