HEADER SUGAR BINDING PROTEIN 02-JUN-20 6Z8L TITLE ALPHA-AMYLASE IN COMPLEX WITH PROBE FRAGMENTS CAVEAT 6Z8L GLC A 901 HAS WRONG CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PANCREATIC ALPHA-AMYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PA,1,4-ALPHA-D-GLUCAN GLUCANOHYDROLASE; COMPND 5 EC: 3.2.1.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS ALPHA-AMYLASE, COMPLEX, MALTOSE, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.ADAM,J.KOEHNKE REVDAT 4 09-OCT-24 6Z8L 1 REMARK REVDAT 3 24-JAN-24 6Z8L 1 REMARK REVDAT 2 07-JUL-21 6Z8L 1 JRNL REVDAT 1 02-DEC-20 6Z8L 0 JRNL AUTH A.AXER,R.P.JUMDE,S.ADAM,A.FAUST,M.SCHAFERS,M.FOBKER, JRNL AUTH 2 J.KOEHNKE,A.K.H.HIRSCH,R.GILMOUR JRNL TITL ENHANCING GLYCAN STABILITY VIA SITE-SELECTIVE FLUORINATION: JRNL TITL 2 MODULATING SUBSTRATE ORIENTATION BY MOLECULAR DESIGN. JRNL REF CHEM SCI V. 12 1286 2020 JRNL REFN ISSN 2041-6520 JRNL PMID 34163891 JRNL DOI 10.1039/D0SC04297H REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.336 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 102448 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.143 REMARK 3 R VALUE (WORKING SET) : 0.142 REMARK 3 FREE R VALUE : 0.154 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.181 REMARK 3 FREE R VALUE TEST SET COUNT : 5308 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 48.4300 - 4.3491 0.98 3430 193 0.1678 0.1695 REMARK 3 2 4.3491 - 3.4523 0.99 3306 182 0.1185 0.1142 REMARK 3 3 3.4523 - 3.0160 0.99 3279 193 0.1297 0.1380 REMARK 3 4 3.0160 - 2.7403 0.99 3252 195 0.1245 0.1393 REMARK 3 5 2.7403 - 2.5439 0.99 3279 152 0.1275 0.1420 REMARK 3 6 2.5439 - 2.3939 1.00 3274 178 0.1312 0.1367 REMARK 3 7 2.3939 - 2.2740 1.00 3245 173 0.1241 0.1465 REMARK 3 8 2.2740 - 2.1750 1.00 3254 179 0.1263 0.1620 REMARK 3 9 2.1750 - 2.0913 1.00 3244 169 0.1288 0.1586 REMARK 3 10 2.0913 - 2.0191 1.00 3235 204 0.1354 0.1427 REMARK 3 11 2.0191 - 1.9560 1.00 3219 173 0.1353 0.1619 REMARK 3 12 1.9560 - 1.9001 1.00 3266 160 0.1374 0.1620 REMARK 3 13 1.9001 - 1.8501 1.00 3210 178 0.1459 0.1601 REMARK 3 14 1.8501 - 1.8049 1.00 3231 170 0.1433 0.1478 REMARK 3 15 1.8049 - 1.7639 1.00 3225 199 0.1442 0.1538 REMARK 3 16 1.7639 - 1.7263 1.00 3231 174 0.1537 0.1720 REMARK 3 17 1.7263 - 1.6918 1.00 3235 177 0.1530 0.1695 REMARK 3 18 1.6918 - 1.6599 1.00 3203 179 0.1558 0.1781 REMARK 3 19 1.6599 - 1.6302 1.00 3223 166 0.1540 0.1751 REMARK 3 20 1.6302 - 1.6026 1.00 3254 147 0.1602 0.1838 REMARK 3 21 1.6026 - 1.5767 1.00 3200 157 0.1619 0.1694 REMARK 3 22 1.5767 - 1.5525 1.00 3237 181 0.1634 0.1801 REMARK 3 23 1.5525 - 1.5297 1.00 3171 195 0.1764 0.2100 REMARK 3 24 1.5297 - 1.5081 1.00 3229 169 0.1827 0.2007 REMARK 3 25 1.5081 - 1.4877 1.00 3230 174 0.1865 0.2171 REMARK 3 26 1.4877 - 1.4684 1.00 3201 193 0.1938 0.2140 REMARK 3 27 1.4684 - 1.4500 1.00 3198 139 0.2089 0.2193 REMARK 3 28 1.4500 - 1.4326 1.00 3232 179 0.2153 0.2712 REMARK 3 29 1.4326 - 1.4159 1.00 3193 204 0.2267 0.2476 REMARK 3 30 1.4159 - 1.4000 1.00 3154 176 0.2288 0.2578 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) : 0.107 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.954 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.76 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 : 0.012 4195 REMARK 3 ANGLE : 1.288 5716 REMARK 3 CHIRALITY : 0.133 604 REMARK 3 PLANARITY : 0.009 735 REMARK 3 DIHEDRAL : 15.082 1486 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 243 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.9467 12.2301 -11.2284 REMARK 3 T TENSOR REMARK 3 T11: 0.1703 T22: 0.1572 REMARK 3 T33: 0.1506 T12: 0.0145 REMARK 3 T13: -0.0221 T23: 0.0192 REMARK 3 L TENSOR REMARK 3 L11: 0.8734 L22: 0.6052 REMARK 3 L33: 0.6735 L12: -0.1305 REMARK 3 L13: 0.1005 L23: -0.0745 REMARK 3 S TENSOR REMARK 3 S11: 0.0303 S12: -0.0675 S13: -0.1695 REMARK 3 S21: 0.0782 S22: 0.0158 S23: -0.0145 REMARK 3 S31: 0.1363 S32: 0.0537 S33: -0.0430 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 244 THROUGH 300 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.3727 20.0449 -20.5498 REMARK 3 T TENSOR REMARK 3 T11: 0.1054 T22: 0.1470 REMARK 3 T33: 0.1498 T12: -0.0292 REMARK 3 T13: 0.0056 T23: 0.0076 REMARK 3 L TENSOR REMARK 3 L11: 1.8348 L22: 1.7753 REMARK 3 L33: 2.6281 L12: -0.6357 REMARK 3 L13: 0.6848 L23: -1.0672 REMARK 3 S TENSOR REMARK 3 S11: 0.0205 S12: 0.0050 S13: -0.1030 REMARK 3 S21: 0.0204 S22: 0.0676 S23: 0.1983 REMARK 3 S31: 0.0743 S32: -0.1679 S33: -0.1043 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 301 THROUGH 350 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.7821 21.4484 -28.8534 REMARK 3 T TENSOR REMARK 3 T11: 0.1037 T22: 0.1216 REMARK 3 T33: 0.1041 T12: -0.0175 REMARK 3 T13: -0.0214 T23: 0.0128 REMARK 3 L TENSOR REMARK 3 L11: 3.6491 L22: 2.1537 REMARK 3 L33: 2.7883 L12: -1.9011 REMARK 3 L13: -1.4369 L23: 0.8211 REMARK 3 S TENSOR REMARK 3 S11: 0.0610 S12: 0.2607 S13: -0.1994 REMARK 3 S21: -0.0961 S22: -0.0790 S23: 0.1091 REMARK 3 S31: 0.2030 S32: -0.0736 S33: 0.0319 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 351 THROUGH 496 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.9728 36.8214 -27.6669 REMARK 3 T TENSOR REMARK 3 T11: 0.1395 T22: 0.1829 REMARK 3 T33: 0.1425 T12: -0.0048 REMARK 3 T13: 0.0047 T23: 0.0472 REMARK 3 L TENSOR REMARK 3 L11: 1.2498 L22: 1.1816 REMARK 3 L33: 0.5134 L12: -0.4808 REMARK 3 L13: 0.1246 L23: 0.0075 REMARK 3 S TENSOR REMARK 3 S11: 0.0038 S12: 0.1347 S13: 0.1537 REMARK 3 S21: -0.0343 S22: 0.0093 S23: 0.0622 REMARK 3 S31: -0.0821 S32: -0.0599 S33: -0.0136 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 6Z8L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1292108946. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-APR-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 102541 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 48.431 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.61600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 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: 5U3A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 60 % MPD, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 25.93650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.60350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.86450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 67.60350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.93650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.86450 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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 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 1040 O HOH A 1298 2.15 REMARK 500 OD1 ASP A 125 O HOH A 1001 2.18 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 OD1 ASN A 363 O6 GLC D 1 1655 1.83 REMARK 500 O HOH A 1007 O HOH A 1128 4555 1.92 REMARK 500 O HOH A 1074 O HOH A 1190 3544 2.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 PRO A 4 CG PRO A 4 CD 0.305 REMARK 500 TYR A 31 CE2 TYR A 31 CD2 -0.093 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 ARG A 252 NE - CZ - NH2 ANGL. DEV. = -3.6 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 TYR A 31 -56.92 -142.77 REMARK 500 MET A 102 -137.30 -99.23 REMARK 500 ASP A 317 59.08 -107.29 REMARK 500 ASN A 350 -117.23 55.92 REMARK 500 THR A 376 2.48 80.66 REMARK 500 SER A 414 -107.43 -135.99 REMARK 500 ASP A 433 34.08 -86.97 REMARK 500 PRO A 486 48.69 -86.96 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 CA A 906 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 100 OD1 REMARK 620 2 ARG A 158 O 156.2 REMARK 620 3 ASP A 167 OD1 82.1 118.6 REMARK 620 4 ASP A 167 OD2 127.5 76.3 52.3 REMARK 620 5 HIS A 201 O 74.7 81.7 139.6 157.3 REMARK 620 6 HOH A1086 O 70.5 122.5 78.1 75.2 122.4 REMARK 620 7 HOH A1169 O 99.9 78.3 70.8 89.2 81.0 148.6 REMARK 620 8 HOH A1266 O 101.6 72.5 135.7 96.3 82.0 62.4 147.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 630 REMARK 630 MOLECULE TYPE: OLIGOSACCHARIDE NUTRIENT REMARK 630 MOLECULE NAME: ALPHA-D-GLUCOPYRANOSE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 GLC A 901 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: NULL REMARK 630 DETAILS: OLIGOSACCHARIDE DBREF 6Z8L A 1 496 UNP P04746 AMYP_HUMAN 16 511 SEQADV 6Z8L MET A 287 UNP P04746 VAL 302 CONFLICT SEQRES 1 A 496 PCA TYR SER PRO ASN THR GLN GLN GLY ARG THR SER ILE SEQRES 2 A 496 VAL HIS LEU PHE GLU TRP ARG TRP VAL ASP ILE ALA LEU SEQRES 3 A 496 GLU CYS GLU ARG TYR LEU ALA PRO LYS GLY PHE GLY GLY SEQRES 4 A 496 VAL GLN VAL SER PRO PRO ASN GLU ASN VAL ALA ILE TYR SEQRES 5 A 496 ASN PRO PHE ARG PRO TRP TRP GLU ARG TYR GLN PRO VAL SEQRES 6 A 496 SER TYR LYS LEU CYS THR ARG SER GLY ASN GLU ASP GLU SEQRES 7 A 496 PHE ARG ASN MET VAL THR ARG CYS ASN ASN VAL GLY VAL SEQRES 8 A 496 ARG ILE TYR VAL ASP ALA VAL ILE ASN HIS MET CYS GLY SEQRES 9 A 496 ASN ALA VAL SER ALA GLY THR SER SER THR CYS GLY SER SEQRES 10 A 496 TYR PHE ASN PRO GLY SER ARG ASP PHE PRO ALA VAL PRO SEQRES 11 A 496 TYR SER GLY TRP ASP PHE ASN ASP GLY LYS CYS LYS THR SEQRES 12 A 496 GLY SER GLY ASP ILE GLU ASN TYR ASN ASP ALA THR GLN SEQRES 13 A 496 VAL ARG ASP CYS ARG LEU THR GLY LEU LEU ASP LEU ALA SEQRES 14 A 496 LEU GLU LYS ASP TYR VAL ARG SER LYS ILE ALA GLU TYR SEQRES 15 A 496 MET ASN HIS LEU ILE ASP ILE GLY VAL ALA GLY PHE ARG SEQRES 16 A 496 LEU ASP ALA SER LYS HIS MET TRP PRO GLY ASP ILE LYS SEQRES 17 A 496 ALA ILE LEU ASP LYS LEU HIS ASN LEU ASN SER ASN TRP SEQRES 18 A 496 PHE PRO ALA GLY SER LYS PRO PHE ILE TYR GLN GLU VAL SEQRES 19 A 496 ILE ASP LEU GLY GLY GLU PRO ILE LYS SER SER ASP TYR SEQRES 20 A 496 PHE GLY ASN GLY ARG VAL THR GLU PHE LYS TYR GLY ALA SEQRES 21 A 496 LYS LEU GLY THR VAL ILE ARG LYS TRP ASN GLY GLU LYS SEQRES 22 A 496 MET SER TYR LEU LYS ASN TRP GLY GLU GLY TRP GLY PHE SEQRES 23 A 496 MET PRO SER ASP ARG ALA LEU VAL PHE VAL ASP ASN HIS SEQRES 24 A 496 ASP ASN GLN ARG GLY HIS GLY ALA GLY GLY ALA SER ILE SEQRES 25 A 496 LEU THR PHE TRP ASP ALA ARG LEU TYR LYS MET ALA VAL SEQRES 26 A 496 GLY PHE MET LEU ALA HIS PRO TYR GLY PHE THR ARG VAL SEQRES 27 A 496 MET SER SER TYR ARG TRP PRO ARG GLN PHE GLN ASN GLY SEQRES 28 A 496 ASN ASP VAL ASN ASP TRP VAL GLY PRO PRO ASN ASN ASN SEQRES 29 A 496 GLY VAL ILE LYS GLU VAL THR ILE ASN PRO ASP THR THR SEQRES 30 A 496 CYS GLY ASN ASP TRP VAL CYS GLU HIS ARG TRP ARG GLN SEQRES 31 A 496 ILE ARG ASN MET VAL ILE PHE ARG ASN VAL VAL ASP GLY SEQRES 32 A 496 GLN PRO PHE THR ASN TRP TYR ASP ASN GLY SER ASN GLN SEQRES 33 A 496 VAL ALA PHE GLY ARG GLY ASN ARG GLY PHE ILE VAL PHE SEQRES 34 A 496 ASN ASN ASP ASP TRP SER PHE SER LEU THR LEU GLN THR SEQRES 35 A 496 GLY LEU PRO ALA GLY THR TYR CYS ASP VAL ILE SER GLY SEQRES 36 A 496 ASP LYS ILE ASN GLY ASN CYS THR GLY ILE LYS ILE TYR SEQRES 37 A 496 VAL SER ASP ASP GLY LYS ALA HIS PHE SER ILE SER ASN SEQRES 38 A 496 SER ALA GLU ASP PRO PHE ILE ALA ILE HIS ALA GLU SER SEQRES 39 A 496 LYS LEU MODRES 6Z8L PCA A 1 GLN MODIFIED RESIDUE HET PCA A 1 14 HET GLC B 1 23 HET GLC B 2 22 HET GLC C 1 23 HET GLC C 2 22 HET GLC D 1 23 HET GLC D 2 22 HET GLC E 1 23 HET GLC E 2 22 HET GLC A 901 24 HET CA A 906 1 HET CL A 907 1 HETNAM PCA PYROGLUTAMIC ACID HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM CA CALCIUM ION HETNAM CL CHLORIDE ION HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 1 PCA C5 H7 N O3 FORMUL 2 GLC 9(C6 H12 O6) FORMUL 7 CA CA 2+ FORMUL 8 CL CL 1- FORMUL 9 HOH *366(H2 O) HELIX 1 AA1 ARG A 20 TYR A 31 1 12 HELIX 2 AA2 PRO A 57 GLN A 63 5 7 HELIX 3 AA3 ASN A 75 VAL A 89 1 15 HELIX 4 AA4 ASN A 120 ARG A 124 5 5 HELIX 5 AA5 SER A 132 PHE A 136 5 5 HELIX 6 AA6 ASP A 153 CYS A 160 1 8 HELIX 7 AA7 ARG A 161 THR A 163 5 3 HELIX 8 AA8 LYS A 172 GLY A 190 1 19 HELIX 9 AA9 ALA A 198 MET A 202 5 5 HELIX 10 AB1 TRP A 203 ASP A 212 1 10 HELIX 11 AB2 LYS A 243 GLY A 251 5 9 HELIX 12 AB3 PHE A 256 ARG A 267 1 12 HELIX 13 AB4 LYS A 273 TRP A 280 5 8 HELIX 14 AB5 GLY A 281 GLY A 285 5 5 HELIX 15 AB6 ASP A 300 GLY A 304 5 5 HELIX 16 AB7 THR A 314 TRP A 316 5 3 HELIX 17 AB8 ASP A 317 HIS A 331 1 15 HELIX 18 AB9 CYS A 384 ARG A 387 5 4 HELIX 19 AC1 TRP A 388 VAL A 401 1 14 HELIX 20 AC2 GLU A 493 LYS A 495 5 3 SHEET 1 AA1 9 SER A 12 LEU A 16 0 SHEET 2 AA1 9 GLY A 39 VAL A 42 1 O GLY A 39 N VAL A 14 SHEET 3 AA1 9 ARG A 92 ALA A 97 1 O TYR A 94 N VAL A 40 SHEET 4 AA1 9 GLY A 193 LEU A 196 1 O ARG A 195 N ALA A 97 SHEET 5 AA1 9 PHE A 229 GLN A 232 1 O PHE A 229 N PHE A 194 SHEET 6 AA1 9 ARG A 252 THR A 254 1 O THR A 254 N GLN A 232 SHEET 7 AA1 9 ALA A 292 VAL A 294 1 O LEU A 293 N VAL A 253 SHEET 8 AA1 9 PHE A 335 SER A 340 1 O PHE A 335 N VAL A 294 SHEET 9 AA1 9 SER A 12 LEU A 16 1 N ILE A 13 O VAL A 338 SHEET 1 AA2 2 HIS A 101 GLY A 104 0 SHEET 2 AA2 2 LEU A 165 ASP A 167 -1 O LEU A 166 N CYS A 103 SHEET 1 AA3 2 PHE A 348 GLN A 349 0 SHEET 2 AA3 2 ASN A 352 ASP A 353 -1 O ASN A 352 N GLN A 349 SHEET 1 AA4 2 ASN A 362 ASN A 363 0 SHEET 2 AA4 2 VAL A 366 ILE A 367 -1 O VAL A 366 N ASN A 363 SHEET 1 AA5 4 PHE A 406 ASP A 411 0 SHEET 2 AA5 4 GLN A 416 ARG A 421 -1 O GLY A 420 N THR A 407 SHEET 3 AA5 4 GLY A 425 ASN A 430 -1 O PHE A 429 N VAL A 417 SHEET 4 AA5 4 PHE A 487 HIS A 491 -1 O ILE A 490 N PHE A 426 SHEET 1 AA6 2 PHE A 436 GLN A 441 0 SHEET 2 AA6 2 LYS A 474 ILE A 479 -1 O ALA A 475 N LEU A 440 SHEET 1 AA7 2 GLY A 447 CYS A 450 0 SHEET 2 AA7 2 LYS A 466 VAL A 469 -1 O ILE A 467 N TYR A 449 SHEET 1 AA8 2 LYS A 457 ILE A 458 0 SHEET 2 AA8 2 ASN A 461 CYS A 462 -1 O ASN A 461 N ILE A 458 SSBOND 1 CYS A 28 CYS A 86 1555 1555 2.08 SSBOND 2 CYS A 70 CYS A 115 1555 1555 2.11 SSBOND 3 CYS A 141 CYS A 160 1555 1555 2.08 SSBOND 4 CYS A 378 CYS A 384 1555 1555 2.03 SSBOND 5 CYS A 450 CYS A 462 1555 1555 2.04 LINK C PCA A 1 N TYR A 2 1555 1555 1.33 LINK O4 GLC B 1 C1 GLC B 2 1555 1555 1.41 LINK O4 GLC C 1 C1 GLC C 2 1555 1555 1.42 LINK O4 GLC D 1 C1 GLC D 2 1555 1555 1.41 LINK O4 GLC E 1 C1 GLC E 2 1555 1555 1.41 LINK OD1 ASN A 100 CA CA A 906 1555 1555 2.39 LINK O ARG A 158 CA CA A 906 1555 1555 2.36 LINK OD1 ASP A 167 CA CA A 906 1555 1555 2.49 LINK OD2 ASP A 167 CA CA A 906 1555 1555 2.47 LINK O HIS A 201 CA CA A 906 1555 1555 2.41 LINK CA CA A 906 O HOH A1086 1555 1555 2.57 LINK CA CA A 906 O HOH A1169 1555 1555 2.45 LINK CA CA A 906 O HOH A1266 1555 1555 2.57 CISPEP 1 ASN A 53 PRO A 54 0 -2.35 CISPEP 2 VAL A 129 PRO A 130 0 -0.22 CRYST1 51.873 73.729 135.207 90.00 90.00 90.00 P 21 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 0.019278 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013563 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007396 0.00000 CONECT 1 2 5 9 CONECT 2 1 3 7 10 CONECT 3 2 4 11 12 CONECT 4 3 5 13 14 CONECT 5 1 4 6 CONECT 6 5 CONECT 7 2 8 15 CONECT 8 7 CONECT 9 1 CONECT 10 2 CONECT 11 3 CONECT 12 3 CONECT 13 4 CONECT 14 4 CONECT 15 7 CONECT 446 1384 CONECT 1133 1782 CONECT 1384 446 CONECT 1599 7908 CONECT 1782 1133 CONECT 2157 2428 CONECT 2390 7908 CONECT 2428 2157 CONECT 2541 7908 CONECT 2542 7908 CONECT 3095 7908 CONECT 5886 5969 CONECT 5969 5886 CONECT 7026 7189 CONECT 7189 7026 CONECT 7704 7705 7710 7714 7716 CONECT 7705 7704 7706 7711 7717 CONECT 7706 7705 7707 7712 7718 CONECT 7707 7706 7708 7713 7719 CONECT 7708 7707 7709 7714 7720 CONECT 7709 7708 7715 7721 7722 CONECT 7710 7704 7723 CONECT 7711 7705 7724 CONECT 7712 7706 7725 CONECT 7713 7707 7727 CONECT 7714 7704 7708 CONECT 7715 7709 7726 CONECT 7716 7704 CONECT 7717 7705 CONECT 7718 7706 CONECT 7719 7707 CONECT 7720 7708 CONECT 7721 7709 CONECT 7722 7709 CONECT 7723 7710 CONECT 7724 7711 CONECT 7725 7712 CONECT 7726 7715 CONECT 7727 7713 7728 7736 7738 CONECT 7728 7727 7729 7733 7739 CONECT 7729 7728 7730 7734 7740 CONECT 7730 7729 7731 7735 7741 CONECT 7731 7730 7732 7736 7742 CONECT 7732 7731 7737 7743 7744 CONECT 7733 7728 7745 CONECT 7734 7729 7746 CONECT 7735 7730 7747 CONECT 7736 7727 7731 CONECT 7737 7732 7748 CONECT 7738 7727 CONECT 7739 7728 CONECT 7740 7729 CONECT 7741 7730 CONECT 7742 7731 CONECT 7743 7732 CONECT 7744 7732 CONECT 7745 7733 CONECT 7746 7734 CONECT 7747 7735 CONECT 7748 7737 CONECT 7749 7750 7755 7759 7761 CONECT 7750 7749 7751 7756 7762 CONECT 7751 7750 7752 7757 7763 CONECT 7752 7751 7753 7758 7764 CONECT 7753 7752 7754 7759 7765 CONECT 7754 7753 7760 7766 7767 CONECT 7755 7749 7768 CONECT 7756 7750 7769 CONECT 7757 7751 7770 CONECT 7758 7752 7772 CONECT 7759 7749 7753 CONECT 7760 7754 7771 CONECT 7761 7749 CONECT 7762 7750 CONECT 7763 7751 CONECT 7764 7752 CONECT 7765 7753 CONECT 7766 7754 CONECT 7767 7754 CONECT 7768 7755 CONECT 7769 7756 CONECT 7770 7757 CONECT 7771 7760 CONECT 7772 7758 7773 7781 7783 CONECT 7773 7772 7774 7778 7784 CONECT 7774 7773 7775 7779 7785 CONECT 7775 7774 7776 7780 7786 CONECT 7776 7775 7777 7781 7787 CONECT 7777 7776 7782 7788 7789 CONECT 7778 7773 7790 CONECT 7779 7774 7791 CONECT 7780 7775 7792 CONECT 7781 7772 7776 CONECT 7782 7777 7793 CONECT 7783 7772 CONECT 7784 7773 CONECT 7785 7774 CONECT 7786 7775 CONECT 7787 7776 CONECT 7788 7777 CONECT 7789 7777 CONECT 7790 7778 CONECT 7791 7779 CONECT 7792 7780 CONECT 7793 7782 CONECT 7794 7795 7800 7804 7806 CONECT 7795 7794 7796 7801 7807 CONECT 7796 7795 7797 7802 7808 CONECT 7797 7796 7798 7803 7809 CONECT 7798 7797 7799 7804 7810 CONECT 7799 7798 7805 7811 7812 CONECT 7800 7794 7813 CONECT 7801 7795 7814 CONECT 7802 7796 7815 CONECT 7803 7797 7817 CONECT 7804 7794 7798 CONECT 7805 7799 7816 CONECT 7806 7794 CONECT 7807 7795 CONECT 7808 7796 CONECT 7809 7797 CONECT 7810 7798 CONECT 7811 7799 CONECT 7812 7799 CONECT 7813 7800 CONECT 7814 7801 CONECT 7815 7802 CONECT 7816 7805 CONECT 7817 7803 7818 7826 7828 CONECT 7818 7817 7819 7823 7829 CONECT 7819 7818 7820 7824 7830 CONECT 7820 7819 7821 7825 7831 CONECT 7821 7820 7822 7826 7832 CONECT 7822 7821 7827 7833 7834 CONECT 7823 7818 7835 CONECT 7824 7819 7836 CONECT 7825 7820 7837 CONECT 7826 7817 7821 CONECT 7827 7822 7838 CONECT 7828 7817 CONECT 7829 7818 CONECT 7830 7819 CONECT 7831 7820 CONECT 7832 7821 CONECT 7833 7822 CONECT 7834 7822 CONECT 7835 7823 CONECT 7836 7824 CONECT 7837 7825 CONECT 7838 7827 CONECT 7839 7840 7845 7849 7851 CONECT 7840 7839 7841 7846 7852 CONECT 7841 7840 7842 7847 7853 CONECT 7842 7841 7843 7848 7854 CONECT 7843 7842 7844 7849 7855 CONECT 7844 7843 7850 7856 7857 CONECT 7845 7839 7858 CONECT 7846 7840 7859 CONECT 7847 7841 7860 CONECT 7848 7842 7862 CONECT 7849 7839 7843 CONECT 7850 7844 7861 CONECT 7851 7839 CONECT 7852 7840 CONECT 7853 7841 CONECT 7854 7842 CONECT 7855 7843 CONECT 7856 7844 CONECT 7857 7844 CONECT 7858 7845 CONECT 7859 7846 CONECT 7860 7847 CONECT 7861 7850 CONECT 7862 7848 7863 7871 7873 CONECT 7863 7862 7864 7868 7874 CONECT 7864 7863 7865 7869 7875 CONECT 7865 7864 7866 7870 7876 CONECT 7866 7865 7867 7871 7877 CONECT 7867 7866 7872 7878 7879 CONECT 7868 7863 7880 CONECT 7869 7864 7881 CONECT 7870 7865 7882 CONECT 7871 7862 7866 CONECT 7872 7867 7883 CONECT 7873 7862 CONECT 7874 7863 CONECT 7875 7864 CONECT 7876 7865 CONECT 7877 7866 CONECT 7878 7867 CONECT 7879 7867 CONECT 7880 7868 CONECT 7881 7869 CONECT 7882 7870 CONECT 7883 7872 CONECT 7884 7885 7890 7894 7896 CONECT 7885 7884 7886 7891 7897 CONECT 7886 7885 7887 7892 7898 CONECT 7887 7886 7888 7893 7899 CONECT 7888 7887 7889 7894 7900 CONECT 7889 7888 7895 7901 7902 CONECT 7890 7884 7903 CONECT 7891 7885 7904 CONECT 7892 7886 7905 CONECT 7893 7887 7906 CONECT 7894 7884 7888 CONECT 7895 7889 7907 CONECT 7896 7884 CONECT 7897 7885 CONECT 7898 7886 CONECT 7899 7887 CONECT 7900 7888 CONECT 7901 7889 CONECT 7902 7889 CONECT 7903 7890 CONECT 7904 7891 CONECT 7905 7892 CONECT 7906 7893 CONECT 7907 7895 CONECT 7908 1599 2390 2541 2542 CONECT 7908 3095 7995 8078 8175 CONECT 7995 7908 CONECT 8078 7908 CONECT 8175 7908 MASTER 406 0 12 20 25 0 0 6 4419 1 239 39 END