HEADER TOXIN 21-NOV-16 5MG9 TITLE PUTATIVE ANCESTRAL MAMBA TOXIN 1 (ANCTX1-W28R/I38S) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANCTX1-W28R/I38S; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TOXIN ADTX1,RHO-ELAPITOXIN-DA1A,RHO-EPTX-DA1A; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: PUTATIVE ANCETRAL MAMBA TOXIN, RESIDUES 1 TO 6 (LEU COMPND 7 THR CYS VAL LYS SER ) MATCH TO UNP Q8QGR0 NXM11_DENAN 22 TO 28, COMPND 8 RESIDUES 7 TO 11 (LYS SER ILE PHE GLY ) MATCH TO UNP P85092 COMPND 9 TXAD1_DENAN 7 TO 11, RESIDUES 12 TO 17 (VAL THR THR GLU ASP CYS ) COMPND 10 MATCH TO UNP P18328 TXM2_DENAN 12 TO 17, RESIDUES 18 TO 26 (PRO ASP COMPND 11 GLY GLN ASN LEU CYS PHE LYS ) MATCH TO UNP P81030 TXM1_DENAN 18 TO COMPND 12 26, RESIDUES 27 TO 31 (ARG ARG HIS TYR ILE ) MATCH TO UNP P86419 COMPND 13 3SI1B_DENAN 27 TO 31, RESIDUES 32 TO 34 (VAL PRO LYS ) MATCH TO UNP COMPND 14 P85092 TXAD1_DENAN 32 TO 34, RESIDUES 35 TO 37 (MET TYR ASP ) MATCH COMPND 15 TO UNP Q8QGR0 NXM11_DENAN 56 TO 58, RESIDUES 38 TO 48 (SER THR ARG COMPND 16 GLY CYS ALA ALA THR CYS PRO ILE ) MATCH TO UNP P85092 TXAD1_DENAN 38 COMPND 17 TO 48, RESIDUES 49 TO 50 (ALA GLU ) MATCH TO UNP Q8QGR0 NXM11_DENAN COMPND 18 61 TO 62, RESIDUES 51 TO 54 (ASN ARG ASP VAL ) MATCH TO UNP P82462 COMPND 19 3SUC1_NAJKA 51 TO 54, RESIDUES 55 TO 58 (ILE HIS CYS CYS ) MATCH TO COMPND 20 UNP P85092 TXAD1_DENAN 55 TO 58, RESIDUES 59 TO 62 (GLY THR ASP LYS ) COMPND 21 MATCH TO UNP P18328 TXM2_DENAN 59 TO 62, RESIDUES 63 TO 65 (CYS ASN COMPND 22 GLU ) MATCH TO UNP P85092 TXAD1_DENAN 63 TO 65, SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: DENDROASPIS ANGUSTICEPS; SOURCE 4 ORGANISM_COMMON: EASTERN GREEN MAMBA; SOURCE 5 ORGANISM_TAXID: 8618 KEYWDS ANCESTRAL MAMBA SNAKE TOXIN, THREE-FINGER FOLD, ANCESTRAL TOXIN KEYWDS 2 RESURRECTION AND ENGINEERING, AMINERGIC TOXIN, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR E.A.STURA,L.TEPSHI,G.BLANCHET,G.MOURIER,D.SERVENT REVDAT 3 17-JAN-24 5MG9 1 REMARK REVDAT 2 14-JUN-17 5MG9 1 JRNL REVDAT 1 03-MAY-17 5MG9 0 JRNL AUTH G.BLANCHET,D.ALILI,A.PROTTE,G.UPERT,N.GILLES,L.TEPSHI, JRNL AUTH 2 E.A.STURA,G.MOURIER,D.SERVENT JRNL TITL ANCESTRAL PROTEIN RESURRECTION AND ENGINEERING OPPORTUNITIES JRNL TITL 2 OF THE MAMBA AMINERGIC TOXINS. JRNL REF SCI REP V. 7 2701 2017 JRNL REFN ESSN 2045-2322 JRNL PMID 28578406 JRNL DOI 10.1038/S41598-017-02953-0 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 11685 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.040 REMARK 3 FREE R VALUE TEST SET COUNT : 823 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 35.5633 - 3.2711 1.00 1828 140 0.1617 0.2059 REMARK 3 2 3.2711 - 2.5966 1.00 1809 136 0.1990 0.2297 REMARK 3 3 2.5966 - 2.2685 1.00 1802 143 0.2127 0.2244 REMARK 3 4 2.2685 - 2.0611 1.00 1812 128 0.2361 0.2715 REMARK 3 5 2.0611 - 1.9134 1.00 1826 138 0.2928 0.2992 REMARK 3 6 1.9134 - 1.8006 0.99 1785 138 0.3869 0.4117 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.620 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.004 551 REMARK 3 ANGLE : 0.809 746 REMARK 3 CHIRALITY : 0.047 80 REMARK 3 PLANARITY : 0.004 93 REMARK 3 DIHEDRAL : 14.383 339 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 20.7852 -8.8910 -8.7359 REMARK 3 T TENSOR REMARK 3 T11: 0.2677 T22: 0.2705 REMARK 3 T33: 0.2316 T12: 0.0655 REMARK 3 T13: -0.0015 T23: 0.0205 REMARK 3 L TENSOR REMARK 3 L11: 0.9453 L22: 0.9564 REMARK 3 L33: 0.8977 L12: -0.0395 REMARK 3 L13: -0.6787 L23: 0.5933 REMARK 3 S TENSOR REMARK 3 S11: -0.0078 S12: 0.0458 S13: 0.1231 REMARK 3 S21: 0.0705 S22: 0.0276 S23: 0.0113 REMARK 3 S31: -0.1580 S32: -0.1611 S33: 0.0001 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 5MG9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1200002428. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JAN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.965 REMARK 200 MONOCHROMATOR : DIAMOND BEAM SPLITTER REMARK 200 OPTICS : COMPOUND REFRACTIVE LENS FULLY REMARK 200 AUTOMATIC DATA COLLECTION REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11687 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 35.556 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.300 REMARK 200 R MERGE (I) : 0.11100 REMARK 200 R SYM (I) : 0.10400 REMARK 200 FOR THE DATA SET : 12.2400 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) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : 1.53000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.160 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: 4IYE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN: LYOPHILIZED SYNTHETIC TOXIN REMARK 280 AT 5 MG/ML IN 1 M NA ACETATE PH 5.5. PRECIPITANT: 1.9 M AMMONIUM REMARK 280 SULFATE, 4 % MPD, 2 % 1,4-DIOXANE, 2 % GAMMA-VALEROLACTONE, REMARK 280 0.132 M SODIUM CITRATE, PH 5.5. CRYOPROTECTANT: 80% SATURATED REMARK 280 LITHIUM SULFATE, 10% DIOXANE, 10% GAMMA-VALEROLACTONE, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 22.37267 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 44.74533 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 44.74533 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 22.37267 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: 660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGO A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue YVR A 107 DBREF 5MG9 A 1 65 PDB 5MG9 5MG9 1 65 SEQRES 1 A 65 LEU THR CYS VAL LYS SER LYS SER ILE PHE GLY VAL THR SEQRES 2 A 65 THR GLU ASP CYS PRO ASP GLY GLN ASN LEU CYS PHE LYS SEQRES 3 A 65 ARG ARG HIS TYR ILE VAL PRO LYS MET TYR ASP SER THR SEQRES 4 A 65 ARG GLY CYS ALA ALA THR CYS PRO ILE ALA GLU ASN ARG SEQRES 5 A 65 ASP VAL ILE HIS CYS CYS GLY THR ASP LYS CYS ASN GLU HET PGO A 101 5 HET EDO A 102 4 HET SO4 A 103 5 HET SO4 A 104 5 HET SO4 A 105 5 HET SO4 A 106 5 HET YVR A 107 7 HETNAM PGO S-1,2-PROPANEDIOL HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETNAM YVR GAMMA-VALEROLACTONE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 PGO C3 H8 O2 FORMUL 3 EDO C2 H6 O2 FORMUL 4 SO4 4(O4 S 2-) FORMUL 8 YVR C5 H8 O2 FORMUL 9 HOH *87(H2 O) SHEET 1 AA1 2 THR A 2 LYS A 7 0 SHEET 2 AA1 2 VAL A 12 ASP A 16 -1 O THR A 13 N LYS A 5 SHEET 1 AA2 3 MET A 35 ALA A 43 0 SHEET 2 AA2 3 LEU A 23 VAL A 32 -1 N ARG A 27 O THR A 39 SHEET 3 AA2 3 ASP A 53 CYS A 58 -1 O VAL A 54 N ARG A 28 SSBOND 1 CYS A 3 CYS A 24 1555 1555 2.03 SSBOND 2 CYS A 17 CYS A 42 1555 1555 2.02 SSBOND 3 CYS A 46 CYS A 57 1555 1555 2.04 SSBOND 4 CYS A 58 CYS A 63 1555 1555 2.03 SITE 1 AC1 6 LYS A 26 ARG A 28 VAL A 54 HIS A 56 SITE 2 AC1 6 SO4 A 105 HOH A 210 SITE 1 AC2 6 SER A 8 HIS A 29 TYR A 30 ARG A 52 SITE 2 AC2 6 HOH A 217 HOH A 222 SITE 1 AC3 7 LYS A 26 ARG A 28 TYR A 36 SER A 38 SITE 2 AC3 7 ARG A 40 HOH A 204 HOH A 243 SITE 1 AC4 8 PHE A 10 ASP A 19 ASN A 51 ARG A 52 SITE 2 AC4 8 HIS A 56 CYS A 63 HOH A 216 HOH A 244 SITE 1 AC5 10 ASP A 16 LYS A 26 ARG A 28 GLU A 50 SITE 2 AC5 10 ASN A 51 PGO A 101 HOH A 210 HOH A 218 SITE 3 AC5 10 HOH A 227 HOH A 264 SITE 1 AC6 6 GLY A 20 ASN A 22 LYS A 62 GLU A 65 SITE 2 AC6 6 HOH A 201 HOH A 215 SITE 1 AC7 5 GLU A 15 ASP A 16 ARG A 52 VAL A 54 SITE 2 AC7 5 HOH A 203 CRYST1 41.057 41.057 67.118 90.00 90.00 120.00 P 31 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 0.024356 0.014062 0.000000 0.00000 SCALE2 0.000000 0.028124 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014899 0.00000