HEADER HYDROLASE 06-NOV-19 6UX6 TITLE CRUZAIN COVALENTLY BOUND BY A VINYLSULFONE COMPOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: CRUZIPAIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CRUZAINE,MAJOR CYSTEINE PROTEINASE; COMPND 5 EC: 3.4.22.51; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA CRUZI; SOURCE 3 ORGANISM_TAXID: 5693; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CRUZAIN, VINYLSULFONE, COVALENT, INHIBITOR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR X.ZHAI,S.TANG,B.C.CHENNA,T.D.MEEK,J.C.SACCHETTINI REVDAT 3 06-NOV-24 6UX6 1 REMARK REVDAT 2 11-OCT-23 6UX6 1 REMARK REVDAT 1 25-NOV-20 6UX6 0 JRNL AUTH X.ZHAI,S.TANG,B.C.CHENNA,T.D.MEEK,J.C.SACCHETTINI JRNL TITL CRUZAIN COVALENTLY BOUND BY A VINYLSULFONE COMPOUND JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.490 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 13156 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 645 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 33.7500 - 3.3115 0.99 2675 131 0.1767 0.1851 REMARK 3 2 3.3115 - 2.6288 0.99 2526 145 0.2403 0.3397 REMARK 3 3 2.6288 - 2.2966 0.99 2478 130 0.2604 0.3022 REMARK 3 4 2.2966 - 2.0866 0.99 2503 117 0.2706 0.3122 REMARK 3 5 2.0866 - 1.9400 0.94 2329 122 0.2741 0.3726 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) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.66 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 : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 2.9971 -15.3025 -12.9272 REMARK 3 T TENSOR REMARK 3 T11: 0.1775 T22: 0.1831 REMARK 3 T33: 0.1725 T12: 0.0312 REMARK 3 T13: 0.0164 T23: 0.0011 REMARK 3 L TENSOR REMARK 3 L11: 0.1593 L22: 0.2264 REMARK 3 L33: 0.1441 L12: 0.2159 REMARK 3 L13: 0.0119 L23: -0.0255 REMARK 3 S TENSOR REMARK 3 S11: -0.0315 S12: -0.0195 S13: -0.0328 REMARK 3 S21: -0.0087 S22: 0.0125 S23: 0.0124 REMARK 3 S31: 0.0138 S32: -0.0016 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 6UX6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1000245349. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13196 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.940 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 (%) : 98.2 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.12500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.24100 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: MOLREP REMARK 200 STARTING MODEL: 1ME4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: BIS-TRIS, PEG3350, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 290K 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 20.25450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 61.06350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.25450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 61.06350 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 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 LYS A 58 CG CD CE NZ 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 GLN A 120 70.41 -68.69 REMARK 500 ASP A 161 -2.23 -146.00 REMARK 500 THR A 185 165.85 64.84 REMARK 500 CYS A 203 15.33 58.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TM8 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 302 DBREF 6UX6 A 1 215 UNP P25779 CYSP_TRYCR 123 337 SEQRES 1 A 215 ALA PRO ALA ALA VAL ASP TRP ARG ALA ARG GLY ALA VAL SEQRES 2 A 215 THR ALA VAL LYS ASP GLN GLY GLN CYS GLY SER CYS TRP SEQRES 3 A 215 ALA PHE SER ALA ILE GLY ASN VAL GLU CYS GLN TRP PHE SEQRES 4 A 215 LEU ALA GLY HIS PRO LEU THR ASN LEU SER GLU GLN MET SEQRES 5 A 215 LEU VAL SER CYS ASP LYS THR ASP SER GLY CYS SER GLY SEQRES 6 A 215 GLY LEU MET ASN ASN ALA PHE GLU TRP ILE VAL GLN GLU SEQRES 7 A 215 ASN ASN GLY ALA VAL TYR THR GLU ASP SER TYR PRO TYR SEQRES 8 A 215 ALA SER GLY GLU GLY ILE SER PRO PRO CYS THR THR SER SEQRES 9 A 215 GLY HIS THR VAL GLY ALA THR ILE THR GLY HIS VAL GLU SEQRES 10 A 215 LEU PRO GLN ASP GLU ALA GLN ILE ALA ALA TRP LEU ALA SEQRES 11 A 215 VAL ASN GLY PRO VAL ALA VAL ALA VAL ASP ALA SER SER SEQRES 12 A 215 TRP MET THR TYR THR GLY GLY VAL MET THR SER CYS VAL SEQRES 13 A 215 SER GLU GLN LEU ASP HIS GLY VAL LEU LEU VAL GLY TYR SEQRES 14 A 215 ASN ASP SER ALA ALA VAL PRO TYR TRP ILE ILE LYS ASN SEQRES 15 A 215 SER TRP THR THR GLN TRP GLY GLU GLU GLY TYR ILE ARG SEQRES 16 A 215 ILE ALA LYS GLY SER ASN GLN CYS LEU VAL LYS GLU GLU SEQRES 17 A 215 ALA SER SER ALA VAL VAL GLY HET TM8 A 301 41 HET GOL A 302 6 HETNAM TM8 NALPHA-[(BENZYLOXY)CARBONYL]-N-[(2S)-1-PHENYL-4- HETNAM 2 TM8 (PHENYLSULFONYL)BUTAN-2-YL]-L-PHENYLALANINAMIDE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 TM8 C33 H34 N2 O5 S FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *70(H2 O) HELIX 1 AA1 SER A 24 ALA A 41 1 18 HELIX 2 AA2 SER A 49 ASP A 57 1 9 HELIX 3 AA3 SER A 61 GLY A 65 5 5 HELIX 4 AA4 LEU A 67 ASN A 79 1 13 HELIX 5 AA5 ASP A 121 GLY A 133 1 13 HELIX 6 AA6 ALA A 141 MET A 145 5 5 HELIX 7 AA7 ASN A 201 VAL A 205 5 5 SHEET 1 AA1 5 ALA A 4 ASP A 6 0 SHEET 2 AA1 5 HIS A 162 ASN A 170 -1 O TYR A 169 N VAL A 5 SHEET 3 AA1 5 VAL A 135 VAL A 139 -1 N VAL A 135 O LEU A 166 SHEET 4 AA1 5 ALA A 209 VAL A 213 -1 O SER A 210 N ALA A 136 SHEET 5 AA1 5 GLY A 114 GLU A 117 -1 N VAL A 116 O SER A 211 SHEET 1 AA2 5 ALA A 4 ASP A 6 0 SHEET 2 AA2 5 HIS A 162 ASN A 170 -1 O TYR A 169 N VAL A 5 SHEET 3 AA2 5 TYR A 177 LYS A 181 -1 O LYS A 181 N LEU A 165 SHEET 4 AA2 5 TYR A 193 ALA A 197 -1 O ILE A 196 N TRP A 178 SHEET 5 AA2 5 VAL A 151 MET A 152 1 N MET A 152 O ARG A 195 SHEET 1 AA3 2 ALA A 82 TYR A 84 0 SHEET 2 AA3 2 VAL A 108 THR A 111 -1 O GLY A 109 N VAL A 83 SSBOND 1 CYS A 22 CYS A 63 1555 1555 2.03 SSBOND 2 CYS A 56 CYS A 101 1555 1555 2.04 SSBOND 3 CYS A 155 CYS A 203 1555 1555 2.03 LINK SG CYS A 25 CAQ TM8 A 301 1555 1555 1.77 SITE 1 AC1 19 GLN A 19 CYS A 25 TRP A 26 THR A 59 SITE 2 AC1 19 SER A 61 SER A 64 GLY A 65 GLY A 66 SITE 3 AC1 19 LEU A 67 ASN A 70 ALA A 138 ALA A 141 SITE 4 AC1 19 SER A 142 LEU A 160 ASP A 161 HIS A 162 SITE 5 AC1 19 TRP A 184 GLU A 208 GOL A 302 SITE 1 AC2 3 GLY A 20 TRP A 184 TM8 A 301 CRYST1 40.509 122.127 34.585 90.00 90.00 90.00 P 21 21 2 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 0.024686 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008188 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028914 0.00000