PDB Short entry for 5YFI HEADER IMMUNE SYSTEM 21-SEP-17 5YFI TITLE CRYSTAL STRUCTURE OF THE ANTI-HUMAN PROSTAGLANDIN E RECEPTOR EP4 TITLE 2 ANTIBODY FAB FRAGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIGHT CHAIN OF FAB FRAGMENT; COMPND 3 CHAIN: L; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: HEAVY CHAIN OF FAB FRAGMENT; COMPND 6 CHAIN: H SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_TAXID: 10090; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 6 ORGANISM_TAXID: 10090 KEYWDS ANTIBODY, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR Y.TOYODA,K.MORIMOTO,R.SUNO,S.HORITA,S.IWATA,T.KOBAYASHI REVDAT 3 06-MAR-19 5YFI 1 JRNL REVDAT 2 12-DEC-18 5YFI 1 TITLE REVDAT 1 05-DEC-18 5YFI 0 JRNL AUTH Y.TOYODA,K.MORIMOTO,R.SUNO,S.HORITA,K.YAMASHITA,K.HIRATA, JRNL AUTH 2 Y.SEKIGUCHI,S.YASUDA,M.SHIROISHI,T.SHIMIZU,Y.URUSHIBATA, JRNL AUTH 3 Y.KAJIWARA,T.INAZUMI,Y.HOTTA,H.ASADA,T.NAKANE,Y.SHIIMURA, JRNL AUTH 4 T.NAKAGITA,K.TSUGE,S.YOSHIDA,T.KURIBARA,T.HOSOYA,Y.SUGIMOTO, JRNL AUTH 5 N.NOMURA,M.SATO,T.HIROKAWA,M.KINOSHITA,T.MURATA,K.TAKAYAMA, JRNL AUTH 6 M.YAMAMOTO,S.NARUMIYA,S.IWATA,T.KOBAYASHI JRNL TITL LIGAND BINDING TO HUMAN PROSTAGLANDIN E RECEPTOR EP4AT THE JRNL TITL 2 LIPID-BILAYER INTERFACE. JRNL REF NAT. CHEM. BIOL. V. 15 18 2019 JRNL REFN ESSN 1552-4469 JRNL PMID 30510193 JRNL DOI 10.1038/S41589-018-0131-3 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829) 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.700 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 81114 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 4067 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 44.9486 - 5.6741 0.96 2586 137 0.1782 0.1783 REMARK 3 2 5.6741 - 4.5051 0.97 2596 137 0.1399 0.1585 REMARK 3 3 4.5051 - 3.9360 0.98 2665 143 0.1469 0.1799 REMARK 3 4 3.9360 - 3.5763 0.96 2574 137 0.1607 0.2054 REMARK 3 5 3.5763 - 3.3200 0.98 2627 144 0.1670 0.2053 REMARK 3 6 3.3200 - 3.1243 1.00 2660 146 0.1882 0.2145 REMARK 3 7 3.1243 - 2.9679 1.00 2710 143 0.1795 0.2714 REMARK 3 8 2.9679 - 2.8387 1.00 2691 135 0.1772 0.2405 REMARK 3 9 2.8387 - 2.7295 1.00 2649 138 0.1811 0.2300 REMARK 3 10 2.7295 - 2.6353 0.99 2693 147 0.1845 0.2218 REMARK 3 11 2.6353 - 2.5529 0.97 2583 135 0.1926 0.2520 REMARK 3 12 2.5529 - 2.4799 0.99 2709 144 0.2132 0.2404 REMARK 3 13 2.4799 - 2.4146 0.99 2619 138 0.2057 0.2688 REMARK 3 14 2.4146 - 2.3557 1.00 2694 143 0.2143 0.2542 REMARK 3 15 2.3557 - 2.3022 1.00 2685 139 0.2085 0.2567 REMARK 3 16 2.3022 - 2.2532 0.99 2656 138 0.2058 0.3161 REMARK 3 17 2.2532 - 2.2081 1.00 2683 142 0.2211 0.2380 REMARK 3 18 2.2081 - 2.1664 1.00 2698 142 0.2203 0.2573 REMARK 3 19 2.1664 - 2.1278 1.00 2676 146 0.2245 0.2754 REMARK 3 20 2.1278 - 2.0917 1.00 2691 139 0.2461 0.2654 REMARK 3 21 2.0917 - 2.0580 1.00 2712 145 0.2506 0.3110 REMARK 3 22 2.0580 - 2.0263 0.98 2564 135 0.2557 0.3019 REMARK 3 23 2.0263 - 1.9965 0.98 2722 143 0.2557 0.2487 REMARK 3 24 1.9965 - 1.9684 1.00 2638 142 0.2611 0.3029 REMARK 3 25 1.9684 - 1.9418 0.99 2664 133 0.2687 0.3170 REMARK 3 26 1.9418 - 1.9165 1.00 2687 141 0.2911 0.3356 REMARK 3 27 1.9165 - 1.8926 1.00 2697 141 0.2995 0.3521 REMARK 3 28 1.8926 - 1.8698 1.00 2674 142 0.3163 0.3255 REMARK 3 29 1.8698 - 1.8480 0.96 2544 132 0.3192 0.3746 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.660 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 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 : 0.005 3507 REMARK 3 ANGLE : 0.766 4784 REMARK 3 CHIRALITY : 0.051 524 REMARK 3 PLANARITY : 0.004 607 REMARK 3 DIHEDRAL : 11.487 2101 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 23 THROUGH 123 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.7916 22.0954 -30.4114 REMARK 3 T TENSOR REMARK 3 T11: 0.2345 T22: 0.1723 REMARK 3 T33: 0.1539 T12: -0.0238 REMARK 3 T13: 0.0074 T23: -0.0108 REMARK 3 L TENSOR REMARK 3 L11: 1.9216 L22: 2.5573 REMARK 3 L33: 2.9847 L12: 0.1581 REMARK 3 L13: -0.8455 L23: -0.3719 REMARK 3 S TENSOR REMARK 3 S11: 0.1015 S12: -0.2730 S13: 0.0221 REMARK 3 S21: 0.5026 S22: -0.0481 S23: 0.0736 REMARK 3 S31: -0.1321 S32: -0.0102 S33: -0.0529 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 124 THROUGH 150 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.9615 -3.2395 -14.3633 REMARK 3 T TENSOR REMARK 3 T11: 0.4496 T22: 0.2792 REMARK 3 T33: 0.1755 T12: -0.0203 REMARK 3 T13: 0.0733 T23: 0.0009 REMARK 3 L TENSOR REMARK 3 L11: 1.2658 L22: 1.2397 REMARK 3 L33: 2.8231 L12: -0.0441 REMARK 3 L13: -0.7261 L23: -1.7087 REMARK 3 S TENSOR REMARK 3 S11: 0.0371 S12: -0.1742 S13: 0.0031 REMARK 3 S21: 0.0963 S22: 0.0116 S23: 0.2674 REMARK 3 S31: 0.2309 S32: -0.1223 S33: -0.0558 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 151 THROUGH 236 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.8421 -9.3561 -10.2884 REMARK 3 T TENSOR REMARK 3 T11: 0.4909 T22: 0.3158 REMARK 3 T33: 0.2234 T12: 0.0191 REMARK 3 T13: 0.0187 T23: 0.0376 REMARK 3 L TENSOR REMARK 3 L11: 1.8212 L22: 7.6245 REMARK 3 L33: 3.6611 L12: -0.2087 REMARK 3 L13: -0.0018 L23: -0.6894 REMARK 3 S TENSOR REMARK 3 S11: 0.0767 S12: -0.2848 S13: -0.1903 REMARK 3 S21: 0.7093 S22: -0.0758 S23: -0.1908 REMARK 3 S31: 0.5373 S32: 0.2182 S33: 0.0021 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 20 THROUGH 51 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.0251 8.1884 -48.5901 REMARK 3 T TENSOR REMARK 3 T11: 0.1074 T22: 0.1645 REMARK 3 T33: 0.2065 T12: 0.0022 REMARK 3 T13: -0.0041 T23: -0.0095 REMARK 3 L TENSOR REMARK 3 L11: 0.4068 L22: 8.8798 REMARK 3 L33: 1.0856 L12: -1.6148 REMARK 3 L13: 0.3766 L23: -1.9225 REMARK 3 S TENSOR REMARK 3 S11: 0.0379 S12: -0.0658 S13: -0.1388 REMARK 3 S21: 0.0612 S22: 0.0084 S23: 0.4786 REMARK 3 S31: -0.0531 S32: -0.0977 S33: -0.0378 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 52 THROUGH 86 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.8511 10.7996 -46.6802 REMARK 3 T TENSOR REMARK 3 T11: 0.0910 T22: 0.1172 REMARK 3 T33: 0.2112 T12: -0.0109 REMARK 3 T13: -0.0239 T23: -0.0286 REMARK 3 L TENSOR REMARK 3 L11: 3.7268 L22: 3.4878 REMARK 3 L33: 5.6920 L12: 0.4774 REMARK 3 L13: -1.2268 L23: -0.9498 REMARK 3 S TENSOR REMARK 3 S11: -0.0556 S12: -0.0958 S13: -0.1326 REMARK 3 S21: 0.1351 S22: -0.0531 S23: -0.2675 REMARK 3 S31: 0.0415 S32: 0.2109 S33: 0.0919 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 87 THROUGH 151 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.8997 5.3148 -43.8599 REMARK 3 T TENSOR REMARK 3 T11: 0.1036 T22: 0.1417 REMARK 3 T33: 0.1612 T12: 0.0093 REMARK 3 T13: 0.0022 T23: -0.0119 REMARK 3 L TENSOR REMARK 3 L11: 0.6883 L22: 2.0231 REMARK 3 L33: 1.3312 L12: 0.4362 REMARK 3 L13: -0.1977 L23: -0.6368 REMARK 3 S TENSOR REMARK 3 S11: 0.0411 S12: -0.0768 S13: -0.0088 REMARK 3 S21: 0.1217 S22: -0.0798 S23: -0.0472 REMARK 3 S31: -0.0576 S32: 0.0603 S33: 0.0483 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 152 THROUGH 172 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.2575 -8.7668 -13.6894 REMARK 3 T TENSOR REMARK 3 T11: 0.4443 T22: 0.5294 REMARK 3 T33: 0.2675 T12: -0.1199 REMARK 3 T13: 0.1254 T23: -0.0160 REMARK 3 L TENSOR REMARK 3 L11: 3.2001 L22: 3.4898 REMARK 3 L33: 3.0492 L12: -0.6062 REMARK 3 L13: -0.2870 L23: -2.0489 REMARK 3 S TENSOR REMARK 3 S11: -0.2283 S12: -0.8443 S13: -0.3246 REMARK 3 S21: 0.8999 S22: -0.0543 S23: 0.4438 REMARK 3 S31: 0.2475 S32: -0.4973 S33: 0.2373 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 173 THROUGH 242 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.4334 -5.8590 -23.7966 REMARK 3 T TENSOR REMARK 3 T11: 0.2336 T22: 0.3409 REMARK 3 T33: 0.2336 T12: 0.0106 REMARK 3 T13: 0.0876 T23: -0.0221 REMARK 3 L TENSOR REMARK 3 L11: 2.5594 L22: 1.7300 REMARK 3 L33: 4.1446 L12: -0.0160 REMARK 3 L13: -0.1102 L23: 1.0657 REMARK 3 S TENSOR REMARK 3 S11: -0.0527 S12: -0.4375 S13: 0.0247 REMARK 3 S21: 0.3330 S22: -0.1344 S23: 0.3387 REMARK 3 S31: -0.0109 S32: -0.7890 S33: 0.1022 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE ENTRY CONTAINS FRIEDEL PAIRS IN REMARK 3 F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS REMARK 4 REMARK 4 5YFI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1300005184. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-APR-16 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 : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 81114 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.848 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.0000 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS REMARK 200 AND I_PLUS/MINUS COLUMNS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 4000, 200 MM ZINC ACETATE, 100 REMARK 280 MM MES (PH 6.5), 100 MM GUANIDINE HYDROCHLORIDE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K 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 20.35150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 100.09100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.39200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 100.09100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.35150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.39200 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: 4300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -171.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET L 1 REMARK 465 ASP L 2 REMARK 465 MET L 3 REMARK 465 ARG L 4 REMARK 465 THR L 5 REMARK 465 PRO L 6 REMARK 465 ALA L 7 REMARK 465 GLN L 8 REMARK 465 PHE L 9 REMARK 465 LEU L 10 REMARK 465 GLY L 11 REMARK 465 ILE L 12 REMARK 465 LEU L 13 REMARK 465 LEU L 14 REMARK 465 LEU L 15 REMARK 465 TRP L 16 REMARK 465 PHE L 17 REMARK 465 PRO L 18 REMARK 465 GLY L 19 REMARK 465 ILE L 20 REMARK 465 LYS L 21 REMARK 465 CYS L 22 REMARK 465 MET H 1 REMARK 465 GLU H 2 REMARK 465 TRP H 3 REMARK 465 ARG H 4 REMARK 465 TRP H 5 REMARK 465 ILE H 6 REMARK 465 PHE H 7 REMARK 465 LEU H 8 REMARK 465 PHE H 9 REMARK 465 LEU H 10 REMARK 465 LEU H 11 REMARK 465 SER H 12 REMARK 465 GLY H 13 REMARK 465 THR H 14 REMARK 465 THR H 15 REMARK 465 GLY H 16 REMARK 465 VAL H 17 REMARK 465 HIS H 18 REMARK 465 SER H 19 REMARK 465 TYR H 122 REMARK 465 ASP H 123 REMARK 465 THR H 243 REMARK 465 ILE H 244 REMARK 465 LYS H 245 REMARK 465 PRO H 246 REMARK 465 CYS H 247 REMARK 465 PRO H 248 REMARK 465 PRO H 249 REMARK 465 CYS H 250 REMARK 465 LYS H 251 REMARK 465 CYS H 252 REMARK 465 PRO H 253 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 OD2 ASP L 206 O HOH L 401 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 O HOH H 460 O HOH H 510 3444 2.10 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 L 72 50.26 37.20 REMARK 500 ALA L 73 -42.72 72.37 REMARK 500 ARG L 233 -9.16 -58.58 REMARK 500 ALA H 35 -157.51 -92.34 REMARK 500 LYS H 62 -109.00 -113.85 REMARK 500 ASN H 103 -168.55 -126.97 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 ZN L 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU L 101 OE2 REMARK 620 2 ASP L 206 OD2 19.3 REMARK 620 3 HOH L 401 O 60.3 52.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN L 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS L 171 NZ REMARK 620 2 GLU L 217 OE1 85.2 REMARK 620 3 CYS L 236 O 145.0 94.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN H 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP L 189 OD2 REMARK 620 2 HIS H 191 NE2 98.4 REMARK 620 3 HOH L 513 O 99.5 106.6 REMARK 620 4 HOH L 518 O 133.3 100.1 115.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN L 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU L 207 OE1 REMARK 620 2 HIS L 211 NE2 106.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN H 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU H 20 OE1 REMARK 620 2 HOH H 444 O 103.3 REMARK 620 3 ASP L 23 N 67.6 65.0 REMARK 620 4 ASP L 23 O 68.4 61.0 4.2 REMARK 620 5 ASP L 23 OD1 71.5 62.2 4.0 4.3 REMARK 620 6 HOH L 448 O 94.9 106.9 58.7 62.3 58.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN H 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER H 36 OG REMARK 620 2 HIS H 101 NE2 92.6 REMARK 620 3 HOH H 507 O 86.5 109.7 REMARK 620 4 ASP L 114 OD1 94.7 9.2 118.7 REMARK 620 5 ASP L 114 OD2 92.6 12.0 121.7 3.6 REMARK 620 6 HOH L 450 O 172.5 89.2 86.0 88.3 90.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN L 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN L 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN L 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN H 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN H 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN H 303 DBREF 5YFI L 1 236 PDB 5YFI 5YFI 1 236 DBREF 5YFI H 1 253 PDB 5YFI 5YFI 1 253 SEQRES 1 L 236 MET ASP MET ARG THR PRO ALA GLN PHE LEU GLY ILE LEU SEQRES 2 L 236 LEU LEU TRP PHE PRO GLY ILE LYS CYS ASP ILE LYS MET SEQRES 3 L 236 THR GLN SER PRO SER SER MET TYR VAL SER LEU GLY GLU SEQRES 4 L 236 ARG VAL THR ILE THR CYS LYS ALA SER GLN ASP ILE ASN SEQRES 5 L 236 ARG TYR LEU SER TRP PHE GLN GLN LYS PRO GLY LYS SER SEQRES 6 L 236 PRO LYS THR LEU ILE TYR ARG ALA ASN ARG MET LEU ASP SEQRES 7 L 236 GLY VAL PRO SER ARG PHE SER GLY SER GLY SER GLY GLN SEQRES 8 L 236 ASP TYR SER LEU THR ILE SER SER LEU GLU TYR GLU ASP SEQRES 9 L 236 MET GLY ASN TYR TYR CYS LEU GLN TYR ASP GLU PHE PRO SEQRES 10 L 236 PHE THR PHE GLY SER GLY THR LYS LEU GLU ILE LYS ARG SEQRES 11 L 236 ALA ASP ALA ALA PRO THR VAL SER ILE PHE PRO PRO SER SEQRES 12 L 236 SER GLU GLN LEU THR SER GLY GLY ALA SER VAL VAL CYS SEQRES 13 L 236 PHE LEU ASN ASN PHE TYR PRO LYS ASP ILE ASN VAL LYS SEQRES 14 L 236 TRP LYS ILE ASP GLY SER GLU ARG GLN ASN GLY VAL LEU SEQRES 15 L 236 ASN SER TRP THR ASP GLN ASP SER LYS ASP SER THR TYR SEQRES 16 L 236 SER MET SER SER THR LEU THR LEU THR LYS ASP GLU TYR SEQRES 17 L 236 GLU ARG HIS ASN SER TYR THR CYS GLU ALA THR HIS LYS SEQRES 18 L 236 THR SER THR SER PRO ILE VAL LYS SER PHE ASN ARG ASN SEQRES 19 L 236 GLU CYS SEQRES 1 H 253 MET GLU TRP ARG TRP ILE PHE LEU PHE LEU LEU SER GLY SEQRES 2 H 253 THR THR GLY VAL HIS SER GLU ILE GLN LEU GLN GLN SER SEQRES 3 H 253 GLY PRO GLU LEU VAL LYS PRO GLY ALA SER VAL LYS VAL SEQRES 4 H 253 SER CYS LYS ALA SER GLY PHE PRO PHE SER THR TYR ASN SEQRES 5 H 253 ILE TYR TRP VAL ILE GLN SER HIS GLY LYS SER LEU GLU SEQRES 6 H 253 TRP ILE GLY TYR ILE ASP PRO TYR ASN GLY GLY THR SER SEQRES 7 H 253 TYR ASN GLN LYS PHE ARG GLY LYS ALA THR LEU THR VAL SEQRES 8 H 253 ASP LYS SER SER SER THR ALA TYR MET HIS LEU ASN SER SEQRES 9 H 253 LEU THR SER GLU ASP SER ALA VAL TYR TYR CYS ALA ARG SEQRES 10 H 253 ARG TRP TYR THR TYR ASP GLY ASP TRP PHE ALA TYR TRP SEQRES 11 H 253 GLY GLN GLY THR LEU VAL THR VAL SER ALA ALA LYS THR SEQRES 12 H 253 THR ALA PRO SER VAL TYR PRO LEU ALA PRO VAL CYS GLY SEQRES 13 H 253 ASP THR THR GLY SER SER VAL THR LEU GLY CYS LEU VAL SEQRES 14 H 253 LYS GLY TYR PHE PRO GLU PRO VAL THR LEU THR TRP ASN SEQRES 15 H 253 SER GLY SER LEU SER SER GLY VAL HIS THR PHE PRO ALA SEQRES 16 H 253 VAL LEU GLN SER ASP LEU TYR THR LEU SER SER SER VAL SEQRES 17 H 253 THR VAL THR SER SER THR TRP PRO SER GLN SER ILE THR SEQRES 18 H 253 CYS ASN VAL ALA HIS PRO ALA SER SER THR LYS VAL ASP SEQRES 19 H 253 LYS LYS ILE GLU PRO ARG GLY PRO THR ILE LYS PRO CYS SEQRES 20 H 253 PRO PRO CYS LYS CYS PRO HET ZN L 301 1 HET ZN L 302 1 HET ZN L 303 1 HET ZN H 301 1 HET ZN H 302 1 HET ZN H 303 1 HETNAM ZN ZINC ION FORMUL 3 ZN 6(ZN 2+) FORMUL 9 HOH *315(H2 O) HELIX 1 AA1 GLU L 101 MET L 105 5 5 HELIX 2 AA2 SER L 143 GLY L 150 1 8 HELIX 3 AA3 LYS L 205 ARG L 210 1 6 HELIX 4 AA4 PRO H 72 GLY H 75 5 4 HELIX 5 AA5 GLN H 81 ARG H 84 5 4 HELIX 6 AA6 THR H 106 SER H 110 5 5 HELIX 7 AA7 SER H 183 SER H 185 5 3 HELIX 8 AA8 PRO H 227 SER H 230 5 4 SHEET 1 AA1 4 MET L 26 SER L 29 0 SHEET 2 AA1 4 VAL L 41 ALA L 47 -1 O THR L 44 N SER L 29 SHEET 3 AA1 4 ASP L 92 ILE L 97 -1 O LEU L 95 N ILE L 43 SHEET 4 AA1 4 PHE L 84 SER L 89 -1 N SER L 85 O THR L 96 SHEET 1 AA2 6 SER L 32 VAL L 35 0 SHEET 2 AA2 6 THR L 124 ILE L 128 1 O GLU L 127 N MET L 33 SHEET 3 AA2 6 GLY L 106 GLN L 112 -1 N GLY L 106 O LEU L 126 SHEET 4 AA2 6 LEU L 55 GLN L 60 -1 N PHE L 58 O TYR L 109 SHEET 5 AA2 6 LYS L 67 TYR L 71 -1 O LEU L 69 N TRP L 57 SHEET 6 AA2 6 ARG L 75 MET L 76 -1 O ARG L 75 N TYR L 71 SHEET 1 AA3 4 SER L 32 VAL L 35 0 SHEET 2 AA3 4 THR L 124 ILE L 128 1 O GLU L 127 N MET L 33 SHEET 3 AA3 4 GLY L 106 GLN L 112 -1 N GLY L 106 O LEU L 126 SHEET 4 AA3 4 THR L 119 PHE L 120 -1 O THR L 119 N GLN L 112 SHEET 1 AA4 4 THR L 136 PHE L 140 0 SHEET 2 AA4 4 GLY L 151 PHE L 161 -1 O PHE L 157 N SER L 138 SHEET 3 AA4 4 TYR L 195 THR L 204 -1 O LEU L 203 N ALA L 152 SHEET 4 AA4 4 VAL L 181 TRP L 185 -1 N SER L 184 O SER L 198 SHEET 1 AA5 4 SER L 175 ARG L 177 0 SHEET 2 AA5 4 ASN L 167 ILE L 172 -1 N ILE L 172 O SER L 175 SHEET 3 AA5 4 SER L 213 HIS L 220 -1 O THR L 219 N ASN L 167 SHEET 4 AA5 4 SER L 223 ASN L 232 -1 O PHE L 231 N TYR L 214 SHEET 1 AA6 4 GLN H 22 GLN H 25 0 SHEET 2 AA6 4 VAL H 37 SER H 44 -1 O LYS H 42 N GLN H 24 SHEET 3 AA6 4 THR H 97 LEU H 102 -1 O ALA H 98 N CYS H 41 SHEET 4 AA6 4 ALA H 87 ASP H 92 -1 N ASP H 92 O THR H 97 SHEET 1 AA7 6 GLU H 29 VAL H 31 0 SHEET 2 AA7 6 THR H 134 VAL H 138 1 O LEU H 135 N GLU H 29 SHEET 3 AA7 6 ALA H 111 TRP H 119 -1 N TYR H 113 O THR H 134 SHEET 4 AA7 6 ILE H 53 GLN H 58 -1 N VAL H 56 O TYR H 114 SHEET 5 AA7 6 LEU H 64 ASP H 71 -1 O ILE H 67 N TRP H 55 SHEET 6 AA7 6 GLY H 76 TYR H 79 -1 O GLY H 76 N ASP H 71 SHEET 1 AA8 4 GLU H 29 VAL H 31 0 SHEET 2 AA8 4 THR H 134 VAL H 138 1 O LEU H 135 N GLU H 29 SHEET 3 AA8 4 ALA H 111 TRP H 119 -1 N TYR H 113 O THR H 134 SHEET 4 AA8 4 TRP H 126 TRP H 130 -1 O TRP H 126 N TRP H 119 SHEET 1 AA9 4 SER H 147 LEU H 151 0 SHEET 2 AA9 4 SER H 162 TYR H 172 -1 O GLY H 166 N LEU H 151 SHEET 3 AA9 4 LEU H 201 THR H 211 -1 O LEU H 204 N VAL H 169 SHEET 4 AA9 4 VAL H 190 THR H 192 -1 N HIS H 191 O SER H 207 SHEET 1 AB1 4 SER H 147 LEU H 151 0 SHEET 2 AB1 4 SER H 162 TYR H 172 -1 O GLY H 166 N LEU H 151 SHEET 3 AB1 4 LEU H 201 THR H 211 -1 O LEU H 204 N VAL H 169 SHEET 4 AB1 4 VAL H 196 GLN H 198 -1 N GLN H 198 O LEU H 201 SHEET 1 AB2 3 THR H 178 TRP H 181 0 SHEET 2 AB2 3 THR H 221 HIS H 226 -1 O ASN H 223 N THR H 180 SHEET 3 AB2 3 THR H 231 LYS H 236 -1 O VAL H 233 N VAL H 224 SSBOND 1 CYS L 45 CYS L 110 1555 1555 2.06 SSBOND 2 CYS L 156 CYS L 216 1555 1555 2.05 SSBOND 3 CYS L 236 CYS H 155 1555 1555 2.04 SSBOND 4 CYS H 41 CYS H 115 1555 1555 2.09 SSBOND 5 CYS H 167 CYS H 222 1555 1555 2.03 LINK OE2 GLU L 101 ZN ZN L 303 1555 1555 2.18 LINK NZ LYS L 171 ZN ZN L 302 1555 1555 2.25 LINK OD2 ASP L 189 ZN ZN H 301 1555 1555 1.89 LINK OE1 GLU L 207 ZN ZN L 301 1555 1555 2.09 LINK NE2 HIS L 211 ZN ZN L 301 1555 1555 2.25 LINK OE1 GLU L 217 ZN ZN L 302 1555 1555 2.55 LINK OE1 GLU H 20 ZN ZN H 303 1555 1555 2.18 LINK OG SER H 36 ZN ZN H 302 1555 1555 2.19 LINK NE2 HIS H 101 ZN ZN H 302 1555 1555 2.08 LINK NE2 HIS H 191 ZN ZN H 301 1555 1555 2.19 LINK ZN ZN H 301 O HOH L 513 1555 1555 2.39 LINK ZN ZN H 301 O HOH L 518 1555 1555 2.49 LINK ZN ZN H 302 O HOH H 507 1555 1555 2.06 LINK ZN ZN H 303 O HOH H 444 1555 1555 1.89 LINK N ASP L 23 ZN ZN H 303 1555 1655 2.21 LINK O ASP L 23 ZN ZN H 303 1555 1655 2.28 LINK OD1 ASP L 23 ZN ZN H 303 1555 1655 2.06 LINK OD1 ASP L 114 ZN ZN H 302 1555 3554 2.52 LINK OD2 ASP L 114 ZN ZN H 302 1555 3554 2.12 LINK OD2 ASP L 206 ZN ZN L 303 1555 1545 2.69 LINK O CYS L 236 ZN ZN L 302 1555 4445 2.50 LINK ZN ZN L 303 O HOH L 401 1555 1565 2.49 LINK ZN ZN H 302 O HOH L 450 1555 3544 2.05 LINK ZN ZN H 303 O HOH L 448 1555 1455 2.21 CISPEP 1 SER L 29 PRO L 30 0 -3.09 CISPEP 2 PHE L 116 PRO L 117 0 1.58 CISPEP 3 TYR L 162 PRO L 163 0 6.04 CISPEP 4 PHE H 173 PRO H 174 0 -7.83 CISPEP 5 GLU H 175 PRO H 176 0 1.08 CISPEP 6 TRP H 215 PRO H 216 0 6.10 SITE 1 AC1 2 GLU L 207 HIS L 211 SITE 1 AC2 3 LYS L 171 GLU L 217 CYS L 236 SITE 1 AC3 3 GLU L 101 ASP L 206 HOH L 401 SITE 1 AC4 4 HIS H 191 ASP L 189 HOH L 513 HOH L 518 SITE 1 AC5 5 SER H 36 HIS H 101 HOH H 507 ASP L 114 SITE 2 AC5 5 HOH L 450 SITE 1 AC6 4 GLU H 20 HOH H 444 ASP L 23 HOH L 448 CRYST1 40.703 60.784 200.182 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 0.024568 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016452 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004995 0.00000