HEADER TOXIN 21-JUL-21 7RJZ TITLE BTHTX-II VARIANT A, FROM BOTHROPS JARARACUSSU VENOM, COMPLEXED WITH TITLE 2 BENZOIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: BTHTX-IIA; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.1.1.4; COMPND 5 OTHER_DETAILS: SEQUENCE DETERMINED USING SEQUENCE SLIDER, A COMPND 6 METHODOLOGY THAT INTEGRATES MASS SPECTROMETRY, CRYSTALLOGRAPHIC AND COMPND 7 GENETIC DATA. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOTHROPS JARARACUSSU; SOURCE 3 ORGANISM_TAXID: 8726 KEYWDS BASIC PHOSPHOLIPASE A2, BTHTX-II VARIANT A, BOTHROPS JARARACUSSU, KEYWDS 2 TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR R.J.BORGES,M.R.M.FONTES REVDAT 2 18-OCT-23 7RJZ 1 REMARK REVDAT 1 05-JAN-22 7RJZ 0 JRNL AUTH R.J.BORGES,G.H.M.SALVADOR,H.B.CAMPANELLI,D.C.PIMENTA, JRNL AUTH 2 M.DE OLIVEIRA NETO,I.USON,M.R.M.FONTES JRNL TITL BTHTX-II FROM BOTHROPS JARARACUSSU VENOM HAS VARIANTS WITH JRNL TITL 2 DIFFERENT OLIGOMERIC ASSEMBLIES: AN EXAMPLE OF SNAKE VENOM JRNL TITL 3 PHOSPHOLIPASES A 2 VERSATILITY. JRNL REF INT.J.BIOL.MACROMOL. V. 191 255 2021 JRNL REFN ISSN 0141-8130 JRNL PMID 34547312 JRNL DOI 10.1016/J.IJBIOMAC.2021.09.083 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.18.2_3874: ???) 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 3 NUMBER OF REFLECTIONS : 30316 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1516 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 40.1300 - 3.7800 0.99 2982 157 0.1626 0.1865 REMARK 3 2 3.7800 - 3.0000 0.99 2838 149 0.1609 0.1870 REMARK 3 3 3.0000 - 2.6200 0.99 2797 147 0.1827 0.2155 REMARK 3 4 2.6200 - 2.3800 0.99 2794 147 0.1805 0.1974 REMARK 3 5 2.3800 - 2.2100 0.98 2738 144 0.2021 0.2653 REMARK 3 6 2.2100 - 2.0800 0.98 2719 144 0.2013 0.2559 REMARK 3 7 2.0800 - 1.9700 0.98 2729 143 0.2182 0.2429 REMARK 3 8 1.9700 - 1.8900 0.97 2707 143 0.2816 0.3498 REMARK 3 9 1.8900 - 1.8200 0.96 2643 139 0.2623 0.2942 REMARK 3 10 1.8200 - 1.7500 0.78 2170 114 0.2760 0.3420 REMARK 3 11 1.7500 - 1.7000 0.61 1683 89 0.3025 0.3503 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.700 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 : 0.003 1972 REMARK 3 ANGLE : 0.650 2665 REMARK 3 CHIRALITY : 0.043 268 REMARK 3 PLANARITY : 0.005 347 REMARK 3 DIHEDRAL : 30.094 278 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 7RJZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1000258364. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 5.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0781 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20210323 REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57103 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 40.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 66.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.15 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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 2.8.3 REMARK 200 STARTING MODEL: 2OQD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE PH 5.2, 25% REMARK 280 PEG4000 (W/V), 0.21 M AMMONIUM SULPHATE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 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 -X+1/2,Y+1/2,-Z 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 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 -1.000000 0.000000 0.000000 30.20000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.68500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.20000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.68500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 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 345 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 351 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 425 LIES ON A SPECIAL POSITION. 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 GLU A 119 CG CD OE1 OE2 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 LEU A 54 60.14 -102.18 REMARK 500 ARG A 68 49.93 -149.15 REMARK 500 LEU B 54 64.88 -100.32 REMARK 500 LYS B 58 78.52 -119.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7RJI RELATED DB: PDB REMARK 900 VARIANT B DBREF 7RJZ A 1 121 PDB 7RJZ 7RJZ 1 121 DBREF 7RJZ B 1 121 PDB 7RJZ 7RJZ 1 121 SEQRES 1 A 121 ASP LEU TRP GLN PHE GLY GLN MET ILE LEU LYS GLU THR SEQRES 2 A 121 GLY LYS LEU PRO PHE PRO TYR TYR THR THR TYR GLY CYS SEQRES 3 A 121 TYR CYS GLY TRP GLY GLY GLN GLY GLN PRO LYS ASP ALA SEQRES 4 A 121 THR ASP ARG CYS CYS PHE VAL HIS ASP CYS CYS TYR GLY SEQRES 5 A 121 LYS LEU THR ALA CYS LYS PRO LYS THR ASP ARG TYR SER SEQRES 6 A 121 TYR SER ARG GLU ASN GLY VAL ILE ILE CYS GLY GLU GLY SEQRES 7 A 121 THR PRO CYS GLN LYS GLN ILE CYS GLU CYS ASP LYS ALA SEQRES 8 A 121 ALA ALA VAL CYS PHE ARG GLU ASN LEU ARG THR TYR LEU SEQRES 9 A 121 ALA ARG TYR MET ALA TYR PRO ASP VAL LEU CYS ALA VAL SEQRES 10 A 121 PRO GLU LYS CYS SEQRES 1 B 121 ASP LEU TRP GLN PHE GLY GLN MET ILE LEU LYS GLU THR SEQRES 2 B 121 GLY LYS LEU PRO PHE PRO TYR TYR THR THR TYR GLY CYS SEQRES 3 B 121 TYR CYS GLY TRP GLY GLY GLN GLY GLN PRO LYS ASP ALA SEQRES 4 B 121 THR ASP ARG CYS CYS PHE VAL HIS ASP CYS CYS TYR GLY SEQRES 5 B 121 LYS LEU THR ALA CYS LYS PRO LYS THR ASP ARG TYR SER SEQRES 6 B 121 TYR SER ARG GLU ASN GLY VAL ILE ILE CYS GLY GLU GLY SEQRES 7 B 121 THR PRO CYS GLN LYS GLN ILE CYS GLU CYS ASP LYS ALA SEQRES 8 B 121 ALA ALA VAL CYS PHE ARG GLU ASN LEU ARG THR TYR LEU SEQRES 9 B 121 ALA ARG TYR MET ALA TYR PRO ASP VAL LEU CYS ALA VAL SEQRES 10 B 121 PRO GLU LYS CYS HET BEZ A 201 9 HET BEZ B 201 9 HETNAM BEZ BENZOIC ACID FORMUL 3 BEZ 2(C7 H6 O2) FORMUL 5 HOH *311(H2 O) HELIX 1 AA1 ASP A 1 GLY A 14 1 14 HELIX 2 AA2 LEU A 16 TYR A 21 1 6 HELIX 3 AA3 TYR A 27 GLY A 31 5 5 HELIX 4 AA4 ASP A 38 LYS A 53 1 16 HELIX 5 AA5 THR A 79 ASN A 99 1 21 HELIX 6 AA6 LEU A 100 TYR A 103 5 4 HELIX 7 AA7 LEU A 104 MET A 108 5 5 HELIX 8 AA8 PRO A 111 CYS A 115 5 5 HELIX 9 AA9 LEU B 2 GLY B 14 1 13 HELIX 10 AB1 LEU B 16 TYR B 21 1 6 HELIX 11 AB2 TYR B 27 GLY B 31 5 5 HELIX 12 AB3 ASP B 38 LYS B 53 1 16 HELIX 13 AB4 THR B 79 ASN B 99 1 21 HELIX 14 AB5 LEU B 100 TYR B 103 5 4 HELIX 15 AB6 LEU B 104 MET B 108 5 5 HELIX 16 AB7 PRO B 111 CYS B 115 5 5 SHEET 1 AA1 2 TYR A 66 SER A 67 0 SHEET 2 AA1 2 ILE A 74 CYS A 75 -1 O ILE A 74 N SER A 67 SHEET 1 AA2 2 TYR B 66 GLU B 69 0 SHEET 2 AA2 2 VAL B 72 CYS B 75 -1 O ILE B 74 N SER B 67 SSBOND 1 CYS A 26 CYS A 115 1555 1555 2.03 SSBOND 2 CYS A 28 CYS A 44 1555 1555 2.03 SSBOND 3 CYS A 43 CYS A 95 1555 1555 2.03 SSBOND 4 CYS A 49 CYS A 121 1555 1555 2.03 SSBOND 5 CYS A 50 CYS A 88 1555 1555 2.03 SSBOND 6 CYS A 57 CYS A 81 1555 1555 2.03 SSBOND 7 CYS A 75 CYS A 86 1555 1555 2.03 SSBOND 8 CYS B 26 CYS B 115 1555 1555 2.03 SSBOND 9 CYS B 28 CYS B 44 1555 1555 2.03 SSBOND 10 CYS B 43 CYS B 95 1555 1555 2.04 SSBOND 11 CYS B 49 CYS B 121 1555 1555 2.03 SSBOND 12 CYS B 50 CYS B 88 1555 1555 2.03 SSBOND 13 CYS B 57 CYS B 81 1555 1555 2.03 SSBOND 14 CYS B 75 CYS B 86 1555 1555 2.03 CISPEP 1 PHE A 18 PRO A 19 0 -0.55 CISPEP 2 PHE B 18 PRO B 19 0 -1.14 CRYST1 60.400 107.370 44.300 90.00 90.00 90.00 P 21 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 0.016556 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009314 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022573 0.00000