HEADER TOXIN 01-AUG-19 6PZL TITLE P. MIRABILIS HEMOLYSIN A MUTANT - Q125A COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMOLYSIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PROTEUS MIRABILIS; SOURCE 3 ORGANISM_TAXID: 584; SOURCE 4 GENE: HPMA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS HEMOLYSIN, TWO-PARTNER SECRETION, BETA-HELIX, TOXIN, PROTEIN KEYWDS 2 SECRETION EXPDTA X-RAY DIFFRACTION AUTHOR T.M.WEAVER,W.R.P.NOVAK,B.BHATTACHARYYA REVDAT 2 11-OCT-23 6PZL 1 REMARK REVDAT 1 05-AUG-20 6PZL 0 JRNL AUTH T.M.WEAVER,W.R.P.NOVAK,D.P.GRILLEY,M.R.WIMMER,C.N.WOODS, JRNL AUTH 2 B.BHATTACHARYYA JRNL TITL STRUCTURE OF THE HPMA265 Q125A VARIANT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.17 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15_3459 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) : 1.17 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.1 REMARK 3 NUMBER OF REFLECTIONS : 71047 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.820 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 32.6770 - 2.8203 1.00 5983 173 0.1755 0.1904 REMARK 3 2 2.8203 - 2.2387 1.00 5767 167 0.1819 0.2012 REMARK 3 3 2.2387 - 1.9558 1.00 5730 166 0.1546 0.1811 REMARK 3 4 1.9558 - 1.7770 1.00 5672 164 0.1524 0.1627 REMARK 3 5 1.7770 - 1.6496 1.00 5671 165 0.1505 0.1602 REMARK 3 6 1.6496 - 1.5524 1.00 5611 163 0.1327 0.1692 REMARK 3 7 1.5524 - 1.4746 1.00 5638 163 0.1388 0.1815 REMARK 3 8 1.4746 - 1.4104 1.00 5609 162 0.1419 0.1655 REMARK 3 9 1.4104 - 1.3561 0.98 5497 160 0.1445 0.1777 REMARK 3 10 1.3561 - 1.3093 0.89 4987 143 0.1417 0.2098 REMARK 3 11 1.3093 - 1.2684 0.80 4491 131 0.1373 0.1616 REMARK 3 12 1.2684 - 1.2321 0.68 3803 110 0.1352 0.1836 REMARK 3 13 1.2321 - 1.1997 0.52 2884 83 0.1578 0.2416 REMARK 3 14 1.1997 - 1.1704 0.31 1704 50 0.2388 0.2913 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.310 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.59 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 6PZL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1000243334. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 71123 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.170 REMARK 200 RESOLUTION RANGE LOW (A) : 32.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.2 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 44.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.17 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.20 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.24100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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: 4W8Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, PH 5.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.11200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.17500 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.11200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 58.17500 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: 1590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 232.70000 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 GLU A 257 REMARK 465 GLY A 258 REMARK 465 SER A 259 REMARK 465 GLY A 260 REMARK 465 ALA A 264 REMARK 465 GLY A 265 REMARK 465 HIS A 266 REMARK 465 HIS A 267 REMARK 465 HIS A 268 REMARK 465 HIS A 269 REMARK 465 HIS A 270 REMARK 465 HIS A 271 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 301 DBREF 6PZL A 30 265 UNP P16466 HLYA_PROMI 30 265 SEQADV 6PZL ALA A 125 UNP P16466 GLN 125 ENGINEERED MUTATION SEQADV 6PZL HIS A 266 UNP P16466 EXPRESSION TAG SEQADV 6PZL HIS A 267 UNP P16466 EXPRESSION TAG SEQADV 6PZL HIS A 268 UNP P16466 EXPRESSION TAG SEQADV 6PZL HIS A 269 UNP P16466 EXPRESSION TAG SEQADV 6PZL HIS A 270 UNP P16466 EXPRESSION TAG SEQADV 6PZL HIS A 271 UNP P16466 EXPRESSION TAG SEQRES 1 A 242 ASN GLY ILE VAL PRO ASP ALA GLY HIS GLN GLY PRO ASP SEQRES 2 A 242 VAL SER ALA VAL ASN GLY GLY THR GLN VAL ILE ASN ILE SEQRES 3 A 242 VAL THR PRO ASN ASN GLU GLY ILE SER HIS ASN GLN TYR SEQRES 4 A 242 GLN ASP PHE ASN VAL GLY LYS PRO GLY ALA VAL PHE ASN SEQRES 5 A 242 ASN ALA LEU GLU ALA GLY GLN SER GLN LEU ALA GLY HIS SEQRES 6 A 242 LEU ASN ALA ASN SER ASN LEU ASN GLY GLN ALA ALA SER SEQRES 7 A 242 LEU ILE LEU ASN GLU VAL VAL SER ARG ASN PRO SER PHE SEQRES 8 A 242 LEU LEU GLY GLN ALA GLU VAL PHE GLY ILE ALA ALA GLU SEQRES 9 A 242 TYR VAL LEU SER ASN PRO ASN GLY ILE THR CYS ASP GLY SEQRES 10 A 242 CYS GLY PHE ILE ASN THR SER ARG SER SER LEU VAL VAL SEQRES 11 A 242 GLY ASN PRO LEU PHE GLU ASN GLY GLN LEU LYS GLY TYR SEQRES 12 A 242 SER THR LEU ASN ASN THR ASN LEU LEU SER LEU GLY LYS SEQRES 13 A 242 ASN GLY LEU ASN THR THR GLY LEU LEU ASP LEU ILE ALA SEQRES 14 A 242 PRO ARG ILE ASP SER ARG GLY LYS ILE THR ALA ALA GLU SEQRES 15 A 242 ILE SER ALA PHE THR GLY GLN ASN THR PHE SER GLN HIS SEQRES 16 A 242 PHE ASP ILE LEU SER SER GLN LYS PRO VAL SER ALA LEU SEQRES 17 A 242 ASP SER TYR PHE PHE GLY SER MET GLN SER GLY ARG ILE SEQRES 18 A 242 ARG ILE ILE ASN THR ALA GLU GLY SER GLY VAL LYS LEU SEQRES 19 A 242 ALA GLY HIS HIS HIS HIS HIS HIS HET GOL A 301 14 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *231(H2 O) HELIX 1 AA1 ASN A 98 ASN A 102 5 5 SHEET 1 AA1 8 VAL A 33 PRO A 34 0 SHEET 2 AA1 8 ILE A 63 ASP A 70 -1 O ASP A 70 N VAL A 33 SHEET 3 AA1 8 LEU A 108 VAL A 113 1 O LEU A 110 N ASN A 66 SHEET 4 AA1 8 ALA A 132 SER A 137 1 O VAL A 135 N ASN A 111 SHEET 5 AA1 8 THR A 152 VAL A 158 1 O VAL A 158 N LEU A 136 SHEET 6 AA1 8 LEU A 193 ALA A 198 1 O ILE A 197 N LEU A 157 SHEET 7 AA1 8 GLU A 211 THR A 216 1 O SER A 213 N LEU A 196 SHEET 8 AA1 8 ILE A 250 ASN A 254 1 O ILE A 253 N THR A 216 SHEET 1 AA2 8 ASP A 42 ASN A 47 0 SHEET 2 AA2 8 THR A 50 ASN A 54 -1 O ASN A 54 N ASP A 42 SHEET 3 AA2 8 ALA A 78 ASN A 82 1 O VAL A 79 N ILE A 53 SHEET 4 AA2 8 GLN A 124 GLY A 129 1 O GLU A 126 N PHE A 80 SHEET 5 AA2 8 CYS A 147 ILE A 150 1 O ILE A 150 N VAL A 127 SHEET 6 AA2 8 LEU A 188 THR A 190 1 O ASN A 189 N CYS A 147 SHEET 7 AA2 8 LYS A 206 THR A 208 1 O THR A 208 N LEU A 188 SHEET 8 AA2 8 SER A 244 GLN A 246 1 O GLN A 246 N ILE A 207 SHEET 1 AA3 2 GLY A 87 GLN A 88 0 SHEET 2 AA3 2 HIS A 94 LEU A 95 -1 O LEU A 95 N GLY A 87 SHEET 1 AA4 5 SER A 119 LEU A 121 0 SHEET 2 AA4 5 ILE A 142 CYS A 144 1 O THR A 143 N LEU A 121 SHEET 3 AA4 5 LEU A 180 LEU A 183 1 O SER A 182 N CYS A 144 SHEET 4 AA4 5 ARG A 200 SER A 203 1 O ASP A 202 N LEU A 183 SHEET 5 AA4 5 TYR A 240 PHE A 241 1 O TYR A 240 N SER A 203 SHEET 1 AA5 4 ASN A 161 GLU A 165 0 SHEET 2 AA5 4 GLN A 168 SER A 173 -1 O LYS A 170 N LEU A 163 SHEET 3 AA5 4 GLN A 218 PHE A 221 -1 O PHE A 221 N TYR A 172 SHEET 4 AA5 4 ILE A 227 GLN A 231 -1 O LEU A 228 N THR A 220 SSBOND 1 CYS A 144 CYS A 147 1555 1555 2.06 SITE 1 AC1 5 LYS A 170 LEU A 180 ARG A 200 HOH A 423 SITE 2 AC1 5 HOH A 578 CRYST1 34.047 60.224 116.350 90.00 90.00 90.00 P 2 21 21 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 0.029371 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016605 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008595 0.00000