HEADER HYDROLASE/HYDROLASE INHIBITOR 22-FEB-16 5IB9 TITLE CRYSTAL STRUCTURE OF AMINOPEPTIDASE EQUIPPED WITH PAD FROM TITLE 2 ANEURINIBACILLUS SP. AM-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMINOPEPTIDASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 36-456; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ANEURINIBACILLUS SP. AM-1; SOURCE 3 ORGANISM_TAXID: 400761; SOURCE 4 STRAIN: AM-1; SOURCE 5 GENE: AMP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS AMINOPEPTIDASE PROTEASE-ASSOCIATED DOMAIN HOMO-DIMERIZATION KEYWDS 2 INHIBITOR, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.TAGAWA,H.NAKANO,K.WATANABE REVDAT 3 08-NOV-23 5IB9 1 LINK REVDAT 2 19-FEB-20 5IB9 1 REMARK REVDAT 1 22-FEB-17 5IB9 0 JRNL AUTH R.TAGAWA,H.NAKANO,K.WATANABE JRNL TITL CRYSTAL STRUCTURE OF AMINOPEPTIDASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 3 NUMBER OF REFLECTIONS : 85042 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4444 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5334 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.97 REMARK 3 BIN R VALUE (WORKING SET) : 0.3560 REMARK 3 BIN FREE R VALUE SET COUNT : 286 REMARK 3 BIN FREE R VALUE : 0.4010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3119 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 590 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.060 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.068 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.046 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.195 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3192 ; 0.026 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4319 ; 2.268 ; 1.968 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 411 ; 6.224 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 138 ;36.594 ;25.217 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 545 ;14.890 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;16.062 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 493 ; 0.153 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2403 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2038 ; 1.473 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3267 ; 2.353 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1154 ; 3.568 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1052 ; 5.919 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5IB9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1000218573. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAY-12 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER SMART 6000 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 89717 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 2EK9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 13% PEG 6000, 0.2M ZINC ACETATE, 0.1M REMARK 280 MES-NAOH, PH 5.8, LIQUID DIFFUSION, TEMPERATURE 293K 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 46.59000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.22150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 46.59000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.22150 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -295.0 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 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 ALA A 1 REMARK 465 PRO A 2 REMARK 465 ALA A 3 REMARK 465 HIS A 4 REMARK 465 VAL A 417 REMARK 465 GLU A 418 REMARK 465 LEU A 419 REMARK 465 GLN A 420 REMARK 465 ASN A 421 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 O HOH A 1111 O HOH A 1146 0.99 REMARK 500 O HOH A 1200 O HOH A 1380 1.03 REMARK 500 O HOH A 1214 O HOH A 1389 1.12 REMARK 500 O HOH A 1358 O HOH A 1370 1.14 REMARK 500 O HOH A 1500 O HOH A 1578 1.14 REMARK 500 O HOH A 1142 O HOH A 1479 1.23 REMARK 500 O HOH A 1145 O HOH A 1335 1.26 REMARK 500 O HOH A 1109 O HOH A 1312 1.28 REMARK 500 O HOH A 1376 O HOH A 1483 1.30 REMARK 500 O HOH A 1187 O HOH A 1217 1.32 REMARK 500 O HOH A 1488 O HOH A 1526 1.33 REMARK 500 O HOH A 1105 O HOH A 1395 1.33 REMARK 500 O HOH A 1131 O HOH A 1354 1.35 REMARK 500 O HOH A 1128 O HOH A 1208 1.38 REMARK 500 O HOH A 1483 O HOH A 1496 1.38 REMARK 500 O HOH A 1102 O HOH A 1171 1.40 REMARK 500 O HOH A 1152 O HOH A 1323 1.44 REMARK 500 O HOH A 1314 O HOH A 1363 1.44 REMARK 500 O HOH A 1452 O HOH A 1498 1.44 REMARK 500 O HOH A 1209 O HOH A 1243 1.46 REMARK 500 O HOH A 1205 O HOH A 1490 1.47 REMARK 500 O HOH A 1369 O HOH A 1534 1.48 REMARK 500 O HOH A 1300 O HOH A 1568 1.50 REMARK 500 O HOH A 1184 O HOH A 1501 1.50 REMARK 500 O HOH A 1278 O HOH A 1372 1.53 REMARK 500 O HOH A 1183 O HOH A 1219 1.55 REMARK 500 O HOH A 1281 O HOH A 1508 1.57 REMARK 500 O HOH A 1256 O HOH A 1359 1.60 REMARK 500 O HOH A 1139 O HOH A 1198 1.60 REMARK 500 O HOH A 1386 O HOH A 1441 1.60 REMARK 500 O HOH A 1397 O HOH A 1534 1.64 REMARK 500 O HOH A 1161 O HOH A 1431 1.65 REMARK 500 O HOH A 1222 O HOH A 1293 1.66 REMARK 500 O HOH A 1106 O HOH A 1421 1.67 REMARK 500 O HOH A 1298 O HOH A 1342 1.68 REMARK 500 O HOH A 1488 O HOH A 1493 1.71 REMARK 500 O HOH A 1279 O HOH A 1534 1.74 REMARK 500 O HOH A 1140 O HOH A 1339 1.75 REMARK 500 O HOH A 1125 O HOH A 1395 1.75 REMARK 500 O HOH A 1167 O HOH A 1198 1.77 REMARK 500 O HOH A 1526 O HOH A 1556 1.77 REMARK 500 O HOH A 1416 O HOH A 1495 1.80 REMARK 500 O HOH A 1281 O HOH A 1596 1.82 REMARK 500 O HOH A 1211 O HOH A 1371 1.83 REMARK 500 O HOH A 1291 O HOH A 1487 1.84 REMARK 500 O HOH A 1191 O HOH A 1386 1.85 REMARK 500 NE2 HIS A 7 O HOH A 1101 1.85 REMARK 500 O HOH A 1294 O HOH A 1463 1.86 REMARK 500 O HOH A 1493 O HOH A 1526 1.86 REMARK 500 OE1 GLU A 56 O HOH A 1102 1.87 REMARK 500 REMARK 500 THIS ENTRY HAS 94 CLOSE CONTACTS 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 HOH A 1409 O HOH A 1526 2555 1.24 REMARK 500 O HOH A 1202 O HOH A 1227 3455 1.62 REMARK 500 O HOH A 1585 O HOH A 1640 1554 1.80 REMARK 500 O HOH A 1465 O HOH A 1493 2555 1.82 REMARK 500 O HOH A 1260 O HOH A 1465 2555 1.84 REMARK 500 O HOH A 1483 O HOH A 1554 3455 1.94 REMARK 500 O HOH A 1298 O HOH A 1298 2555 1.99 REMARK 500 O HOH A 1260 O HOH A 1458 2555 1.99 REMARK 500 O HOH A 1110 O HOH A 1260 2555 2.04 REMARK 500 O HOH A 1333 O HOH A 1364 2565 2.06 REMARK 500 O HOH A 1429 O HOH A 1555 2555 2.07 REMARK 500 O HOH A 1244 O HOH A 1495 3455 2.11 REMARK 500 OE2 GLU A 36 O HOH A 1101 3445 2.11 REMARK 500 O HOH A 1588 O HOH A 1590 3445 2.12 REMARK 500 O HOH A 1409 O HOH A 1493 2555 2.19 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 ASP A 14 CB - CG - OD2 ANGL. DEV. = -8.0 DEGREES REMARK 500 TYR A 19 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ASP A 240 CB - CG - OD1 ANGL. DEV. = -6.2 DEGREES REMARK 500 ASP A 240 CB - CG - OD2 ANGL. DEV. = 13.5 DEGREES REMARK 500 ASP A 241 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG A 265 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 265 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 GLU A 290 OE1 - CD - OE2 ANGL. DEV. = -7.4 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 ARG A 30 72.13 -118.00 REMARK 500 TYR A 87 9.97 80.16 REMARK 500 ASP A 92 83.92 -154.67 REMARK 500 ASN A 124 -55.59 69.56 REMARK 500 ASP A 160 119.93 -171.18 REMARK 500 ASN A 215 -120.96 56.29 REMARK 500 LYS A 234 -2.56 69.47 REMARK 500 MET A 302 76.02 62.64 REMARK 500 SER A 335 -31.69 -139.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1686 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH A1687 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH A1688 DISTANCE = 6.65 ANGSTROMS REMARK 525 HOH A1689 DISTANCE = 6.90 ANGSTROMS REMARK 525 HOH A1690 DISTANCE = 8.15 ANGSTROMS 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 ZN A1004 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 13 O REMARK 620 2 THR A 13 OG1 86.3 REMARK 620 3 ASP A 386 OD1 90.4 89.2 REMARK 620 4 HOH A1234 O 84.9 95.9 172.8 REMARK 620 5 HOH A1263 O 169.7 88.2 98.3 86.9 REMARK 620 6 HOH A1318 O 91.0 176.8 89.1 85.5 94.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1005 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 45 OE2 REMARK 620 2 GLU A 383 OE1 21.0 REMARK 620 3 HOH A1266 O 25.1 4.2 REMARK 620 4 HOH A1383 O 22.7 3.0 4.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1006 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 204 NE2 REMARK 620 2 GLU A 288 OE2 65.3 REMARK 620 3 HOH A1409 O 123.1 100.8 REMARK 620 4 HOH A1465 O 115.1 147.9 104.0 REMARK 620 5 HOH A1493 O 107.3 158.3 65.2 53.6 REMARK 620 6 HOH A1526 O 102.7 113.2 29.2 98.3 46.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 228 NE2 REMARK 620 2 ASP A 240 OD1 99.0 REMARK 620 3 ASP A 301 OD1 100.4 94.0 REMARK 620 4 ASP A 301 OD2 89.9 151.7 57.9 REMARK 620 5 BES A1007 N2 159.0 101.0 84.4 75.2 REMARK 620 6 BES A1007 O2 105.4 97.7 149.6 105.8 65.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 240 OD2 REMARK 620 2 GLU A 273 OE1 150.5 REMARK 620 3 GLU A 273 OE2 94.4 58.1 REMARK 620 4 HIS A 371 NE2 87.8 90.9 108.4 REMARK 620 5 BES A1007 O2 101.2 93.2 96.4 153.0 REMARK 620 6 BES A1007 O3 136.6 72.0 128.9 81.1 74.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1003 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 386 OD2 REMARK 620 2 ASP A 390 OD2 100.6 REMARK 620 3 HOH A1263 O 104.5 125.7 REMARK 620 4 HOH A1376 O 96.8 112.1 111.7 REMARK 620 5 HOH A1483 O 128.7 95.4 104.6 32.8 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 ZN A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BES A 1007 DBREF 5IB9 A 1 421 UNP A2V759 A2V759_9BACL 36 456 SEQRES 1 A 421 ALA PRO ALA HIS ALA ASP HIS GLN ILE THR LYS ARG THR SEQRES 2 A 421 ASP ALA GLU ASN MET TYR ASN THR ILE GLN PHE LEU SER SEQRES 3 A 421 GLN ALA PRO ARG VAL ALA GLY SER PRO GLU GLU LEU LYS SEQRES 4 A 421 ALA VAL ARG TYR ILE GLU GLN GLN PHE LYS SER TYR GLY SEQRES 5 A 421 TYR HIS VAL GLU VAL GLN PRO PHE GLN PHE GLU GLY TYR SEQRES 6 A 421 THR ALA PRO SER GLU VAL THR LEU LYS ILE GLY THR GLU SEQRES 7 A 421 LYS LYS GLU GLY GLU ALA PHE THR TYR SER PRO ASN SER SEQRES 8 A 421 ASP VAL THR ALA GLU LEU VAL TYR VAL GLY LEU GLY THR SEQRES 9 A 421 THR ALA ASP VAL ALA GLY LYS ASP LEU ASN GLY LYS ILE SEQRES 10 A 421 ALA LEU ILE GLN ARG GLY ASN ILE SER PHE ALA ASP LYS SEQRES 11 A 421 VAL ARG ASN ALA ALA LYS GLN GLY ALA LYS ALA VAL ILE SEQRES 12 A 421 ILE TYR ASN ASN THR ASP GLY LYS LEU ASN GLY THR LEU SEQRES 13 A 421 GLY GLY SER ASP ALA SER PHE VAL ALA ALA VAL GLY ILE SEQRES 14 A 421 THR LYS GLN GLU GLY ASP ALA LEU ALA ALA ASN LEU ARG SEQRES 15 A 421 ALA GLY GLU LYS ILE THR ALA THR VAL LYS VAL ALA GLY SEQRES 16 A 421 ALA GLU VAL LYS THR LEU THR SER HIS ASN VAL ILE ALA SEQRES 17 A 421 THR LYS LYS PRO ASP ALA ASN LYS LYS ASN THR ASN ASP SEQRES 18 A 421 ILE ILE ILE ILE GLY SER HIS HIS ASP SER VAL GLU LYS SEQRES 19 A 421 ALA PRO GLY ALA ASN ASP ASP ALA SER GLY VAL ALA VAL SEQRES 20 A 421 THR LEU GLU LEU ALA ARG VAL MET SER LYS LEU LYS THR SEQRES 21 A 421 ASP THR GLU LEU ARG PHE ILE THR PHE GLY ALA GLU GLU SEQRES 22 A 421 ASN GLY LEU ILE GLY SER LYS LYS TYR ALA ALA SER LEU SEQRES 23 A 421 SER GLU ASP GLU ILE LYS ARG THR ILE GLY MET PHE GLN SEQRES 24 A 421 LEU ASP MET VAL GLY SER LYS ASP ALA GLY ASP LEU ILE SEQRES 25 A 421 MET TYR THR ILE ASP GLY LYS LYS ASN ARG VAL THR ASP SEQRES 26 A 421 LEU GLY ALA ALA ALA SER SER ARG LEU SER GLY VAL LEU SEQRES 27 A 421 PRO TYR GLY GLN GLU GLY ARG SER ASP HIS GLU SER PHE SEQRES 28 A 421 HIS ALA LEU GLY ILE PRO ALA ALA LEU PHE ILE HIS ALA SEQRES 29 A 421 PRO VAL GLU PRO TRP TYR HIS THR PRO ASN ASP THR LEU SEQRES 30 A 421 ASP LYS ILE SER LYS GLU LYS LEU ASP ASN VAL ALA ASP SEQRES 31 A 421 ILE VAL GLY SER ALA VAL TYR GLN ALA ALA ARG PRO GLY SEQRES 32 A 421 GLU LEU VAL ILE GLU PRO ILE ASP TYR PRO ARG ARG ASN SEQRES 33 A 421 VAL GLU LEU GLN ASN HET ZN A1001 1 HET ZN A1002 1 HET ZN A1003 1 HET ZN A1004 1 HET ZN A1005 1 HET ZN A1006 1 HET BES A1007 22 HETNAM ZN ZINC ION HETNAM BES 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL- HETNAM 2 BES PENTANOIC ACID HETSYN BES BESTATIN FORMUL 2 ZN 6(ZN 2+) FORMUL 8 BES C16 H24 N2 O4 FORMUL 9 HOH *590(H2 O) HELIX 1 AA1 ALA A 5 LYS A 11 1 7 HELIX 2 AA2 ASP A 14 SER A 26 1 13 HELIX 3 AA3 SER A 34 TYR A 51 1 18 HELIX 4 AA4 THR A 104 GLY A 110 1 7 HELIX 5 AA5 SER A 126 GLN A 137 1 12 HELIX 6 AA6 THR A 170 ALA A 183 1 14 HELIX 7 AA7 ALA A 214 ASN A 218 5 5 HELIX 8 AA8 ASP A 241 LYS A 257 1 17 HELIX 9 AA9 LEU A 276 ALA A 284 1 9 HELIX 10 AB1 SER A 287 ARG A 293 1 7 HELIX 11 AB2 ASN A 321 SER A 335 1 15 HELIX 12 AB3 ASP A 347 ALA A 353 1 7 HELIX 13 AB4 THR A 376 ILE A 380 5 5 HELIX 14 AB5 SER A 381 ARG A 401 1 21 SHEET 1 AA1 8 VAL A 55 THR A 66 0 SHEET 2 AA1 8 GLU A 197 LYS A 210 -1 O LYS A 199 N GLY A 64 SHEET 3 AA1 8 GLU A 263 PHE A 269 -1 O PHE A 266 N ALA A 208 SHEET 4 AA1 8 ILE A 222 HIS A 228 1 N SER A 227 O PHE A 269 SHEET 5 AA1 8 THR A 294 LEU A 300 1 O PHE A 298 N ILE A 224 SHEET 6 AA1 8 ALA A 358 ALA A 364 1 O PHE A 361 N GLN A 299 SHEET 7 AA1 8 ASP A 310 THR A 315 -1 N TYR A 314 O LEU A 360 SHEET 8 AA1 8 TYR A 340 GLN A 342 1 O GLY A 341 N THR A 315 SHEET 1 AA2 8 GLU A 78 LYS A 80 0 SHEET 2 AA2 8 GLU A 70 ILE A 75 -1 N LEU A 73 O LYS A 80 SHEET 3 AA2 8 ILE A 187 ALA A 194 -1 O LYS A 192 N THR A 72 SHEET 4 AA2 8 SER A 91 TYR A 99 -1 N VAL A 93 O VAL A 191 SHEET 5 AA2 8 ILE A 117 GLN A 121 1 O LEU A 119 N VAL A 98 SHEET 6 AA2 8 ALA A 141 TYR A 145 1 O ILE A 143 N ALA A 118 SHEET 7 AA2 8 ALA A 165 ILE A 169 1 O VAL A 167 N ILE A 144 SHEET 8 AA2 8 GLU A 83 ALA A 84 -1 N GLU A 83 O GLY A 168 LINK O THR A 13 ZN ZN A1004 1555 1555 2.12 LINK OG1 THR A 13 ZN ZN A1004 1555 1555 2.16 LINK OE2 GLU A 45 ZN ZN A1005 1555 3445 1.95 LINK NE2 HIS A 204 ZN ZN A1006 1555 1555 2.02 LINK NE2 HIS A 228 ZN ZN A1002 1555 1555 2.03 LINK OD2 ASP A 240 ZN ZN A1001 1555 1555 1.76 LINK OD1 ASP A 240 ZN ZN A1002 1555 1555 2.01 LINK OE1 GLU A 273 ZN ZN A1001 1555 1555 2.57 LINK OE2 GLU A 273 ZN ZN A1001 1555 1555 2.11 LINK OE2 GLU A 288 ZN ZN A1006 1555 2555 1.90 LINK OD1 ASP A 301 ZN ZN A1002 1555 1555 2.10 LINK OD2 ASP A 301 ZN ZN A1002 1555 1555 2.31 LINK NE2 HIS A 371 ZN ZN A1001 1555 1555 2.05 LINK OE1 GLU A 383 ZN ZN A1005 1555 1555 1.96 LINK OD2 ASP A 386 ZN ZN A1003 1555 1555 1.79 LINK OD1 ASP A 386 ZN ZN A1004 1555 1555 1.98 LINK OD2 ASP A 390 ZN ZN A1003 1555 1555 1.95 LINK ZN ZN A1001 O2 BES A1007 1555 1555 2.10 LINK ZN ZN A1001 O3 BES A1007 1555 1555 2.37 LINK ZN ZN A1002 N2 BES A1007 1555 1555 2.57 LINK ZN ZN A1002 O2 BES A1007 1555 1555 2.06 LINK ZN ZN A1003 O HOH A1263 1555 1555 1.83 LINK ZN ZN A1003 O HOH A1376 1555 1555 2.10 LINK ZN ZN A1003 O HOH A1483 1555 1555 2.40 LINK ZN ZN A1004 O HOH A1234 1555 1555 2.23 LINK ZN ZN A1004 O HOH A1263 1555 1555 2.11 LINK ZN ZN A1004 O HOH A1318 1555 1555 2.07 LINK ZN ZN A1005 O HOH A1266 1555 3455 1.92 LINK ZN ZN A1005 O HOH A1383 1555 1555 1.83 LINK ZN ZN A1006 O HOH A1409 1555 2555 1.97 LINK ZN ZN A1006 O HOH A1465 1555 2555 1.95 LINK ZN ZN A1006 O HOH A1493 1555 1555 2.08 LINK ZN ZN A1006 O HOH A1526 1555 1555 2.51 CISPEP 1 ASP A 240 ASP A 241 0 4.78 CISPEP 2 ALA A 364 PRO A 365 0 -2.95 SITE 1 AC1 5 ASP A 240 GLU A 273 HIS A 371 ZN A1002 SITE 2 AC1 5 BES A1007 SITE 1 AC2 5 HIS A 228 ASP A 240 ASP A 301 ZN A1001 SITE 2 AC2 5 BES A1007 SITE 1 AC3 7 ASP A 386 ASP A 390 ZN A1004 HOH A1263 SITE 2 AC3 7 HOH A1376 HOH A1483 HOH A1496 SITE 1 AC4 7 THR A 10 THR A 13 ASP A 386 ZN A1003 SITE 2 AC4 7 HOH A1234 HOH A1263 HOH A1318 SITE 1 AC5 5 GLU A 45 LYS A 49 GLU A 383 HOH A1266 SITE 2 AC5 5 HOH A1383 SITE 1 AC6 7 HIS A 204 GLU A 288 HOH A1409 HOH A1465 SITE 2 AC6 7 HOH A1488 HOH A1493 HOH A1526 SITE 1 AC7 15 HIS A 228 ASP A 240 GLU A 272 GLU A 273 SITE 2 AC7 15 GLY A 275 ASP A 301 MET A 302 ARG A 345 SITE 3 AC7 15 ILE A 362 VAL A 366 TYR A 370 HIS A 371 SITE 4 AC7 15 ZN A1001 ZN A1002 HOH A1114 CRYST1 93.180 68.443 76.589 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 0.010732 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014611 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013057 0.00000