PDB Short entry for 6ATW HEADER TOXIN 29-AUG-17 6ATW TITLE EXPLORING CYSTINE DENSE PEPTIDE SPACE TO OPEN A UNIQUE MOLECULAR TITLE 2 TOOLBOX COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHLOROTOXIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CLTX; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEIURUS QUINQUESTRIATUS QUINQUESTRIATUS; SOURCE 3 ORGANISM_COMMON: EGYPTIAN SCORPION; SOURCE 4 ORGANISM_TAXID: 6885; 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 2 14-MAR-18 6ATW 1 JRNL REVDAT 1 28-FEB-18 6ATW 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. 1.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0155 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) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.02 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 87.9 REMARK 3 NUMBER OF REFLECTIONS : 3857 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) : 0.136 REMARK 3 R VALUE (WORKING SET) : 0.133 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 196 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) : 1.53 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 52 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 16.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.2270 REMARK 3 BIN FREE R VALUE SET COUNT : 3 REMARK 3 BIN FREE R VALUE : 0.3320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 279 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 55 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.52 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : -0.02000 REMARK 3 B12 (A**2) : 0.00000 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): 0.081 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.087 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.040 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.065 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 299 ; 0.016 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 272 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 400 ; 1.556 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): 638 ; 0.758 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 41 ; 7.501 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 11 ;27.923 ;21.818 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 59 ;13.945 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 3 ;22.270 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 37 ; 0.115 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 339 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 66 ; 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): 155 ; 1.096 ; 0.781 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 154 ; 1.081 ; 0.779 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 193 ; 1.624 ; 1.747 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 194 ; 1.627 ; 1.750 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 144 ; 2.424 ; 1.019 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 144 ; 2.420 ; 1.018 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 205 ; 3.878 ; 2.157 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 339 ; 5.571 ;16.871 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 324 ; 5.183 ;15.455 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 : NULL 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 6ATW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1000229829. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAR-16 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 : 7263 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530 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 (%) : 86.9 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 10.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.12600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 28.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.1 M NA MALONATE PH 7.0, 0.1 M HEPES REMARK 280 PH 7.0, 0.5 % JEFFAMINE ED-2001 PH 7.0, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 298K 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 11.26950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 24.02000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 13.15600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 24.02000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 11.26950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 13.15600 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 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 DBREF 6ATW A 1 36 UNP P45639 CTXL_LEIQU 1 36 SEQADV 6ATW GLY A -1 UNP P45639 EXPRESSION TAG SEQADV 6ATW SER A 0 UNP P45639 EXPRESSION TAG SEQRES 1 A 38 GLY SER MET CYS MET PRO CYS PHE THR THR ASP HIS GLN SEQRES 2 A 38 MET ALA ARG LYS CYS ASP ASP CYS CYS GLY GLY LYS GLY SEQRES 3 A 38 ARG GLY LYS CYS TYR GLY PRO GLN CYS LEU CYS ARG FORMUL 2 HOH *55(H2 O) HELIX 1 AA1 GLN A 11 GLY A 21 1 11 SHEET 1 AA1 3 MET A 3 PRO A 4 0 SHEET 2 AA1 3 GLN A 32 CYS A 35 -1 O CYS A 33 N MET A 3 SHEET 3 AA1 3 GLY A 26 TYR A 29 -1 N LYS A 27 O LEU A 34 SSBOND 1 CYS A 2 CYS A 19 1555 1555 2.05 SSBOND 2 CYS A 5 CYS A 28 1555 1555 2.09 SSBOND 3 CYS A 16 CYS A 33 1555 1555 2.06 SSBOND 4 CYS A 20 CYS A 35 1555 1555 2.03 CRYST1 22.539 26.312 48.040 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 0.044368 0.000000 0.000000 0.00000 SCALE2 0.000000 0.038005 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020816 0.00000