HEADER HYDROLASE/HYDROLASE INHIBITOR 16-JUL-18 6A9U TITLE CRYSTAL STRCTURE OF ICP55 FROM SACCHAROMYCES CEREVISIAE BOUND TO TITLE 2 APSTATIN INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERMEDIATE CLEAVING PEPTIDASE 55; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: INTERMEDIATE CLEAVING PEPTIDASE OF 55 KDA; COMPND 5 EC: 3.4.11.26; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: APSTATIN; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE S288C; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: ICP55, YER078C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PST50STR; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 3263 KEYWDS INTERMEDIATE CLEAVING PEPTIDASE 55, M24B, PEPTIDASE, XAA-PRO KEYWDS 2 AMINOPEPTIDASE, MITOCHONDRIAL, APSTATIN, N-((2S, 3R)-3-AMINO-2- KEYWDS 3 HYDROXY-4-PHENYLBUTANOYL)-PRO-PRO-ALA-NH2, HYDROLASE, HYDROLASE- KEYWDS 4 HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.SINGH,A.KUMAR,V.D.GOYAL,R.D.MAKDE REVDAT 4 22-NOV-23 6A9U 1 REMARK REVDAT 3 15-NOV-23 6A9U 1 LINK ATOM REVDAT 2 13-MAR-19 6A9U 1 JRNL REVDAT 1 16-JAN-19 6A9U 0 JRNL AUTH R.SINGH,V.D.GOYAL,A.KUMAR,N.S.SABHARWAL,R.D.MAKDE JRNL TITL CRYSTAL STRUCTURES AND BIOCHEMICAL ANALYSES OF INTERMEDIATE JRNL TITL 2 CLEAVAGE PEPTIDASE: ROLE OF DYNAMICS IN ENZYMATIC FUNCTION. JRNL REF FEBS LETT. V. 593 443 2019 JRNL REFN ISSN 1873-3468 JRNL PMID 30582634 JRNL DOI 10.1002/1873-3468.13321 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 27365 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 1407 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 47.7673 - 5.1689 0.98 2724 137 0.2114 0.2113 REMARK 3 2 5.1689 - 4.1034 1.00 2639 145 0.1638 0.1825 REMARK 3 3 4.1034 - 3.5849 1.00 2581 159 0.2094 0.2796 REMARK 3 4 3.5849 - 3.2572 1.00 2604 148 0.2388 0.2816 REMARK 3 5 3.2572 - 3.0238 1.00 2566 144 0.2765 0.3661 REMARK 3 6 3.0238 - 2.8455 1.00 2560 154 0.2689 0.3415 REMARK 3 7 2.8455 - 2.7030 1.00 2571 138 0.2688 0.3479 REMARK 3 8 2.7030 - 2.5854 1.00 2579 119 0.2677 0.2848 REMARK 3 9 2.5854 - 2.4859 1.00 2572 133 0.2799 0.3489 REMARK 3 10 2.4859 - 2.4001 1.00 2562 130 0.2831 0.3226 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) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 44.80 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 : 0.004 3319 REMARK 3 ANGLE : 0.600 4488 REMARK 3 CHIRALITY : 0.046 494 REMARK 3 PLANARITY : 0.005 585 REMARK 3 DIHEDRAL : 3.946 2788 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 59 THROUGH 268 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.5146 -46.8757 -7.8225 REMARK 3 T TENSOR REMARK 3 T11: 0.3859 T22: 0.4799 REMARK 3 T33: 0.3141 T12: -0.0256 REMARK 3 T13: -0.0428 T23: -0.0192 REMARK 3 L TENSOR REMARK 3 L11: 2.9009 L22: 2.3666 REMARK 3 L33: 1.8294 L12: 2.1084 REMARK 3 L13: 0.6725 L23: 0.5359 REMARK 3 S TENSOR REMARK 3 S11: 0.3379 S12: -0.6253 S13: -0.0658 REMARK 3 S21: 0.4238 S22: -0.4371 S23: 0.0302 REMARK 3 S31: 0.2432 S32: -0.5436 S33: 0.0993 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 269 THROUGH 498 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.2960 -30.1294 -23.6725 REMARK 3 T TENSOR REMARK 3 T11: 0.3557 T22: 0.2708 REMARK 3 T33: 0.3711 T12: 0.0017 REMARK 3 T13: -0.0935 T23: 0.0151 REMARK 3 L TENSOR REMARK 3 L11: 1.9547 L22: 1.0938 REMARK 3 L33: 2.4559 L12: 0.5383 REMARK 3 L13: 0.1950 L23: 0.2516 REMARK 3 S TENSOR REMARK 3 S11: -0.1731 S12: 0.1213 S13: 0.0074 REMARK 3 S21: -0.1069 S22: 0.0969 S23: -0.1342 REMARK 3 S31: -0.2405 S32: 0.3351 S33: 0.0618 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 6A9U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1300008248. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : RRCAT INDUS-2 REMARK 200 BEAMLINE : PX-BL21 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97947 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27387 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 47.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.82400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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: 1A16 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HIPIS PH 7 , 28% JAGFFAMINE ED REMARK 280 2003 PH7, 2MM MNCL2, PH 7.0, MICROBATCH, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 74.04450 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 74.04450 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 62.49450 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 74.04450 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 74.04450 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 62.49450 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 74.04450 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 74.04450 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 62.49450 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 74.04450 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 74.04450 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 62.49450 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 74.04450 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 74.04450 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 62.49450 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 74.04450 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 74.04450 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 62.49450 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 74.04450 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 74.04450 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 62.49450 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 74.04450 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 74.04450 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 62.49450 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: 1200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 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 762 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE APSTATIN IS PEPTIDE-LIKE, A MEMBER OF ENZYME INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: APSTATIN REMARK 400 CHAIN: B REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 GLY A 57 REMARK 465 SER A 58 REMARK 465 PHE A 96 REMARK 465 ALA A 97 REMARK 465 SER A 98 REMARK 465 GLY A 99 REMARK 465 ALA A 100 REMARK 465 VAL A 101 REMARK 465 PHE A 102 REMARK 465 LYS A 145 REMARK 465 ASP A 146 REMARK 465 ALA A 147 REMARK 465 PHE A 148 REMARK 465 ALA A 149 REMARK 465 GLU A 150 REMARK 465 LYS A 151 REMARK 465 TRP A 152 REMARK 465 GLU A 153 REMARK 465 GLY A 154 REMARK 465 SER A 197 REMARK 465 THR A 198 REMARK 465 SER A 199 REMARK 465 ASN A 200 REMARK 465 PRO A 201 REMARK 465 GLY A 215 REMARK 465 SER A 216 REMARK 465 GLY A 217 REMARK 465 ASN A 218 REMARK 465 SER A 219 REMARK 465 ASN A 220 REMARK 465 ARG A 221 REMARK 465 SER A 222 REMARK 465 LEU A 223 REMARK 465 ASN A 224 REMARK 465 SER A 225 REMARK 465 ILE A 226 REMARK 465 ALA A 227 REMARK 465 LEU A 499 REMARK 465 SER A 500 REMARK 465 THR A 501 REMARK 465 LYS A 502 REMARK 465 PHE A 503 REMARK 465 GLU A 504 REMARK 465 GLU A 505 REMARK 465 ASP A 506 REMARK 465 GLN A 507 REMARK 465 VAL A 508 REMARK 465 ALA A 509 REMARK 465 PRO A 510 REMARK 465 LEU A 511 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 LEU A 133 CG CD1 CD2 REMARK 470 TYR A 160 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 179 CG CD CE NZ REMARK 470 LYS A 183 CG CD CE NZ REMARK 470 ARG A 262 CZ NH1 NH2 REMARK 470 ARG A 273 NE CZ NH1 NH2 REMARK 470 ASP A 321 CG OD1 OD2 REMARK 470 LYS A 401 CG CD CE NZ 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 01B B 1 O - C - N ANGL. DEV. = -22.4 DEGREES REMARK 500 PRO B 2 C - N - CA ANGL. DEV. = 23.4 DEGREES REMARK 500 PRO B 2 C - N - CD ANGL. DEV. = -23.6 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 PRO A 63 105.57 -56.51 REMARK 500 LYS A 84 64.67 64.28 REMARK 500 SER A 115 -36.60 -146.62 REMARK 500 ASN A 121 73.52 58.99 REMARK 500 THR A 130 -155.18 -122.90 REMARK 500 ASN A 167 41.22 72.10 REMARK 500 ILE A 234 -20.34 -147.44 REMARK 500 ASP A 315 34.56 -150.00 REMARK 500 ASP A 338 117.05 -168.62 REMARK 500 VAL A 426 66.86 31.58 REMARK 500 GLU A 444 72.53 -150.66 REMARK 500 THR A 476 -168.34 -170.33 REMARK 500 LYS A 486 -15.60 -148.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 01B B 1 PRO B 2 -141.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 01B B 1 25.77 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 MN A 601 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 327 OD1 REMARK 620 2 ASP A 327 OD2 51.3 REMARK 620 3 ASP A 338 OD1 87.6 138.8 REMARK 620 4 GLU A 467 OE2 99.0 98.1 89.5 REMARK 620 5 01B B 1 N 94.6 86.9 95.4 165.8 REMARK 620 6 01B B 1 O2 157.8 106.6 114.6 81.9 83.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 602 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 338 OD2 REMARK 620 2 HIS A 417 NE2 107.4 REMARK 620 3 GLU A 444 OE1 158.5 86.3 REMARK 620 4 GLU A 467 OE1 84.7 129.8 73.9 REMARK 620 5 01B B 1 O2 101.5 136.1 77.7 84.6 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for APSTATIN chain B DBREF 6A9U A 58 511 UNP P40051 ICP55_YEAST 58 511 DBREF 6A9U B 1 5 PDB 6A9U 6A9U 1 5 SEQADV 6A9U GLY A 57 UNP P40051 EXPRESSION TAG SEQADV 6A9U GLU A 189 UNP P40051 ASP 189 ENGINEERED MUTATION SEQRES 1 A 455 GLY SER GLY GLU LEU THR PRO GLY ILE SER ALA LEU GLU SEQRES 2 A 455 TYR TYR GLU ARG ARG ILE ARG LEU ALA GLU THR LEU PRO SEQRES 3 A 455 PRO LYS SER CYS VAL ILE LEU ALA GLY ASN ASP ILE GLN SEQRES 4 A 455 PHE ALA SER GLY ALA VAL PHE TYR PRO PHE GLN GLN GLU SEQRES 5 A 455 ASN ASP LEU PHE TYR LEU SER GLY TRP ASN GLU PRO ASN SEQRES 6 A 455 SER VAL MET ILE LEU GLU LYS PRO THR ASP SER LEU SER SEQRES 7 A 455 ASP THR ILE PHE HIS MET LEU VAL PRO PRO LYS ASP ALA SEQRES 8 A 455 PHE ALA GLU LYS TRP GLU GLY PHE ARG SER GLY VAL TYR SEQRES 9 A 455 GLY VAL GLN GLU ILE PHE ASN ALA ASP GLU SER ALA SER SEQRES 10 A 455 ILE ASN ASP LEU SER LYS TYR LEU PRO LYS ILE ILE ASN SEQRES 11 A 455 ARG ASN GLU PHE ILE TYR PHE ASP MET LEU SER THR SER SEQRES 12 A 455 ASN PRO SER SER SER ASN PHE LYS HIS ILE LYS SER LEU SEQRES 13 A 455 LEU ASP GLY SER GLY ASN SER ASN ARG SER LEU ASN SER SEQRES 14 A 455 ILE ALA ASN LYS THR ILE LYS PRO ILE SER LYS ARG ILE SEQRES 15 A 455 ALA GLU PHE ARG LYS ILE LYS SER PRO GLN GLU LEU ARG SEQRES 16 A 455 ILE MET ARG ARG ALA GLY GLN ILE SER GLY ARG SER PHE SEQRES 17 A 455 ASN GLN ALA PHE ALA LYS ARG PHE ARG ASN GLU ARG THR SEQRES 18 A 455 LEU ASP SER PHE LEU HIS TYR LYS PHE ILE SER GLY GLY SEQRES 19 A 455 CYS ASP LYS ASP ALA TYR ILE PRO VAL VAL ALA THR GLY SEQRES 20 A 455 SER ASN SER LEU CYS ILE HIS TYR THR ARG ASN ASP ASP SEQRES 21 A 455 VAL MET PHE ASP ASP GLU MET VAL LEU VAL ASP ALA ALA SEQRES 22 A 455 GLY SER LEU GLY GLY TYR CYS ALA ASP ILE SER ARG THR SEQRES 23 A 455 TRP PRO ASN SER GLY LYS PHE THR ASP ALA GLN ARG ASP SEQRES 24 A 455 LEU TYR GLU ALA VAL LEU ASN VAL GLN ARG ASP CYS ILE SEQRES 25 A 455 LYS LEU CYS LYS ALA SER ASN ASN TYR SER LEU HIS ASP SEQRES 26 A 455 ILE HIS GLU LYS SER ILE THR LEU MET LYS GLN GLU LEU SEQRES 27 A 455 LYS ASN LEU GLY ILE ASP LYS VAL SER GLY TRP ASN VAL SEQRES 28 A 455 GLU LYS LEU TYR PRO HIS TYR ILE GLY HIS ASN LEU GLY SEQRES 29 A 455 LEU ASP VAL HIS ASP VAL PRO LYS VAL SER ARG TYR GLU SEQRES 30 A 455 PRO LEU LYS VAL GLY GLN VAL ILE THR ILE GLU PRO GLY SEQRES 31 A 455 LEU TYR ILE PRO ASN GLU GLU SER PHE PRO SER TYR PHE SEQRES 32 A 455 ARG ASN VAL GLY ILE ARG ILE GLU ASP ASP ILE ALA ILE SEQRES 33 A 455 GLY GLU ASP THR TYR THR ASN LEU THR VAL GLU ALA VAL SEQRES 34 A 455 LYS GLU ILE ASP ASP LEU GLU ASN VAL MET GLN ASN GLY SEQRES 35 A 455 LEU SER THR LYS PHE GLU GLU ASP GLN VAL ALA PRO LEU SEQRES 1 B 5 01B PRO PRO ALA NH2 HET 01B B 1 13 HET NH2 B 5 1 HET MN A 601 1 HET MN A 602 1 HETNAM 01B (2S,3R)-3-AMINO-2-HYDROXY-4-PHENYLBUTANOIC ACID HETNAM NH2 AMINO GROUP HETNAM MN MANGANESE (II) ION FORMUL 2 01B C10 H13 N O3 FORMUL 2 NH2 H2 N FORMUL 3 MN 2(MN 2+) FORMUL 5 HOH *88(H2 O) HELIX 1 AA1 SER A 66 GLU A 79 1 14 HELIX 2 AA2 GLU A 108 GLY A 116 1 9 HELIX 3 AA3 SER A 157 ILE A 165 1 9 HELIX 4 AA4 ASP A 176 ASN A 186 1 11 HELIX 5 AA5 SER A 203 LEU A 213 1 11 HELIX 6 AA6 ILE A 234 LYS A 243 1 10 HELIX 7 AA7 SER A 246 ALA A 269 1 24 HELIX 8 AA8 ASN A 274 GLY A 290 1 17 HELIX 9 AA9 SER A 304 CYS A 308 5 5 HELIX 10 AB1 THR A 350 LYS A 369 1 20 HELIX 11 AB2 LEU A 370 CYS A 371 5 2 HELIX 12 AB3 LYS A 372 ASN A 376 5 5 HELIX 13 AB4 SER A 378 LEU A 397 1 20 HELIX 14 AB5 ASN A 406 TYR A 411 1 6 HELIX 15 AB6 GLU A 487 GLY A 498 1 12 SHEET 1 AA1 6 GLU A 170 SER A 173 0 SHEET 2 AA1 6 ILE A 137 VAL A 142 1 N PHE A 138 O GLU A 170 SHEET 3 AA1 6 VAL A 123 LYS A 128 -1 N ILE A 125 O HIS A 139 SHEET 4 AA1 6 SER A 85 ALA A 90 -1 N LEU A 89 O MET A 124 SHEET 5 AA1 6 PHE A 190 TYR A 192 1 O TYR A 192 N CYS A 86 SHEET 6 AA1 6 THR A 230 LYS A 232 1 O LYS A 232 N ILE A 191 SHEET 1 AA2 3 LYS A 293 ASP A 294 0 SHEET 2 AA2 3 GLY A 330 LEU A 332 -1 O SER A 331 N LYS A 293 SHEET 3 AA2 3 TYR A 335 CYS A 336 -1 O TYR A 335 N LEU A 332 SHEET 1 AA3 3 VAL A 299 THR A 302 0 SHEET 2 AA3 3 MET A 323 ASP A 327 -1 O LEU A 325 N ALA A 301 SHEET 3 AA3 3 SER A 340 PRO A 344 -1 O ARG A 341 N VAL A 326 SHEET 1 AA4 3 VAL A 440 ILE A 443 0 SHEET 2 AA4 3 ASP A 468 ILE A 472 -1 O ILE A 470 N ILE A 441 SHEET 3 AA4 3 TYR A 477 ASN A 479 -1 O THR A 478 N ALA A 471 SHEET 1 AA5 2 GLY A 446 ILE A 449 0 SHEET 2 AA5 2 VAL A 462 ARG A 465 -1 O VAL A 462 N ILE A 449 LINK C 01B B 1 N PRO B 2 1555 1555 1.43 LINK C ALA B 4 N NH2 B 5 1555 1555 1.33 LINK OD1 ASP A 327 MN MN A 601 1555 1555 2.58 LINK OD2 ASP A 327 MN MN A 601 1555 1555 2.50 LINK OD1 ASP A 338 MN MN A 601 1555 1555 2.21 LINK OD2 ASP A 338 MN MN A 602 1555 1555 2.31 LINK NE2 HIS A 417 MN MN A 602 1555 1555 2.36 LINK OE1 GLU A 444 MN MN A 602 1555 1555 2.65 LINK OE2 GLU A 467 MN MN A 601 1555 1555 2.56 LINK OE1 GLU A 467 MN MN A 602 1555 1555 2.49 LINK MN MN A 601 N 01B B 1 1555 1555 2.17 LINK MN MN A 601 O2 01B B 1 1555 1555 2.39 LINK MN MN A 602 O2 01B B 1 1555 1555 2.01 SITE 1 AC1 5 ASP A 327 ASP A 338 GLU A 467 MN A 602 SITE 2 AC1 5 01B B 1 SITE 1 AC2 6 ASP A 338 HIS A 417 GLU A 444 GLU A 467 SITE 2 AC2 6 MN A 601 01B B 1 SITE 1 AC3 12 TYR A 296 ASP A 327 ASP A 338 HIS A 413 SITE 2 AC3 12 TYR A 414 GLY A 416 HIS A 417 HIS A 424 SITE 3 AC3 12 GLU A 444 GLU A 467 MN A 601 MN A 602 CRYST1 148.089 148.089 124.989 90.00 90.00 90.00 I 4 2 2 16 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 0.006753 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006753 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008001 0.00000