HEADER IMMUNE SYSTEM 21-AUG-15 5ADO TITLE CRYSTAL STRUCTURE OF THE PARAOXON-MODIFIED A.17 ANTIBODY FAB FRAGMENT TITLE 2 - LIGHT CHAIN S35R MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: FAB A.17; COMPND 3 CHAIN: H; COMPND 4 FRAGMENT: HEAVY CHAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: FAB A.17; COMPND 8 CHAIN: L; COMPND 9 FRAGMENT: LIGHT CHAIN; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 644223; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: GS115; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPICZALPHA JK1; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 644223; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: GS115; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PPICZALPHA JK1 KEYWDS IMMUNE SYSTEM, ENZYME REPROGRAMMING, ANTIBODIES, IG SUPERFAMILY, IN KEYWDS 2 SILICO ANTIBODY MATURATION EXPDTA X-RAY DIFFRACTION AUTHOR S.D.CHATZIEFTHIMIOU,I.V.SMIRNOV,A.V.GOLOVIN,A.V.STEPANOVA,Y.PENG, AUTHOR 2 O.I.ZOLOTAREVA,A.A.BELOGUROV,N.A.PONOMARENKO,G.M.BLACKBURN, AUTHOR 3 A.A.GABIBOV,R.LERNER,M.WILMANNS REVDAT 3 10-JAN-24 5ADO 1 REMARK LINK REVDAT 2 07-MAR-18 5ADO 1 SOURCE REMARK REVDAT 1 09-NOV-16 5ADO 0 JRNL AUTH I.V.SMIRNOV,A.V.GOLOVIN,S.D.CHATZIEFTHIMIOU,A.V.STEPANOVA, JRNL AUTH 2 Y.PENG,O.I.ZOLOTAREVA,A.A.BELOGUROV,I.N.KURKOVA, JRNL AUTH 3 N.A.PONOMARENKO,M.WILMANNS,G.M.BLACKBURN,A.G.GABIBOV, JRNL AUTH 4 R.A.LERNER JRNL TITL ROBOTIC QM/MM-DRIVEN MATURATION OF ANTIBODY COMBINING SITES. JRNL REF SCI.ADV. V. 2 01695 2016 JRNL REFN ESSN 2375-2548 JRNL PMID 27774510 JRNL DOI 10.1126/SCIADV.1501695 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 60774 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3246 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 40.2134 - 4.4062 0.99 2712 127 0.1357 0.1297 REMARK 3 2 4.4062 - 3.4980 0.98 2628 146 0.1338 0.1853 REMARK 3 3 3.4980 - 3.0560 1.00 2631 162 0.1650 0.1864 REMARK 3 4 3.0560 - 2.7766 1.00 2634 161 0.1731 0.1962 REMARK 3 5 2.7766 - 2.5777 1.00 2653 142 0.1789 0.1921 REMARK 3 6 2.5777 - 2.4257 1.00 2683 130 0.1826 0.2389 REMARK 3 7 2.4257 - 2.3042 1.00 2623 127 0.1766 0.2048 REMARK 3 8 2.3042 - 2.2039 1.00 2681 127 0.1794 0.2443 REMARK 3 9 2.2039 - 2.1191 1.00 2671 146 0.1749 0.2007 REMARK 3 10 2.1191 - 2.0460 1.00 2610 143 0.1847 0.2144 REMARK 3 11 2.0460 - 1.9820 1.00 2659 140 0.1759 0.2129 REMARK 3 12 1.9820 - 1.9254 1.00 2608 157 0.1852 0.2212 REMARK 3 13 1.9254 - 1.8747 1.00 2673 126 0.1764 0.2329 REMARK 3 14 1.8747 - 1.8289 1.00 2629 146 0.1778 0.2340 REMARK 3 15 1.8289 - 1.7874 1.00 2623 138 0.1959 0.2284 REMARK 3 16 1.7874 - 1.7493 1.00 2629 146 0.1992 0.2369 REMARK 3 17 1.7493 - 1.7143 1.00 2613 153 0.2099 0.2561 REMARK 3 18 1.7143 - 1.6820 1.00 2681 135 0.2220 0.2711 REMARK 3 19 1.6820 - 1.6519 1.00 2634 150 0.2277 0.2836 REMARK 3 20 1.6519 - 1.6239 1.00 2640 136 0.2365 0.2676 REMARK 3 21 1.6239 - 1.5977 1.00 2623 121 0.2453 0.2568 REMARK 3 22 1.5977 - 1.5732 1.00 2662 147 0.2575 0.3175 REMARK 3 23 1.5732 - 1.5500 1.00 2554 140 0.2813 0.3615 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.380 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.00 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 : 0.010 NULL REMARK 3 ANGLE : 1.200 NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN H AND RESID 2:99) REMARK 3 ORIGIN FOR THE GROUP (A): 1.0434 -2.5708 -2.6536 REMARK 3 T TENSOR REMARK 3 T11: 0.2345 T22: 0.3620 REMARK 3 T33: 0.2085 T12: -0.0020 REMARK 3 T13: 0.0237 T23: -0.0726 REMARK 3 L TENSOR REMARK 3 L11: 4.0470 L22: 2.7946 REMARK 3 L33: 4.7330 L12: -0.2279 REMARK 3 L13: 1.4705 L23: -0.6796 REMARK 3 S TENSOR REMARK 3 S11: 0.1124 S12: 0.6218 S13: -0.4155 REMARK 3 S21: -0.3269 S22: -0.1129 S23: 0.0987 REMARK 3 S31: 0.5070 S32: -0.2045 S33: 0.0289 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN H AND RESID 100:222) REMARK 3 ORIGIN FOR THE GROUP (A): 8.7633 -7.4885 24.4737 REMARK 3 T TENSOR REMARK 3 T11: 0.1606 T22: 0.1015 REMARK 3 T33: 0.1740 T12: -0.0235 REMARK 3 T13: 0.0079 T23: 0.0019 REMARK 3 L TENSOR REMARK 3 L11: 1.3281 L22: 1.2270 REMARK 3 L33: 2.1933 L12: 0.0117 REMARK 3 L13: 0.0400 L23: -0.7532 REMARK 3 S TENSOR REMARK 3 S11: 0.0140 S12: -0.0086 S13: -0.0807 REMARK 3 S21: 0.0680 S22: -0.0215 S23: 0.0702 REMARK 3 S31: 0.1368 S32: -0.0509 S33: 0.0268 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN L AND RESID 4:108) REMARK 3 ORIGIN FOR THE GROUP (A): -17.4907 4.5734 10.1825 REMARK 3 T TENSOR REMARK 3 T11: 0.1292 T22: 0.1574 REMARK 3 T33: 0.1963 T12: 0.0271 REMARK 3 T13: 0.0196 T23: -0.0004 REMARK 3 L TENSOR REMARK 3 L11: 3.9316 L22: 1.4757 REMARK 3 L33: 5.0084 L12: -0.0350 REMARK 3 L13: -2.1070 L23: -0.2513 REMARK 3 S TENSOR REMARK 3 S11: 0.1233 S12: 0.2275 S13: 0.1197 REMARK 3 S21: -0.0082 S22: 0.0438 S23: 0.0834 REMARK 3 S31: -0.1878 S32: -0.0538 S33: -0.1548 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN L AND RESID 109:216) REMARK 3 ORIGIN FOR THE GROUP (A): 7.9935 4.4170 37.6108 REMARK 3 T TENSOR REMARK 3 T11: 0.1843 T22: 0.1178 REMARK 3 T33: 0.1543 T12: 0.0012 REMARK 3 T13: 0.0201 T23: 0.0106 REMARK 3 L TENSOR REMARK 3 L11: 6.1369 L22: 0.8264 REMARK 3 L33: 1.9008 L12: 0.1353 REMARK 3 L13: 1.2961 L23: -0.0756 REMARK 3 S TENSOR REMARK 3 S11: -0.0799 S12: -0.2135 S13: 0.0648 REMARK 3 S21: 0.1055 S22: 0.0432 S23: 0.0749 REMARK 3 S31: -0.0636 S32: -0.1497 S33: 0.0289 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 5ADO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1290064760. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P14 (MX2) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8266 REMARK 200 MONOCHROMATOR : SI(III) CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64020 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.93000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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: PDB ENTRY 2XZA REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.18 M MGCL2 16% (W/V) POLYETHYLENE REMARK 280 GLYCOL 6000 0.1 M N-(2-ACETAMIDO) IMINODIACETIC ACID (ADA) PH REMARK 280 7.5, PH 6.5 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 33.53750 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: 3570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L 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 GLN H 1 REMARK 465 GLN H 101 REMARK 465 SER H 102 REMARK 465 SER H 103 REMARK 465 HIS H 104 REMARK 465 SER H 134 REMARK 465 LYS H 135 REMARK 465 SER H 136 REMARK 465 THR H 137 REMARK 465 SER H 138 REMARK 465 GLY H 139 REMARK 465 LEU H 223 REMARK 465 ALA H 224 REMARK 465 MET H 225 REMARK 465 ASP H 226 REMARK 465 TYR H 227 REMARK 465 LYS H 228 REMARK 465 ASP H 229 REMARK 465 HIS H 230 REMARK 465 ASP H 231 REMARK 465 GLY H 232 REMARK 465 ASP H 233 REMARK 465 TYR H 234 REMARK 465 LYS H 235 REMARK 465 ASP H 236 REMARK 465 HIS H 237 REMARK 465 ASP H 238 REMARK 465 ILE H 239 REMARK 465 ASP H 240 REMARK 465 TYR H 241 REMARK 465 LYS H 242 REMARK 465 ASP H 243 REMARK 465 ASP H 244 REMARK 465 ASP H 245 REMARK 465 ASP H 246 REMARK 465 LYS H 247 REMARK 465 VAL H 248 REMARK 465 ASP H 249 REMARK 465 HIS H 250 REMARK 465 HIS H 251 REMARK 465 HIS H 252 REMARK 465 HIS H 253 REMARK 465 HIS H 254 REMARK 465 HIS H 255 REMARK 465 GLN L 1 REMARK 465 SER L 2 REMARK 465 VAL L 3 REMARK 465 ILE L 217 REMARK 465 ASP L 218 REMARK 465 ALA L 219 REMARK 465 ALA L 220 REMARK 465 ALA L 221 REMARK 465 ALA L 222 REMARK 465 ALA L 223 REMARK 465 SER L 224 REMARK 465 PHE L 225 REMARK 465 LEU L 226 REMARK 465 GLU L 227 REMARK 465 GLN L 228 REMARK 465 LYS L 229 REMARK 465 LEU L 230 REMARK 465 ILE L 231 REMARK 465 SER L 232 REMARK 465 GLU L 233 REMARK 465 GLU L 234 REMARK 465 ASP L 235 REMARK 465 LEU L 236 REMARK 465 ASN L 237 REMARK 465 SER L 238 REMARK 465 ALA L 239 REMARK 465 VAL L 240 REMARK 465 ASP L 241 REMARK 465 HIS L 242 REMARK 465 HIS L 243 REMARK 465 HIS L 244 REMARK 465 HIS L 245 REMARK 465 HIS L 246 REMARK 465 HIS L 247 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 L 37 O3 DEP L 1356 2.11 REMARK 500 OG SER H 185 O HOH H 2212 2.15 REMARK 500 OG SER L 178 O HOH L 2199 2.17 REMARK 500 O HOH H 2095 O HOH H 2101 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 CYS H 202 CA - CB - SG ANGL. DEV. = 8.5 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 SER H 15 -4.27 79.27 REMARK 500 ASN L 28 -90.62 -106.66 REMARK 500 ASN L 52 -42.07 77.31 REMARK 500 ASN L 53 11.09 -147.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 DIETHYL PHOSPHONATE (DEP): 1-ETHOXYPHOSPHONOYLOXYETHANE REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DEP L 1356 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5ADP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE A.17 ANTIBODY FAB FRAGMENT - LIGHT CHAIN REMARK 900 S35R MUTANT REMARK 999 REMARK 999 SEQUENCE REMARK 999 CHAIN L HAS MUTATION S35R DBREF 5ADO H 1 255 PDB 5ADO 5ADO 1 255 DBREF 5ADO L 1 247 PDB 5ADO 5ADO 1 247 SEQRES 1 H 255 GLN VAL GLN LEU GLN GLU SER GLY PRO GLY LEU VAL LYS SEQRES 2 H 255 PRO SER GLU THR LEU SER LEU THR CYS ALA VAL SER GLY SEQRES 3 H 255 TYR SER ILE SER SER GLY TYR TYR TRP GLY TRP ILE ARG SEQRES 4 H 255 GLN PRO PRO GLY LYS GLY LEU GLU TRP ILE GLY SER ILE SEQRES 5 H 255 TYR HIS SER GLY SER THR TYR TYR ASN PRO SER LEU LYS SEQRES 6 H 255 SER ARG VAL THR ILE SER VAL ASP THR SER LYS ASN GLN SEQRES 7 H 255 PHE SER LEU LYS LEU SER SER VAL THR ALA ALA ASP THR SEQRES 8 H 255 ALA VAL TYR TYR CYS ALA GLY LEU THR GLN SER SER HIS SEQRES 9 H 255 ASN ASP ALA ASN TRP GLY GLN GLY THR LEU THR THR VAL SEQRES 10 H 255 SER SER ALA SER THR LYS GLY PRO SER VAL PHE PRO LEU SEQRES 11 H 255 ALA PRO SER SER LYS SER THR SER GLY GLY THR ALA ALA SEQRES 12 H 255 LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL SEQRES 13 H 255 THR VAL SER TRP ASN SER GLY ALA LEU THR SER GLY VAL SEQRES 14 H 255 HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU TYR SEQRES 15 H 255 SER LEU SER SER VAL VAL THR VAL PRO SER SER SER LEU SEQRES 16 H 255 GLY THR GLN THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SEQRES 17 H 255 SER ASN THR LYS VAL ASP LYS LYS VAL GLU PRO LYS SER SEQRES 18 H 255 CYS LEU ALA MET ASP TYR LYS ASP HIS ASP GLY ASP TYR SEQRES 19 H 255 LYS ASP HIS ASP ILE ASP TYR LYS ASP ASP ASP ASP LYS SEQRES 20 H 255 VAL ASP HIS HIS HIS HIS HIS HIS SEQRES 1 L 247 GLN SER VAL LEU THR GLN PRO PRO SER VAL SER ALA ALA SEQRES 2 L 247 PRO GLY GLN LYS VAL THR ILE SER CYS SER GLY SER SER SEQRES 3 L 247 SER ASN ILE GLY ASN ASN TYR VAL ARG TRP TYR GLN GLN SEQRES 4 L 247 LEU PRO GLY THR ALA PRO LYS LEU LEU ILE TYR ASP ASN SEQRES 5 L 247 ASN LYS ARG PRO SER GLY ILE PRO ASP ARG PHE SER GLY SEQRES 6 L 247 SER LYS SER GLY THR SER ALA THR LEU GLY ILE THR GLY SEQRES 7 L 247 LEU GLN THR GLY ASP GLU ALA ASP TYR TYR CYS GLY THR SEQRES 8 L 247 TRP ASP SER SER LEU ASN PRO VAL PHE GLY GLY GLY THR SEQRES 9 L 247 LYS LEU GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL SEQRES 10 L 247 PHE ILE PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY SEQRES 11 L 247 THR ALA SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO SEQRES 12 L 247 ARG GLU ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU SEQRES 13 L 247 GLN SER GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SEQRES 14 L 247 SER LYS ASP SER THR TYR SER LEU SER SER THR LEU THR SEQRES 15 L 247 LEU SER LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA SEQRES 16 L 247 CYS GLU VAL THR HIS GLN GLY LEU SER SER PRO VAL THR SEQRES 17 L 247 LYS SER PHE ASN ARG GLY GLU CYS ILE ASP ALA ALA ALA SEQRES 18 L 247 ALA ALA SER PHE LEU GLU GLN LYS LEU ILE SER GLU GLU SEQRES 19 L 247 ASP LEU ASN SER ALA VAL ASP HIS HIS HIS HIS HIS HIS HET DEP L1356 8 HETNAM DEP DIETHYL PHOSPHONATE FORMUL 3 DEP C4 H11 O3 P FORMUL 4 HOH *494(H2 O) HELIX 1 1 SER H 28 GLY H 32 5 5 HELIX 2 2 LEU H 64 SER H 66 5 3 HELIX 3 3 THR H 87 THR H 91 5 5 HELIX 4 4 SER H 162 ALA H 164 5 3 HELIX 5 5 SER H 193 LEU H 195 5 3 HELIX 6 6 LYS H 207 ASN H 210 5 4 HELIX 7 7 GLN L 80 GLU L 84 5 5 HELIX 8 8 SER L 123 SER L 129 1 7 HELIX 9 9 LYS L 185 GLU L 189 1 5 SHEET 1 HA 4 GLN H 3 SER H 7 0 SHEET 2 HA 4 LEU H 18 SER H 25 -1 O THR H 21 N SER H 7 SHEET 3 HA 4 GLN H 78 LEU H 83 -1 O PHE H 79 N CYS H 22 SHEET 4 HA 4 VAL H 68 ASP H 73 -1 O THR H 69 N LYS H 82 SHEET 1 HB 4 LEU H 11 VAL H 12 0 SHEET 2 HB 4 THR H 113 VAL H 117 1 O THR H 116 N VAL H 12 SHEET 3 HB 4 ALA H 92 LEU H 99 -1 O ALA H 92 N THR H 115 SHEET 4 HB 4 ALA H 107 TRP H 109 -1 O ASN H 108 N GLY H 98 SHEET 1 HC 6 LEU H 11 VAL H 12 0 SHEET 2 HC 6 THR H 113 VAL H 117 1 O THR H 116 N VAL H 12 SHEET 3 HC 6 ALA H 92 LEU H 99 -1 O ALA H 92 N THR H 115 SHEET 4 HC 6 TYR H 34 GLN H 40 -1 O TYR H 34 N LEU H 99 SHEET 5 HC 6 GLU H 47 TYR H 53 -1 O GLU H 47 N ARG H 39 SHEET 6 HC 6 THR H 58 TYR H 60 -1 O TYR H 59 N SER H 51 SHEET 1 HD 2 ALA H 107 TRP H 109 0 SHEET 2 HD 2 ALA H 92 LEU H 99 -1 O GLY H 98 N ASN H 108 SHEET 1 HE 4 SER H 126 LEU H 130 0 SHEET 2 HE 4 THR H 141 TYR H 151 -1 O GLY H 145 N LEU H 130 SHEET 3 HE 4 TYR H 182 PRO H 191 -1 O TYR H 182 N TYR H 151 SHEET 4 HE 4 VAL H 175 LEU H 176 1 O VAL H 175 N SER H 183 SHEET 1 HF 4 SER H 126 LEU H 130 0 SHEET 2 HF 4 THR H 141 TYR H 151 -1 O GLY H 145 N LEU H 130 SHEET 3 HF 4 TYR H 182 PRO H 191 -1 O TYR H 182 N TYR H 151 SHEET 4 HF 4 VAL H 169 THR H 171 -1 O HIS H 170 N VAL H 187 SHEET 1 HG 2 VAL H 175 LEU H 176 0 SHEET 2 HG 2 TYR H 182 PRO H 191 1 O SER H 183 N VAL H 175 SHEET 1 HH 3 THR H 157 TRP H 160 0 SHEET 2 HH 3 ILE H 201 HIS H 206 -1 O ASN H 203 N SER H 159 SHEET 3 HH 3 THR H 211 LYS H 216 -1 O THR H 211 N HIS H 206 SHEET 1 LA 4 SER L 9 ALA L 12 0 SHEET 2 LA 4 THR L 104 ILE L 108 1 O LYS L 105 N VAL L 10 SHEET 3 LA 4 ALA L 85 TRP L 92 -1 O ALA L 85 N LEU L 106 SHEET 4 LA 4 PRO L 98 PHE L 100 1 O VAL L 99 N THR L 91 SHEET 1 LB 5 SER L 9 ALA L 12 0 SHEET 2 LB 5 THR L 104 ILE L 108 1 O LYS L 105 N VAL L 10 SHEET 3 LB 5 ALA L 85 TRP L 92 -1 O ALA L 85 N LEU L 106 SHEET 4 LB 5 ARG L 35 GLN L 39 -1 O ARG L 35 N GLY L 90 SHEET 5 LB 5 LYS L 46 ILE L 49 -1 O LYS L 46 N GLN L 38 SHEET 1 LC 2 PRO L 98 PHE L 100 0 SHEET 2 LC 2 ALA L 85 TRP L 92 1 O THR L 91 N VAL L 99 SHEET 1 LD 3 VAL L 18 SER L 23 0 SHEET 2 LD 3 SER L 71 ILE L 76 -1 O ALA L 72 N CYS L 22 SHEET 3 LD 3 PHE L 63 SER L 68 -1 O SER L 64 N GLY L 75 SHEET 1 LE 4 SER L 116 PHE L 120 0 SHEET 2 LE 4 THR L 131 PHE L 141 -1 O VAL L 135 N PHE L 120 SHEET 3 LE 4 TYR L 175 SER L 184 -1 O TYR L 175 N PHE L 141 SHEET 4 LE 4 SER L 161 VAL L 165 -1 O GLN L 162 N THR L 180 SHEET 1 LF 4 ALA L 155 LEU L 156 0 SHEET 2 LF 4 LYS L 147 VAL L 152 -1 O VAL L 152 N ALA L 155 SHEET 3 LF 4 VAL L 193 THR L 199 -1 O ALA L 195 N LYS L 151 SHEET 4 LF 4 VAL L 207 ASN L 212 -1 O VAL L 207 N VAL L 198 SSBOND 1 CYS H 22 CYS H 96 1555 1555 2.08 SSBOND 2 CYS H 146 CYS H 202 1555 1555 2.04 SSBOND 3 CYS H 222 CYS L 216 1555 1555 2.03 SSBOND 4 CYS L 22 CYS L 89 1555 1555 2.04 SSBOND 5 CYS L 136 CYS L 196 1555 1555 2.04 LINK OH TYR L 37 P DEP L1356 1555 1555 1.42 CISPEP 1 PHE H 152 PRO H 153 0 -7.22 CISPEP 2 GLU H 154 PRO H 155 0 0.07 CISPEP 3 TYR L 142 PRO L 143 0 0.54 SITE 1 AC1 7 ALA H 107 TRP H 109 ARG L 35 TYR L 37 SITE 2 AC1 7 GLY L 90 THR L 91 TRP L 92 CRYST1 52.661 67.075 66.698 90.00 107.52 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.018989 0.000000 0.005995 0.00000 SCALE2 0.000000 0.014909 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015722 0.00000