HEADER TOXIN 31-MAR-20 6YHY TITLE A LID BLOCKING MECHANISM OF A CONE SNAIL TOXIN REVEALED AT THE ATOMIC TITLE 2 LEVEL COMPND MOL_ID: 1; COMPND 2 MOLECULE: CONK-S1; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CONUS CONSORS; SOURCE 3 ORGANISM_TAXID: 101297; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CONK-S1, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR C.SAIKIA,H.ALTMAN-GUETA,O.DYM,F.FROLOW,M.GUREVITZ,D.GORDON,E.REUVENY, AUTHOR 2 I.KARBAT REVDAT 3 24-JAN-24 6YHY 1 REMARK REVDAT 2 27-OCT-21 6YHY 1 TITLE COMPND SOURCE JRNL REVDAT 2 2 1 DBREF SEQADV REVDAT 1 14-APR-21 6YHY 0 JRNL AUTH C.SAIKIA,O.DYM,H.ALTMAN-GUETA,D.GORDON,E.REUVENY,I.KARBAT JRNL TITL A MOLECULAR LID MECHANISM OF K + CHANNEL BLOCKER ACTION JRNL TITL 2 REVEALED BY A CONE PEPTIDE. JRNL REF J.MOL.BIOL. V. 433 66957 2021 JRNL REFN ESSN 1089-8638 JRNL PMID 33771569 JRNL DOI 10.1016/J.JMB.2021.166957 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 33433 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1686 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 19.1300 - 3.5500 0.94 2550 134 0.1573 0.1748 REMARK 3 2 3.5500 - 2.8200 0.98 2649 151 0.1843 0.2049 REMARK 3 3 2.8200 - 2.4600 0.99 2707 124 0.1943 0.2444 REMARK 3 4 2.4600 - 2.2400 0.98 2661 138 0.1963 0.3045 REMARK 3 5 2.2400 - 2.0800 0.98 2657 141 0.1918 0.2408 REMARK 3 6 2.0800 - 1.9600 0.98 2692 132 0.1848 0.2189 REMARK 3 7 1.9600 - 1.8600 0.98 2635 151 0.1963 0.2088 REMARK 3 8 1.8600 - 1.7800 0.98 2688 144 0.2167 0.2488 REMARK 3 9 1.7800 - 1.7100 0.98 2631 137 0.2378 0.2747 REMARK 3 10 1.7100 - 1.6500 0.98 2654 156 0.2594 0.2881 REMARK 3 11 1.6500 - 1.6000 0.98 2668 117 0.2780 0.3210 REMARK 3 12 1.6000 - 1.5500 0.94 2555 161 0.2942 0.3360 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.32 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 : NULL 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 6YHY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1292107651. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35688 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 19.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.02800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.2600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.41330 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.300 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: 1Y62 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.100M SODIUM CITRATE TRIBASIC REMARK 280 DIHYDRATE PH 5.6 20.00% V/V ISOPROPANOL 20.00% W/V POLYETHYLENE REMARK 280 GLYCOL 4,000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K 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 20.88800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.07450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.14250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.07450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.88800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.14250 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 GLN A 40 CD OE1 NE2 REMARK 470 ARG A 55 CD NE CZ NH1 NH2 REMARK 470 ASP B 2 CG OD1 OD2 REMARK 470 LYS B 18 CE NZ REMARK 470 GLU B 20 CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER B 19 73.33 40.11 REMARK 500 ASN B 46 105.33 -162.60 REMARK 500 REMARK 500 REMARK: NULL DBREF 6YHY A 2 60 PDB 6YHY 6YHY 2 60 DBREF 6YHY B 2 60 PDB 6YHY 6YHY 2 60 SEQRES 1 A 59 ASP ARG PRO SER TYR CYS ASN LEU PRO ALA ASP SER GLY SEQRES 2 A 59 SER GLY THR LYS SER GLU GLN ARG ILE TYR TYR ASN SER SEQRES 3 A 59 ALA ARG LYS GLN CYS LEU THR PHE THR TYR ASN GLY GLN SEQRES 4 A 59 GLY GLY ASN GLU ASN ASN PHE ARG ARG THR TYR ASP CYS SEQRES 5 A 59 ARG ARG THR CYS GLN TYR PRO SEQRES 1 B 59 ASP ARG PRO SER TYR CYS ASN LEU PRO ALA ASP SER GLY SEQRES 2 B 59 SER GLY THR LYS SER GLU GLN ARG ILE TYR TYR ASN SER SEQRES 3 B 59 ALA ARG LYS GLN CYS LEU THR PHE THR TYR ASN GLY GLN SEQRES 4 B 59 GLY GLY ASN GLU ASN ASN PHE ARG ARG THR TYR ASP CYS SEQRES 5 B 59 ARG ARG THR CYS GLN TYR PRO FORMUL 3 HOH *80(H2 O) HELIX 1 AA1 PRO A 4 LEU A 9 5 6 HELIX 2 AA2 ARG A 49 CYS A 57 1 9 HELIX 3 AA3 PRO B 4 LEU B 9 5 6 HELIX 4 AA4 ARG B 49 CYS B 57 1 9 SHEET 1 AA1 2 GLU A 20 ASN A 26 0 SHEET 2 AA1 2 GLN A 31 TYR A 37 -1 O GLN A 31 N ASN A 26 SHEET 1 AA2 2 GLU B 20 ASN B 26 0 SHEET 2 AA2 2 GLN B 31 TYR B 37 -1 O TYR B 37 N GLU B 20 SSBOND 1 CYS A 7 CYS A 57 1555 1555 2.06 SSBOND 2 CYS A 32 CYS A 53 1555 1555 2.13 SSBOND 3 CYS B 7 CYS B 57 1555 1555 2.06 SSBOND 4 CYS B 32 CYS B 53 1555 1555 2.10 CRYST1 41.776 52.285 56.149 90.00 90.00 90.00 P 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 0.023937 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019126 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017810 0.00000