HEADER TOXIN 19-APR-12 4AQN TITLE CRYSTAL STRUCTURE OF PESTICIN FROM Y. PESTIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PESTICIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA PESTIS; SOURCE 3 ORGANISM_TAXID: 632; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS TOXIN, BACTERIOCIN, COLICIN, THREE DOMAINS, MURAMIDASE EXPDTA X-RAY DIFFRACTION AUTHOR K.ZETH,R.ALBRECHT REVDAT 3 18-JUL-12 4AQN 1 JRNL REVDAT 2 30-MAY-12 4AQN 1 JRNL REVDAT 1 02-MAY-12 4AQN 0 JRNL AUTH S.I.PATZER,R.ALBRECHT,V.BRAUN,K.ZETH JRNL TITL STRUCTURE AND MECHANISTIC STUDIES OF PESTICIN, A BACTERIAL JRNL TITL 2 HOMOLOG OF PHAGE LYSOZYMES. JRNL REF J.BIOL.CHEM. V. 287 23381 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22593569 JRNL DOI 10.1074/JBC.M112.362913 REMARK 2 REMARK 2 RESOLUTION. 1.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT 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) : 1.980 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.819 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.99 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.75 REMARK 3 NUMBER OF REFLECTIONS : 52797 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1920 REMARK 3 R VALUE (WORKING SET) : 0.1896 REMARK 3 FREE R VALUE : 0.2369 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 2640 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 29.8221 - 5.2742 0.98 2663 140 0.1685 0.2017 REMARK 3 2 5.2742 - 4.1900 0.99 2653 140 0.1427 0.1824 REMARK 3 3 4.1900 - 3.6614 1.00 2622 138 0.1529 0.1980 REMARK 3 4 3.6614 - 3.3271 1.00 2636 139 0.1734 0.2230 REMARK 3 5 3.3271 - 3.0889 1.00 2671 140 0.1865 0.2163 REMARK 3 6 3.0889 - 2.9070 1.00 2649 140 0.2036 0.2638 REMARK 3 7 2.9070 - 2.7615 1.00 2629 138 0.2083 0.2734 REMARK 3 8 2.7615 - 2.6414 1.00 2647 139 0.1997 0.2734 REMARK 3 9 2.6414 - 2.5397 1.00 2639 139 0.2029 0.2619 REMARK 3 10 2.5397 - 2.4521 1.00 2621 138 0.2011 0.2804 REMARK 3 11 2.4521 - 2.3755 1.00 2684 141 0.2126 0.2692 REMARK 3 12 2.3755 - 2.3076 1.00 2586 136 0.2119 0.2618 REMARK 3 13 2.3076 - 2.2469 1.00 2631 139 0.2179 0.2498 REMARK 3 14 2.2469 - 2.1921 1.00 2641 139 0.2314 0.2888 REMARK 3 15 2.1921 - 2.1423 1.00 2599 137 0.2555 0.3363 REMARK 3 16 2.1423 - 2.0967 1.00 2664 140 0.2647 0.3118 REMARK 3 17 2.0967 - 2.0548 1.00 2623 138 0.2737 0.3191 REMARK 3 18 2.0548 - 2.0160 1.00 2616 138 0.2972 0.3323 REMARK 3 19 2.0160 - 1.9800 1.00 2683 141 0.3242 0.3593 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.309 REMARK 3 B_SOL : 42.153 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.29 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.32 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) : 1.4564 REMARK 3 B22 (A**2) : -1.1051 REMARK 3 B33 (A**2) : -0.3513 REMARK 3 B12 (A**2) : 0.0000 REMARK 3 B13 (A**2) : 0.9968 REMARK 3 B23 (A**2) : 0.0000 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 : 0.008 5520 REMARK 3 ANGLE : 1.133 7459 REMARK 3 CHIRALITY : 0.079 824 REMARK 3 PLANARITY : 0.004 977 REMARK 3 DIHEDRAL : 14.788 2075 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 13:164) REMARK 3 ORIGIN FOR THE GROUP (A): 16.4256 10.8567 21.8774 REMARK 3 T TENSOR REMARK 3 T11: 0.2118 T22: 0.5013 REMARK 3 T33: 0.1910 T12: -0.0729 REMARK 3 T13: -0.0079 T23: -0.0992 REMARK 3 L TENSOR REMARK 3 L11: 2.1009 L22: 1.5549 REMARK 3 L33: 5.1459 L12: -0.1215 REMARK 3 L13: -0.1947 L23: -1.4610 REMARK 3 S TENSOR REMARK 3 S11: 0.0158 S12: 0.7360 S13: -0.3115 REMARK 3 S21: -0.1754 S22: 0.1408 S23: -0.0183 REMARK 3 S31: -0.0328 S32: 0.0050 S33: -0.1233 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 165:357) REMARK 3 ORIGIN FOR THE GROUP (A): -0.7579 -0.8065 52.2974 REMARK 3 T TENSOR REMARK 3 T11: 0.2397 T22: 0.2020 REMARK 3 T33: 0.1871 T12: 0.0567 REMARK 3 T13: 0.0287 T23: 0.0403 REMARK 3 L TENSOR REMARK 3 L11: 2.0961 L22: 3.6850 REMARK 3 L33: 0.6749 L12: 1.0522 REMARK 3 L13: -0.2432 L23: 0.4026 REMARK 3 S TENSOR REMARK 3 S11: 0.1324 S12: -0.1040 S13: -0.0190 REMARK 3 S21: 0.4145 S22: -0.1367 S23: 0.1448 REMARK 3 S31: -0.0113 S32: 0.0355 S33: 0.0150 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN B AND (RESSEQ 13:39) REMARK 3 ORIGIN FOR THE GROUP (A): -21.6444 9.4353 121.6766 REMARK 3 T TENSOR REMARK 3 T11: 0.4563 T22: 1.0298 REMARK 3 T33: 0.4035 T12: -0.1118 REMARK 3 T13: -0.0038 T23: 0.0283 REMARK 3 L TENSOR REMARK 3 L11: 0.9906 L22: 2.1904 REMARK 3 L33: 6.4412 L12: -0.5859 REMARK 3 L13: 0.1833 L23: 0.0097 REMARK 3 S TENSOR REMARK 3 S11: 0.1591 S12: -0.5312 S13: 0.4732 REMARK 3 S21: -0.0206 S22: 0.1265 S23: 0.3228 REMARK 3 S31: 0.4451 S32: -0.0365 S33: -0.3677 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN B AND (RESSEQ 40:164) REMARK 3 ORIGIN FOR THE GROUP (A): -24.9272 12.1576 108.7904 REMARK 3 T TENSOR REMARK 3 T11: 0.3103 T22: 0.8839 REMARK 3 T33: 0.0239 T12: -0.0710 REMARK 3 T13: 0.0570 T23: -0.1406 REMARK 3 L TENSOR REMARK 3 L11: 1.7146 L22: 0.7487 REMARK 3 L33: 4.6646 L12: 0.1578 REMARK 3 L13: -0.1419 L23: 0.8137 REMARK 3 S TENSOR REMARK 3 S11: 0.1413 S12: -0.8138 S13: 0.4176 REMARK 3 S21: 0.1780 S22: -0.3804 S23: 0.1501 REMARK 3 S31: -0.0307 S32: -1.2472 S33: -0.0577 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN B AND (RESSEQ 165:336) REMARK 3 ORIGIN FOR THE GROUP (A): -5.0747 -0.3857 80.9914 REMARK 3 T TENSOR REMARK 3 T11: 0.2160 T22: 0.1438 REMARK 3 T33: 0.1538 T12: -0.0352 REMARK 3 T13: -0.0121 T23: -0.0039 REMARK 3 L TENSOR REMARK 3 L11: 2.6297 L22: 3.7958 REMARK 3 L33: 1.6080 L12: -1.8668 REMARK 3 L13: -0.9167 L23: 1.0230 REMARK 3 S TENSOR REMARK 3 S11: -0.1177 S12: -0.0509 S13: -0.1272 REMARK 3 S21: 0.0962 S22: 0.1254 S23: -0.1921 REMARK 3 S31: 0.2510 S32: 0.0776 S33: -0.0192 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN B AND (RESSEQ 337:357) REMARK 3 ORIGIN FOR THE GROUP (A): -21.9676 6.2970 77.9668 REMARK 3 T TENSOR REMARK 3 T11: 0.2801 T22: 0.2952 REMARK 3 T33: 0.2869 T12: -0.0153 REMARK 3 T13: -0.0815 T23: -0.0310 REMARK 3 L TENSOR REMARK 3 L11: 6.2730 L22: 3.4917 REMARK 3 L33: 8.0521 L12: -1.0410 REMARK 3 L13: -2.6594 L23: 2.0417 REMARK 3 S TENSOR REMARK 3 S11: 0.4348 S12: 0.1589 S13: -0.2764 REMARK 3 S21: -0.3883 S22: -0.4850 S23: 0.5508 REMARK 3 S31: -0.3622 S32: -1.1672 S33: 0.0731 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 4AQN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-APR-12. REMARK 100 THE PDBE ID CODE IS EBI-52128. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD (MX-225) REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52797 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.00 REMARK 200 RESOLUTION RANGE LOW (A) : 48.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.7 REMARK 200 R MERGE (I) : 0.10 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.30 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.5 REMARK 200 R MERGE FOR SHELL (I) : 0.65 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.00 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHARP, DM, BUCCANEER REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.8 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 8000, 0.2 M MGCL2, 0.1 M REMARK 280 HEPES PH 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 43.39000 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: 1560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.6 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 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 MET A 1 REMARK 465 SER A 2 REMARK 465 ASP A 3 REMARK 465 THR A 4 REMARK 465 MET A 5 REMARK 465 VAL A 6 REMARK 465 VAL A 7 REMARK 465 ASN A 8 REMARK 465 GLY A 9 REMARK 465 SER A 10 REMARK 465 GLY A 11 REMARK 465 GLY A 12 REMARK 465 PHE A 30 REMARK 465 GLU A 31 REMARK 465 ALA A 32 REMARK 465 ASN A 33 REMARK 465 SER A 34 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 ASP B 3 REMARK 465 THR B 4 REMARK 465 MET B 5 REMARK 465 VAL B 6 REMARK 465 VAL B 7 REMARK 465 ASN B 8 REMARK 465 GLY B 9 REMARK 465 SER B 10 REMARK 465 GLY B 11 REMARK 465 GLY B 12 REMARK 465 PRO B 28 REMARK 465 ASN B 29 REMARK 465 PHE B 30 REMARK 465 GLU B 31 REMARK 465 ALA B 32 REMARK 465 ASN B 33 REMARK 465 SER B 34 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 ASN A 29 CG OD1 ND2 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 OH TYR A 55 O HOH A 2004 2.07 REMARK 500 OH TYR A 300 O HOH A 2108 2.06 REMARK 500 O LEU A 356 O HOH A 2199 2.14 REMARK 500 OG SER B 79 O HOH B 2019 2.01 REMARK 500 OE1 GLU B 101 OH TYR B 108 2.14 REMARK 500 OE1 GLU B 255 O HOH B 2115 2.11 REMARK 500 OD1B ASN B 279 O HOH B 2139 2.03 REMARK 500 O HOH A 2030 O HOH A 2109 2.13 REMARK 500 O HOH A 2034 O HOH A 2139 2.20 REMARK 500 O HOH A 2074 O HOH A 2197 1.95 REMARK 500 O HOH A 2112 O HOH A 2115 2.13 REMARK 500 O HOH A 2201 O HOH A 2202 2.10 REMARK 500 O HOH B 2041 O HOH B 2107 1.94 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 ILE B 280 O HOH A 2147 2556 2.04 REMARK 500 O HOH A 2061 O HOH B 2162 2546 2.09 REMARK 500 REMARK 500 REMARK: NULL 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 PRO A 28 C - N - CA ANGL. DEV. = 10.4 DEGREES 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 38 53.23 -114.97 REMARK 500 PRO A 46 -87.28 -30.65 REMARK 500 PHE A 51 72.25 -118.39 REMARK 500 MET A 57 -133.88 51.54 REMARK 500 PHE A 177 -114.85 -121.56 REMARK 500 SER A 184 119.36 -39.53 REMARK 500 PRO A 187 44.38 -85.09 REMARK 500 ALA A 310 66.81 -152.11 REMARK 500 PRO B 14 104.08 -40.57 REMARK 500 PRO B 46 -86.31 -38.38 REMARK 500 ARG B 48 -161.72 -128.07 REMARK 500 ASP B 68 152.91 -43.45 REMARK 500 LYS B 102 135.79 -173.96 REMARK 500 PHE B 177 -115.57 -120.48 REMARK 500 PRO B 187 47.89 -77.90 REMARK 500 SER B 192 156.20 -49.86 REMARK 500 ALA B 310 66.17 -151.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ILE B 280 23.0 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1358 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B2182 O REMARK 620 2 HOH B2153 O 62.0 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B1358 REMARK 999 REMARK 999 SEQUENCE REMARK 999 OTHER_DETAILS: PESTICIN FROM Y. PESTIS WAS CLONED INTO E. REMARK 999 COLI WITH NO OVERHANGING RESIDUES. DBREF 4AQN A 1 357 UNP Q57159 Q57159_YERPE 1 357 DBREF 4AQN B 1 357 UNP Q57159 Q57159_YERPE 1 357 SEQRES 1 A 357 MET SER ASP THR MET VAL VAL ASN GLY SER GLY GLY VAL SEQRES 2 A 357 PRO ALA PHE LEU PHE SER GLY SER THR LEU SER SER TYR SEQRES 3 A 357 ARG PRO ASN PHE GLU ALA ASN SER ILE THR ILE ALA LEU SEQRES 4 A 357 PRO HIS TYR VAL ASP LEU PRO GLY ARG SER ASN PHE LYS SEQRES 5 A 357 LEU MET TYR ILE MET GLY PHE PRO ILE ASP THR GLU MET SEQRES 6 A 357 GLU LYS ASP SER GLU TYR SER ASN LYS ILE ARG GLN GLU SEQRES 7 A 357 SER LYS ILE SER LYS THR GLU GLY THR VAL SER TYR GLU SEQRES 8 A 357 GLN LYS ILE THR VAL GLU THR GLY GLN GLU LYS ASP GLY SEQRES 9 A 357 VAL LYS VAL TYR ARG VAL MET VAL LEU GLU GLY THR ILE SEQRES 10 A 357 ALA GLU SER ILE GLU HIS LEU ASP LYS LYS GLU ASN GLU SEQRES 11 A 357 ASP ILE LEU ASN ASN ASN ARG ASN ARG ILE VAL LEU ALA SEQRES 12 A 357 ASP ASN THR VAL ILE ASN PHE ASP ASN ILE SER GLN LEU SEQRES 13 A 357 LYS GLU PHE LEU ARG ARG SER VAL ASN ILE VAL ASP HIS SEQRES 14 A 357 ASP ILE PHE SER SER ASN GLY PHE GLU GLY PHE ASN PRO SEQRES 15 A 357 THR SER HIS PHE PRO SER ASN PRO SER SER ASP TYR PHE SEQRES 16 A 357 ASN SER THR GLY VAL THR PHE GLY SER GLY VAL ASP LEU SEQRES 17 A 357 GLY GLN ARG SER LYS GLN ASP LEU LEU ASN ASP GLY VAL SEQRES 18 A 357 PRO GLN TYR ILE ALA ASP ARG LEU ASP GLY TYR TYR MET SEQRES 19 A 357 LEU ARG GLY LYS GLU ALA TYR ASP LYS VAL ARG THR ALA SEQRES 20 A 357 PRO LEU THR LEU SER ASP ASN GLU ALA HIS LEU LEU SER SEQRES 21 A 357 ASN ILE TYR ILE ASP LYS PHE SER HIS LYS ILE GLU GLY SEQRES 22 A 357 LEU PHE ASN ASP ALA ASN ILE GLY LEU ARG PHE SER ASP SEQRES 23 A 357 LEU PRO LEU ARG THR ARG THR ALA LEU VAL SER ILE GLY SEQRES 24 A 357 TYR GLN LYS GLY PHE LYS LEU SER ARG THR ALA PRO THR SEQRES 25 A 357 VAL TRP ASN LYS VAL ILE ALA LYS ASP TRP ASN GLY LEU SEQRES 26 A 357 VAL ASN ALA PHE ASN ASN ILE VAL ASP GLY MET SER ASP SEQRES 27 A 357 ARG ARG LYS ARG GLU GLY ALA LEU VAL GLN LYS ASP ILE SEQRES 28 A 357 ASP SER GLY LEU LEU LYS SEQRES 1 B 357 MET SER ASP THR MET VAL VAL ASN GLY SER GLY GLY VAL SEQRES 2 B 357 PRO ALA PHE LEU PHE SER GLY SER THR LEU SER SER TYR SEQRES 3 B 357 ARG PRO ASN PHE GLU ALA ASN SER ILE THR ILE ALA LEU SEQRES 4 B 357 PRO HIS TYR VAL ASP LEU PRO GLY ARG SER ASN PHE LYS SEQRES 5 B 357 LEU MET TYR ILE MET GLY PHE PRO ILE ASP THR GLU MET SEQRES 6 B 357 GLU LYS ASP SER GLU TYR SER ASN LYS ILE ARG GLN GLU SEQRES 7 B 357 SER LYS ILE SER LYS THR GLU GLY THR VAL SER TYR GLU SEQRES 8 B 357 GLN LYS ILE THR VAL GLU THR GLY GLN GLU LYS ASP GLY SEQRES 9 B 357 VAL LYS VAL TYR ARG VAL MET VAL LEU GLU GLY THR ILE SEQRES 10 B 357 ALA GLU SER ILE GLU HIS LEU ASP LYS LYS GLU ASN GLU SEQRES 11 B 357 ASP ILE LEU ASN ASN ASN ARG ASN ARG ILE VAL LEU ALA SEQRES 12 B 357 ASP ASN THR VAL ILE ASN PHE ASP ASN ILE SER GLN LEU SEQRES 13 B 357 LYS GLU PHE LEU ARG ARG SER VAL ASN ILE VAL ASP HIS SEQRES 14 B 357 ASP ILE PHE SER SER ASN GLY PHE GLU GLY PHE ASN PRO SEQRES 15 B 357 THR SER HIS PHE PRO SER ASN PRO SER SER ASP TYR PHE SEQRES 16 B 357 ASN SER THR GLY VAL THR PHE GLY SER GLY VAL ASP LEU SEQRES 17 B 357 GLY GLN ARG SER LYS GLN ASP LEU LEU ASN ASP GLY VAL SEQRES 18 B 357 PRO GLN TYR ILE ALA ASP ARG LEU ASP GLY TYR TYR MET SEQRES 19 B 357 LEU ARG GLY LYS GLU ALA TYR ASP LYS VAL ARG THR ALA SEQRES 20 B 357 PRO LEU THR LEU SER ASP ASN GLU ALA HIS LEU LEU SER SEQRES 21 B 357 ASN ILE TYR ILE ASP LYS PHE SER HIS LYS ILE GLU GLY SEQRES 22 B 357 LEU PHE ASN ASP ALA ASN ILE GLY LEU ARG PHE SER ASP SEQRES 23 B 357 LEU PRO LEU ARG THR ARG THR ALA LEU VAL SER ILE GLY SEQRES 24 B 357 TYR GLN LYS GLY PHE LYS LEU SER ARG THR ALA PRO THR SEQRES 25 B 357 VAL TRP ASN LYS VAL ILE ALA LYS ASP TRP ASN GLY LEU SEQRES 26 B 357 VAL ASN ALA PHE ASN ASN ILE VAL ASP GLY MET SER ASP SEQRES 27 B 357 ARG ARG LYS ARG GLU GLY ALA LEU VAL GLN LYS ASP ILE SEQRES 28 B 357 ASP SER GLY LEU LEU LYS HET MG B1358 1 HETNAM MG MAGNESIUM ION FORMUL 3 MG MG 2+ FORMUL 4 HOH *385(H2 O) HELIX 1 1 THR A 116 ASP A 125 1 10 HELIX 2 2 LYS A 126 GLU A 128 5 3 HELIX 3 3 ASN A 129 ASN A 135 1 7 HELIX 4 4 ASN A 152 ASN A 165 1 14 HELIX 5 5 ASP A 168 SER A 173 1 6 HELIX 6 6 TYR A 194 THR A 198 5 5 HELIX 7 7 SER A 212 ASP A 219 1 8 HELIX 8 8 PRO A 222 LEU A 229 1 8 HELIX 9 9 GLY A 237 ALA A 247 1 11 HELIX 10 10 SER A 252 ALA A 278 1 27 HELIX 11 11 ARG A 283 LEU A 287 5 5 HELIX 12 12 PRO A 288 GLY A 303 1 16 HELIX 13 13 LYS A 305 ALA A 310 1 6 HELIX 14 14 ALA A 310 ALA A 319 1 10 HELIX 15 15 ASP A 321 ILE A 332 1 12 HELIX 16 16 MET A 336 SER A 353 1 18 HELIX 17 17 THR B 116 ASP B 125 1 10 HELIX 18 18 LYS B 126 ASN B 135 1 10 HELIX 19 19 ASN B 152 ASN B 165 1 14 HELIX 20 20 ASP B 168 SER B 173 1 6 HELIX 21 21 SER B 212 ASP B 219 1 8 HELIX 22 22 PRO B 222 LEU B 229 1 8 HELIX 23 23 ARG B 236 ALA B 247 1 12 HELIX 24 24 SER B 252 ALA B 278 1 27 HELIX 25 25 ARG B 283 LEU B 287 5 5 HELIX 26 26 PRO B 288 GLY B 303 1 16 HELIX 27 27 LYS B 305 ALA B 310 1 6 HELIX 28 28 ALA B 310 ILE B 318 1 9 HELIX 29 29 ASP B 321 ASN B 331 1 11 HELIX 30 30 MET B 336 SER B 353 1 18 SHEET 1 AA 2 LEU A 23 SER A 24 0 SHEET 2 AA 2 VAL A 105 GLY A 115 -1 O MET A 111 N LEU A 23 SHEET 1 AB 7 HIS A 41 ASP A 44 0 SHEET 2 AB 7 LYS A 52 ILE A 56 -1 O LEU A 53 N VAL A 43 SHEET 3 AB 7 PHE A 59 MET A 65 -1 O PHE A 59 N ILE A 56 SHEET 4 AB 7 VAL A 105 GLY A 115 -1 O LYS A 106 N GLU A 64 SHEET 5 AB 7 ILE A 94 LYS A 102 -1 O ILE A 94 N GLY A 115 SHEET 6 AB 7 ARG A 137 VAL A 141 -1 O ARG A 137 N GLY A 99 SHEET 7 AB 7 VAL A 147 PHE A 150 -1 O ILE A 148 N ILE A 140 SHEET 1 AC 5 HIS A 41 ASP A 44 0 SHEET 2 AC 5 LYS A 52 ILE A 56 -1 O LEU A 53 N VAL A 43 SHEET 3 AC 5 PHE A 59 MET A 65 -1 O PHE A 59 N ILE A 56 SHEET 4 AC 5 VAL A 105 GLY A 115 -1 O LYS A 106 N GLU A 64 SHEET 5 AC 5 LEU A 23 SER A 24 -1 O LEU A 23 N LEU A 113 SHEET 1 AD 3 ASN A 181 HIS A 185 0 SHEET 2 AD 3 THR A 201 GLY A 203 -1 O THR A 201 N HIS A 185 SHEET 3 AD 3 VAL A 206 ASP A 207 -1 O VAL A 206 N PHE A 202 SHEET 1 BA 2 LEU B 23 SER B 24 0 SHEET 2 BA 2 VAL B 105 GLY B 115 -1 O MET B 111 N LEU B 23 SHEET 1 BB 7 HIS B 41 ASP B 44 0 SHEET 2 BB 7 LYS B 52 ILE B 56 -1 O LEU B 53 N VAL B 43 SHEET 3 BB 7 PHE B 59 MET B 65 -1 O PHE B 59 N ILE B 56 SHEET 4 BB 7 VAL B 105 GLY B 115 -1 O LYS B 106 N GLU B 64 SHEET 5 BB 7 ILE B 94 LYS B 102 -1 O ILE B 94 N GLY B 115 SHEET 6 BB 7 ARG B 137 VAL B 141 -1 O ARG B 137 N GLY B 99 SHEET 7 BB 7 VAL B 147 PHE B 150 -1 O ILE B 148 N ILE B 140 SHEET 1 BC 5 HIS B 41 ASP B 44 0 SHEET 2 BC 5 LYS B 52 ILE B 56 -1 O LEU B 53 N VAL B 43 SHEET 3 BC 5 PHE B 59 MET B 65 -1 O PHE B 59 N ILE B 56 SHEET 4 BC 5 VAL B 105 GLY B 115 -1 O LYS B 106 N GLU B 64 SHEET 5 BC 5 LEU B 23 SER B 24 -1 O LEU B 23 N LEU B 113 SHEET 1 BD 3 ASN B 181 HIS B 185 0 SHEET 2 BD 3 THR B 201 GLY B 203 -1 O THR B 201 N HIS B 185 SHEET 3 BD 3 VAL B 206 ASP B 207 -1 O VAL B 206 N PHE B 202 LINK MG MG B1358 O HOH B2182 1555 1555 2.85 LINK MG MG B1358 O HOH B2153 1555 1555 2.98 CISPEP 1 VAL A 13 PRO A 14 0 -1.14 CISPEP 2 SER A 49 ASN A 50 0 2.72 CISPEP 3 ILE B 280 GLY B 281 0 4.48 SITE 1 AC1 4 GLU B 178 HOH B2098 HOH B2153 HOH B2182 CRYST1 36.550 86.780 122.270 90.00 96.14 90.00 P 1 21 1 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 0.027360 0.000000 0.002943 0.00000 SCALE2 0.000000 0.011523 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008226 0.00000