HEADER TOXIN 30-JUL-19 6PYK TITLE P. MIRABILIS HEMOLYSIN A MUTANT - F80L 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; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET24A+ 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 6PYK 1 REMARK REVDAT 1 05-AUG-20 6PYK 0 JRNL AUTH T.M.WEAVER,W.R.P.NOVAK,B.BHATTACHARYYA,C.N.WOODS, JRNL AUTH 2 D.P.GRILLEY,M.R.WIMMER JRNL TITL STRUCTURE OF TRUNCATED HEMOLYSIN A VARIANT F80L JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.35 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 44567 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.134 REMARK 3 R VALUE (WORKING SET) : 0.133 REMARK 3 FREE R VALUE : 0.162 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 2172 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 34.0110 - 3.4010 0.97 2718 130 0.1578 0.1584 REMARK 3 2 3.4010 - 2.6998 1.00 2704 149 0.1466 0.1712 REMARK 3 3 2.6998 - 2.3586 1.00 2679 133 0.1473 0.1604 REMARK 3 4 2.3586 - 2.1430 1.00 2656 141 0.1202 0.1372 REMARK 3 5 2.1430 - 1.9894 1.00 2704 124 0.1100 0.1378 REMARK 3 6 1.9894 - 1.8722 1.00 2644 138 0.1029 0.1633 REMARK 3 7 1.8722 - 1.7784 1.00 2644 146 0.1035 0.1498 REMARK 3 8 1.7784 - 1.7010 1.00 2668 128 0.1065 0.1580 REMARK 3 9 1.7010 - 1.6355 1.00 2672 139 0.1031 0.1654 REMARK 3 10 1.6355 - 1.5791 1.00 2656 139 0.0998 0.1560 REMARK 3 11 1.5791 - 1.5297 1.00 2636 133 0.1029 0.1557 REMARK 3 12 1.5297 - 1.4860 1.00 2645 129 0.1183 0.1613 REMARK 3 13 1.4860 - 1.4469 1.00 2668 134 0.1318 0.2000 REMARK 3 14 1.4469 - 1.4116 1.00 2632 120 0.1561 0.2181 REMARK 3 15 1.4116 - 1.3795 0.99 2649 149 0.1643 0.2233 REMARK 3 16 1.3795 - 1.3501 0.93 2420 140 0.1828 0.2368 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.320 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.38 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 6PYK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1000243155. 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 : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL CRY-COOLED REMARK 200 SI(111) REMARK 200 OPTICS : BERYLLIUM LENSES REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44578 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 34.011 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.80400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 3FY3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 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 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-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 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: 1650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19940 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 114.46970 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -58.38322 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 HIS A 271 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS A 147 CA - CB - SG ANGL. DEV. = 7.0 DEGREES 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 264 -169.74 -113.38 REMARK 500 REMARK 500 REMARK: NULL DBREF 6PYK A 30 265 UNP P16466 HLYA_PROMI 30 265 SEQADV 6PYK LEU A 80 UNP P16466 PHE 80 ENGINEERED MUTATION SEQADV 6PYK HIS A 266 UNP P16466 EXPRESSION TAG SEQADV 6PYK HIS A 267 UNP P16466 EXPRESSION TAG SEQADV 6PYK HIS A 268 UNP P16466 EXPRESSION TAG SEQADV 6PYK HIS A 269 UNP P16466 EXPRESSION TAG SEQADV 6PYK HIS A 270 UNP P16466 EXPRESSION TAG SEQADV 6PYK 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 LEU 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 GLN 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 FORMUL 2 HOH *119(H2 O) 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 SER A 137 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 ALA A 45 0 SHEET 2 AA2 8 GLN A 51 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 LEU A 80 SHEET 5 AA2 8 CYS A 147 ILE A 150 1 O ILE A 150 N GLN A 125 SHEET 6 AA2 8 LEU A 188 THR A 190 1 O ASN A 189 N PHE A 149 SHEET 7 AA2 8 LYS A 206 ALA A 209 1 O THR A 208 N LEU A 188 SHEET 8 AA2 8 SER A 244 SER A 247 1 O GLN A 246 N ILE A 207 SHEET 1 AA3 2 GLY A 87 SER A 89 0 SHEET 2 AA3 2 GLY A 93 LEU A 95 -1 O LEU A 95 N GLY A 87 SHEET 1 AA4 6 SER A 119 LEU A 121 0 SHEET 2 AA4 6 ILE A 142 CYS A 144 1 O THR A 143 N LEU A 121 SHEET 3 AA4 6 LEU A 180 LEU A 183 1 O SER A 182 N CYS A 144 SHEET 4 AA4 6 ARG A 200 SER A 203 1 O ASP A 202 N LEU A 183 SHEET 5 AA4 6 SER A 239 PHE A 241 1 O TYR A 240 N SER A 203 SHEET 6 AA4 6 VAL A 261 LEU A 263 1 O LYS A 262 N SER A 239 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 SER A 222 -1 O PHE A 221 N TYR A 172 SHEET 4 AA5 4 ILE A 227 GLN A 231 -1 O GLN A 231 N GLN A 218 SSBOND 1 CYS A 144 CYS A 147 1555 1555 2.03 CRYST1 51.550 34.011 59.480 90.00 101.02 90.00 P 1 2 1 2 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 0.019399 0.000000 0.003776 0.00000 SCALE2 0.000000 0.029402 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017128 0.00000