HEADER TOXIN 07-DEC-19 6LH8 TITLE STRUCTURE OF AEROLYSIN-LIKE PROTEIN (BOMBINA MAXIMA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: AEROLYSIN-LIKE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOMBINA MAXIMA; SOURCE 3 ORGANISM_TAXID: 161274; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PORE-FORMING, AEROLYSIN, AMPHIBIAN, SECRETION, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR X.L.BIAN,Q.Q.WANG,X.LI,M.Q.TENG,Y.ZHANG REVDAT 4 27-MAR-24 6LH8 1 REMARK REVDAT 3 05-AUG-20 6LH8 1 JRNL REVDAT 2 17-JUN-20 6LH8 1 JRNL REVDAT 1 10-JUN-20 6LH8 0 JRNL AUTH Q.WANG,X.BIAN,L.ZENG,F.PAN,L.LIU,J.LIANG,L.WANG,K.ZHOU, JRNL AUTH 2 W.LEE,Y.XIANG,S.LI,M.TENG,X.LI,X.GUO,Y.ZHANG JRNL TITL A CELLULAR ENDOLYSOSOME-MODULATING PORE-FORMING PROTEIN FROM JRNL TITL 2 A TOAD IS NEGATIVELY REGULATED BY ITS PARALOG UNDER JRNL TITL 3 OXIDIZING CONDITIONS. JRNL REF J.BIOL.CHEM. V. 295 10293 2020 JRNL REFN ESSN 1083-351X JRNL PMID 32499370 JRNL DOI 10.1074/JBC.RA120.013556 REMARK 2 REMARK 2 RESOLUTION. 1.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.420 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 16266 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1628 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 41.5780 - 3.9574 1.00 1371 152 0.1787 0.2092 REMARK 3 2 3.9574 - 3.1414 1.00 1281 142 0.1778 0.2075 REMARK 3 3 3.1414 - 2.7444 1.00 1261 141 0.1932 0.2619 REMARK 3 4 2.7444 - 2.4935 1.00 1240 139 0.2169 0.2522 REMARK 3 5 2.4935 - 2.3148 0.99 1227 133 0.2013 0.2379 REMARK 3 6 2.3148 - 2.1783 0.98 1221 139 0.1923 0.2671 REMARK 3 7 2.1783 - 2.0693 0.99 1210 135 0.1857 0.2097 REMARK 3 8 2.0693 - 1.9792 0.97 1189 133 0.1960 0.2317 REMARK 3 9 1.9792 - 1.9030 0.97 1199 133 0.2050 0.2546 REMARK 3 10 1.9030 - 1.8373 0.96 1181 128 0.2145 0.2340 REMARK 3 11 1.8373 - 1.7799 0.93 1126 129 0.2357 0.2817 REMARK 3 12 1.7799 - 1.7290 0.92 1132 124 0.2701 0.3197 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.710 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.70 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 6LH8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1300013849. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUL-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK HKL2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16266 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.729 REMARK 200 RESOLUTION RANGE LOW (A) : 41.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 41.8800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.620 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M MAGNESIUM CHLORIDE HEXAHYDRATE, REMARK 280 25% PEG 3350, 0.1M BIS-TRIS, PH 6.4, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z REMARK 290 4555 Y+1/2,-X+1/2,Z REMARK 290 5555 -X+1/2,Y+1/2,-Z REMARK 290 6555 X+1/2,-Y+1/2,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.39650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.39650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.39650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.39650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.39650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.39650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.39650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.39650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 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 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 207 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 377 LIES ON A SPECIAL POSITION. 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 SER A 31 REMARK 465 ASN A 32 REMARK 465 VAL A 33 REMARK 465 LEU A 156 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 O HOH A 218 O HOH A 314 1.77 REMARK 500 OD1 ASN A 77 O HOH A 201 1.88 REMARK 500 O HOH A 206 O HOH A 348 1.92 REMARK 500 NE2 GLN A 67 O HOH A 202 2.01 REMARK 500 OE2 GLU A 18 O HOH A 203 2.02 REMARK 500 O HOH A 279 O HOH A 372 2.03 REMARK 500 O HOH A 205 O HOH A 210 2.04 REMARK 500 O HOH A 204 O HOH A 230 2.10 REMARK 500 O HOH A 204 O HOH A 324 2.11 REMARK 500 OD1 ASP A 23 O HOH A 204 2.15 REMARK 500 OG SER A 2 O HOH A 205 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 360 O HOH A 360 8665 1.65 REMARK 500 O HOH A 204 O HOH A 233 7555 2.15 REMARK 500 O HOH A 204 O HOH A 211 7555 2.15 REMARK 500 O HOH A 204 O HOH A 358 7555 2.16 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 ALA A 57 35.36 -96.23 REMARK 500 SER A 87 -26.85 -152.00 REMARK 500 REMARK 500 REMARK: NULL DBREF 6LH8 A 1 156 PDB 6LH8 6LH8 1 156 SEQRES 1 A 156 MET SER ALA SER VAL THR VAL LEU TRP ASP LYS GLU ILE SEQRES 2 A 156 GLU GLY SER ASN GLU VAL VAL LYS VAL ASP GLU MET VAL SEQRES 3 A 156 ALA SER ASN ILE SER ASN VAL LYS VAL GLU PHE TYR LEU SEQRES 4 A 156 LYS GLU ARG HIS PHE ASP ARG THR ILE THR HIS ASN ILE SEQRES 5 A 156 THR LEU PRO ARG ALA THR GLU VAL PRO ILE GLY THR GLU SEQRES 6 A 156 ILE GLN LEU GLU PRO LYS HIS ARG LEU ASN GLY ASN THR SEQRES 7 A 156 GLU PRO ILE THR PHE THR TYR GLY SER LEU GLU SER TYR SEQRES 8 A 156 THR GLU LEU SER GLU ASP LYS VAL THR MET PRO GLU PHE SEQRES 9 A 156 VAL GLU PRO LYS THR LYS LEU ILE VAL ILE LEU THR ARG SEQRES 10 A 156 ASN GLU ASN ILE THR SER ALA PRO VAL GLU ILE SER VAL SEQRES 11 A 156 GLY ASP ILE LYS GLU THR ALA THR TYR ILE CYS GLN SER SEQRES 12 A 156 GLN SER GLY ILE ASN ALA GLU VAL ASN THR GLU PRO LEU FORMUL 2 HOH *177(H2 O) HELIX 1 AA1 TRP A 9 GLU A 12 5 4 SHEET 1 AA1 5 SER A 4 VAL A 7 0 SHEET 2 AA1 5 LYS A 110 VAL A 130 -1 O SER A 129 N SER A 4 SHEET 3 AA1 5 ILE A 133 GLN A 144 -1 O GLU A 135 N ILE A 128 SHEET 4 AA1 5 GLU A 41 THR A 53 -1 N THR A 49 O GLN A 142 SHEET 5 AA1 5 SER A 90 THR A 100 -1 O TYR A 91 N HIS A 50 SHEET 1 AA2 3 ILE A 13 SER A 28 0 SHEET 2 AA2 3 LYS A 110 VAL A 130 -1 O LEU A 111 N ALA A 27 SHEET 3 AA2 3 ASN A 148 GLU A 154 -1 O GLU A 154 N LYS A 110 SHEET 1 AA3 2 GLU A 65 LEU A 68 0 SHEET 2 AA3 2 ILE A 81 THR A 84 -1 O PHE A 83 N ILE A 66 CRYST1 78.793 78.793 48.948 90.00 90.00 90.00 P 4 21 2 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 0.012691 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012691 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020430 0.00000