HEADER TOXIN 01-SEP-17 6AVC TITLE EXPLORING CYSTINE DENSE PEPTIDE SPACE TO OPEN A UNIQUE MOLECULAR TITLE 2 TOOLBOX COMPND MOL_ID: 1; COMPND 2 MOLECULE: POTASSIUM CHANNEL TOXIN ALPHA-KTX 1.5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 21-57; COMPND 5 SYNONYM: BMTX1,NEUROTOXIN TX1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MESOBUTHUS MARTENSII; SOURCE 3 ORGANISM_COMMON: MANCHURIAN SCORPION; SOURCE 4 ORGANISM_TAXID: 34649; SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 7 EXPRESSION_SYSTEM_CELL: HEK-293F KEYWDS KNOTTINS, CYSTINE KNOT, TOXINS, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR M.M.GEWE,P.RUPERT,R.K.STRONG REVDAT 3 04-OCT-23 6AVC 1 REMARK REVDAT 2 14-MAR-18 6AVC 1 JRNL REVDAT 1 28-FEB-18 6AVC 0 JRNL AUTH C.E.CORRENTI,M.M.GEWE,C.MEHLIN,A.D.BANDARANAYAKE, JRNL AUTH 2 W.A.JOHNSEN,P.B.RUPERT,M.Y.BRUSNIAK,M.CLARKE,S.E.BURKE, JRNL AUTH 3 W.DE VAN DER SCHUEREN,K.PILAT,S.M.TURNBAUGH,D.MAY,A.WATSON, JRNL AUTH 4 M.K.CHAN,C.D.BAHL,J.M.OLSON,R.K.STRONG JRNL TITL SCREENING, LARGE-SCALE PRODUCTION AND STRUCTURE-BASED JRNL TITL 2 CLASSIFICATION OF CYSTINE-DENSE PEPTIDES. JRNL REF NAT. STRUCT. MOL. BIOL. V. 25 270 2018 JRNL REFN ESSN 1545-9985 JRNL PMID 29483648 JRNL DOI 10.1038/S41594-018-0033-9 REMARK 2 REMARK 2 RESOLUTION. 1.88 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.63 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 85.8 REMARK 3 NUMBER OF REFLECTIONS : 2443 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 131 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.88 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.93 REMARK 3 REFLECTION IN BIN (WORKING SET) : 83 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 41.51 REMARK 3 BIN R VALUE (WORKING SET) : 0.1700 REMARK 3 BIN FREE R VALUE SET COUNT : 5 REMARK 3 BIN FREE R VALUE : 0.2120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 272 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 37 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.31000 REMARK 3 B22 (A**2) : 0.31000 REMARK 3 B33 (A**2) : -0.99000 REMARK 3 B12 (A**2) : 0.15000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.164 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.171 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.092 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.117 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 280 ; 0.020 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 254 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 374 ; 1.611 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): 596 ; 0.785 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 36 ; 7.691 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 8 ;40.813 ;23.750 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 53 ;17.023 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 1 ;44.922 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 37 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 300 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 53 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 147 ; 1.818 ; 2.117 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 146 ; 1.809 ; 2.107 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 182 ; 2.681 ; 3.528 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 183 ; 2.681 ; 3.539 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 133 ; 2.683 ; 2.505 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 134 ; 2.673 ; 2.515 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 193 ; 4.014 ; 4.045 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 305 ; 6.519 ;19.913 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 297 ; 5.649 ;18.865 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 38 REMARK 3 ORIGIN FOR THE GROUP (A): -3.2738 16.1274 2.2420 REMARK 3 T TENSOR REMARK 3 T11: 0.0085 T22: 0.0432 REMARK 3 T33: 0.0355 T12: 0.0011 REMARK 3 T13: -0.0040 T23: -0.0036 REMARK 3 L TENSOR REMARK 3 L11: 2.4889 L22: 2.3058 REMARK 3 L33: 6.7046 L12: 0.4003 REMARK 3 L13: -2.2434 L23: 0.5442 REMARK 3 S TENSOR REMARK 3 S11: 0.0226 S12: -0.1085 S13: -0.0207 REMARK 3 S21: 0.0411 S22: -0.0305 S23: -0.1138 REMARK 3 S31: 0.1355 S32: 0.3640 S33: 0.0079 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6AVC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1000229893. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2578 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.880 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.2 REMARK 200 DATA REDUNDANCY : 57.70 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 59.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.88 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 38.0 REMARK 200 DATA REDUNDANCY IN SHELL : 40.40 REMARK 200 R MERGE FOR SHELL (I) : 0.41500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 16.20 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: 1C49 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM NA MALONATE PH 7, 17% PEG 3350, REMARK 280 PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.38533 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 10.69267 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 10.69267 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 21.38533 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 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 1 REMARK 465 SER A 39 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 SER A 2 OG REMARK 470 GLN A 3 CG CD OE1 NE2 REMARK 470 PHE A 4 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASN A 27 CG OD1 ND2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6ATL RELATED DB: PDB REMARK 900 RELATED ID: 6ATM RELATED DB: PDB REMARK 900 RELATED ID: 6ATN RELATED DB: PDB REMARK 900 RELATED ID: 6ATS RELATED DB: PDB REMARK 900 RELATED ID: 6ATU RELATED DB: PDB REMARK 900 RELATED ID: 6ATW RELATED DB: PDB REMARK 900 RELATED ID: 6ATY RELATED DB: PDB REMARK 900 RELATED ID: 6AU7 RELATED DB: PDB REMARK 900 RELATED ID: 6AUP RELATED DB: PDB REMARK 900 RELATED ID: 6AV8 RELATED DB: PDB REMARK 900 RELATED ID: 6AVA RELATED DB: PDB DBREF 6AVC A 3 39 UNP Q9NII6 KAX15_MESMA 21 57 SEQADV 6AVC GLY A 1 UNP Q9NII6 EXPRESSION TAG SEQADV 6AVC SER A 2 UNP Q9NII6 EXPRESSION TAG SEQRES 1 A 39 GLY SER GLN PHE THR ASP VAL LYS CYS THR GLY SER LYS SEQRES 2 A 39 GLN CYS TRP PRO VAL CYS LYS GLN MET PHE GLY LYS PRO SEQRES 3 A 39 ASN GLY LYS CYS MET ASN GLY LYS CYS ARG CYS TYR SER FORMUL 2 HOH *37(H2 O) HELIX 1 AA1 GLY A 11 LYS A 13 5 3 HELIX 2 AA2 GLN A 14 GLY A 24 1 11 SHEET 1 AA1 3 GLN A 3 LYS A 8 0 SHEET 2 AA1 3 LYS A 34 CYS A 37 -1 O CYS A 37 N GLN A 3 SHEET 3 AA1 3 GLY A 28 MET A 31 -1 N MET A 31 O LYS A 34 SSBOND 1 CYS A 9 CYS A 30 1555 1555 2.09 SSBOND 2 CYS A 15 CYS A 35 1555 1555 2.06 SSBOND 3 CYS A 19 CYS A 37 1555 1555 2.09 CRYST1 43.454 43.454 32.078 90.00 90.00 120.00 P 32 2 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 0.023013 0.013286 0.000000 0.00000 SCALE2 0.000000 0.026573 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031174 0.00000