HEADER TOXIN 25-SEP-15 5DZ5 TITLE CRYSTAL STRUCTURE OF DENDROASPIS POLYLEPIS MAMBALGIN-1 WILD-TYPE IN TITLE 2 P41212 SPACE GROUP COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAMBALGIN-1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: MAMB-1,PI-DP1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: DENDROASPIS POLYLEPIS POLYLEPIS; SOURCE 4 ORGANISM_COMMON: BLACK MAMBA; SOURCE 5 ORGANISM_TAXID: 8620 KEYWDS PAIN-RELIEVING POLYPEPTIDE, ANALGESIC, ACID-SENSING ION CHANNEL, KEYWDS 2 MAMBALGIN-1, THREE-FINGER-FOLD, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR E.A.STURA,L.TEPSHI,G.MOURIER,P.KESSLER,D.SERVENT REVDAT 3 10-JAN-24 5DZ5 1 REMARK REVDAT 2 17-FEB-16 5DZ5 1 JRNL REVDAT 1 30-DEC-15 5DZ5 0 JRNL AUTH G.MOURIER,M.SALINAS,P.KESSLER,E.A.STURA,M.LEBLANC,L.TEPSHI, JRNL AUTH 2 T.BESSON,S.DIOCHOT,A.BARON,D.DOUGUET,E.LINGUEGLIA,D.SERVENT JRNL TITL MAMBALGIN-1 PAIN-RELIEVING PEPTIDE, STEPWISE SOLID-PHASE JRNL TITL 2 SYNTHESIS, CRYSTAL STRUCTURE, AND FUNCTIONAL DOMAIN FOR JRNL TITL 3 ACID-SENSING ION CHANNEL 1A INHIBITION. JRNL REF J.BIOL.CHEM. V. 291 2616 2016 JRNL REFN ESSN 1083-351X JRNL PMID 26680001 JRNL DOI 10.1074/JBC.M115.702373 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 6979 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 349 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 40.4758 - 2.4568 1.00 3400 179 0.1716 0.2271 REMARK 3 2 2.4568 - 1.9500 1.00 3230 170 0.2524 0.3046 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.450 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 : 0.025 942 REMARK 3 ANGLE : 1.991 1250 REMARK 3 CHIRALITY : 0.112 132 REMARK 3 PLANARITY : 0.008 164 REMARK 3 DIHEDRAL : 16.100 361 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): -0.4511 2.7210 7.7542 REMARK 3 T TENSOR REMARK 3 T11: 0.1421 T22: 0.2007 REMARK 3 T33: 0.1781 T12: -0.0044 REMARK 3 T13: 0.0044 T23: -0.0097 REMARK 3 L TENSOR REMARK 3 L11: 0.1642 L22: 0.0575 REMARK 3 L33: 0.3726 L12: 0.0671 REMARK 3 L13: 0.0385 L23: -0.0645 REMARK 3 S TENSOR REMARK 3 S11: 0.0208 S12: -0.0171 S13: 0.0310 REMARK 3 S21: 0.0502 S22: -0.0005 S23: 0.0255 REMARK 3 S31: 0.0052 S32: -0.0349 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 5DZ5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000214057. 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 : 5.5-7.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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 : AUTOMATIC DATA COLLECTION ON REMARK 200 ESRF MASSIF1 ID30A-1 REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6981 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 46.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.18300 REMARK 200 R SYM (I) : 0.17100 REMARK 200 FOR THE DATA SET : 9.6600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.94 REMARK 200 R MERGE FOR SHELL (I) : 1.67000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.190 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: 5DO6 REMARK 200 REMARK 200 REMARK: PRISMATIC REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 26.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN: 5 MG/ML IN 0.050 M NA REMARK 280 ACETATE, PH 5.5 PRECIPITANT: 30% PEG600, 0.2 M IMIDAZOLE MALATE, REMARK 280 PH 7.0. CRYOPROTECTANT: 40% CRYOSOL SM5, 30% PEG 600, 0.1 M REMARK 280 MIXED (NA ACETATE, ADA, BICINE) PH 7.0, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.28000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 23.40000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 23.40000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 20.14000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 23.40000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 23.40000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 60.42000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 23.40000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 23.40000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 20.14000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 23.40000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 23.40000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 60.42000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 40.28000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 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 SG CYS B 12 SG CYS B 37 1.64 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 ASN A 56 51.64 -95.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 143 DISTANCE = 6.36 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5DU1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DENDROASPIS POLYLEPIS VENOM MAMBALGIN-1 IN REMARK 900 SPACE GROUP P21 CONTAINS 4 MOLECULES IN THE ASYMMETRIC UNIT. REMARK 900 RELATED ID: 5DO6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DENDROASPIS POLYLEPIS VENOM MAMBALGIN-1 T23A REMARK 900 MUTANT WAS USED TO SOLVE THE PHASE PROBLEM. DBREF 5DZ5 A 1 57 UNP P0DKR6 3SX1_DENPO 22 78 DBREF 5DZ5 B 1 57 UNP P0DKR6 3SX1_DENPO 22 78 SEQRES 1 A 57 LEU LYS CYS TYR GLN HIS GLY LYS VAL VAL THR CYS HIS SEQRES 2 A 57 ARG ASP MET LYS PHE CYS TYR HIS ASN THR GLY MET PRO SEQRES 3 A 57 PHE ARG ASN LEU LYS LEU ILE LEU GLN GLY CYS SER SER SEQRES 4 A 57 SER CYS SER GLU THR GLU ASN ASN LYS CYS CYS SER THR SEQRES 5 A 57 ASP ARG CYS ASN LYS SEQRES 1 B 57 LEU LYS CYS TYR GLN HIS GLY LYS VAL VAL THR CYS HIS SEQRES 2 B 57 ARG ASP MET LYS PHE CYS TYR HIS ASN THR GLY MET PRO SEQRES 3 B 57 PHE ARG ASN LEU LYS LEU ILE LEU GLN GLY CYS SER SER SEQRES 4 B 57 SER CYS SER GLU THR GLU ASN ASN LYS CYS CYS SER THR SEQRES 5 B 57 ASP ARG CYS ASN LYS FORMUL 3 HOH *80(H2 O) HELIX 1 AA1 GLU A 45 ASN A 47 5 3 HELIX 2 AA2 GLU B 45 ASN B 47 5 3 SHEET 1 AA1 2 LYS A 2 TYR A 4 0 SHEET 2 AA1 2 VAL A 9 THR A 11 -1 O VAL A 10 N CYS A 3 SHEET 1 AA2 6 CYS A 49 CYS A 50 0 SHEET 2 AA2 6 PHE A 18 PHE A 27 -1 N CYS A 19 O CYS A 50 SHEET 3 AA2 6 LEU A 30 SER A 38 -1 O LEU A 32 N GLY A 24 SHEET 4 AA2 6 LEU B 30 SER B 38 -1 O ILE B 33 N LYS A 31 SHEET 5 AA2 6 PHE B 18 PHE B 27 -1 N GLY B 24 O LEU B 32 SHEET 6 AA2 6 CYS B 49 CYS B 50 -1 O CYS B 50 N CYS B 19 SHEET 1 AA3 2 LYS B 2 TYR B 4 0 SHEET 2 AA3 2 VAL B 9 THR B 11 -1 O VAL B 10 N CYS B 3 SSBOND 1 CYS A 3 CYS A 19 1555 1555 2.01 SSBOND 2 CYS A 12 CYS A 37 1555 1555 2.01 SSBOND 3 CYS A 41 CYS A 49 1555 1555 1.92 SSBOND 4 CYS A 50 CYS A 55 1555 1555 2.05 SSBOND 5 CYS B 3 CYS B 19 1555 1555 1.95 SSBOND 6 CYS B 41 CYS B 49 1555 1555 2.01 SSBOND 7 CYS B 50 CYS B 55 1555 1555 2.04 CRYST1 46.800 46.800 80.560 90.00 90.00 90.00 P 41 21 2 16 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 0.021368 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021368 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012413 0.00000