HEADER VIRAL PROTEIN/IMMUNE SYSTEM 26-NOV-12 4I3R TITLE CRYSTAL STRUCTURE OF THE OUTER DOMAIN OF HIV-1 GP120 IN COMPLEX WITH TITLE 2 VRC-PG04 SPACE GROUP P3221 COMPND MOL_ID: 1; COMPND 2 MOLECULE: OUTER DOMAIN OF HIV-1 GP120 (KER2018 OD4.2.2); COMPND 3 CHAIN: G; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HEAVY CHAIN OF VRC-PG04 FAB; COMPND 7 CHAIN: H; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: LIGHT CHAIN OF VRC-PG04 FAB; COMPND 11 CHAIN: L; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS; SOURCE 3 ORGANISM_TAXID: 12721; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: 293S; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 13 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 15 EXPRESSION_SYSTEM_CELL_LINE: 293F; SOURCE 16 MOL_ID: 3; SOURCE 17 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 18 ORGANISM_COMMON: HUMAN; SOURCE 19 ORGANISM_TAXID: 9606; SOURCE 20 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 21 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 22 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 23 EXPRESSION_SYSTEM_CELL_LINE: 293F KEYWDS ANTIBODY AFFINITY, ANTIBODY SPECIFICITY, BINDING SITES, HIV KEYWDS 2 INFECTIONS, ANTIBODIES, HIV ENVELOPE PROTEIN GP120, AIDS VACCINES, KEYWDS 3 AMINO ACID SEQUENCE, ANTIGENS, EPITOPES, HIV ANTIBODIES, CD4, KEYWDS 4 SOMATIC MUTATION, SEQUENCE ENGINEERING, COMPLEMENTARITY DETERMINING KEYWDS 5 REGIONS, IMMUNOGLOBULIN FAB FRAGMENTS, SERA, VIRAL PROTEIN-IMMUNE KEYWDS 6 SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.G.JOYCE,C.BIERTUMPFEL,G.J.NABEL,P.D.KWONG REVDAT 7 27-NOV-24 4I3R 1 REMARK REVDAT 6 20-SEP-23 4I3R 1 REMARK REVDAT 5 26-MAY-21 4I3R 1 SOURCE HETSYN REVDAT 4 29-JUL-20 4I3R 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE REVDAT 3 13-FEB-13 4I3R 1 JRNL REVDAT 2 23-JAN-13 4I3R 1 JRNL REVDAT 1 09-JAN-13 4I3R 0 JRNL AUTH M.G.JOYCE,M.KANEKIYO,L.XU,C.BIERTUMPFEL,J.C.BOYINGTON, JRNL AUTH 2 S.MOQUIN,W.SHI,X.WU,Y.YANG,Z.Y.YANG,B.ZHANG,A.ZHENG,T.ZHOU, JRNL AUTH 3 J.ZHU,J.R.MASCOLA,P.D.KWONG,G.J.NABEL JRNL TITL OUTER DOMAIN OF HIV-1 GP120: ANTIGENIC OPTIMIZATION, JRNL TITL 2 STRUCTURAL MALLEABILITY, AND CRYSTAL STRUCTURE WITH ANTIBODY JRNL TITL 3 VRC-PG04. JRNL REF J.VIROL. V. 87 2294 2013 JRNL REFN ISSN 0022-538X JRNL PMID 23236069 JRNL DOI 10.1128/JVI.02717-12 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 22971 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1380 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 43.6564 - 6.4592 0.96 2263 113 0.1793 0.2598 REMARK 3 2 6.4592 - 5.1294 0.98 2189 132 0.1724 0.2076 REMARK 3 3 5.1294 - 4.4818 0.98 2175 158 0.1306 0.1870 REMARK 3 4 4.4818 - 4.0723 0.98 2178 132 0.1389 0.1784 REMARK 3 5 4.0723 - 3.7806 0.98 2151 134 0.1750 0.2393 REMARK 3 6 3.7806 - 3.5578 0.99 2188 146 0.1986 0.2865 REMARK 3 7 3.5578 - 3.3797 0.99 2157 135 0.2273 0.3187 REMARK 3 8 3.3797 - 3.2327 0.99 2162 141 0.2604 0.3085 REMARK 3 9 3.2327 - 3.1082 0.98 2143 158 0.2958 0.3998 REMARK 3 10 3.1082 - 3.0010 0.91 1985 131 0.3099 0.3564 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) : 0.430 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.670 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 75.00 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 : 0.009 4994 REMARK 3 ANGLE : 1.299 6774 REMARK 3 CHIRALITY : 0.083 763 REMARK 3 PLANARITY : 0.005 871 REMARK 3 DIHEDRAL : 17.339 1816 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 13 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN G AND RESID 252:257) REMARK 3 ORIGIN FOR THE GROUP (A): 59.6013 -36.2938 -5.3695 REMARK 3 T TENSOR REMARK 3 T11: 1.3534 T22: 0.9015 REMARK 3 T33: 1.1311 T12: -0.3162 REMARK 3 T13: -0.2617 T23: 0.3679 REMARK 3 L TENSOR REMARK 3 L11: 2.0503 L22: 2.0283 REMARK 3 L33: 2.0979 L12: 1.9630 REMARK 3 L13: 4.9553 L23: 4.8250 REMARK 3 S TENSOR REMARK 3 S11: 0.4060 S12: -1.1721 S13: -0.7484 REMARK 3 S21: 2.1364 S22: 0.4371 S23: 1.0845 REMARK 3 S31: 4.0807 S32: -1.3793 S33: -0.7159 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN G AND RESID 258:396) REMARK 3 ORIGIN FOR THE GROUP (A): 61.9825 -38.9028 -22.4094 REMARK 3 T TENSOR REMARK 3 T11: 1.2051 T22: 0.4911 REMARK 3 T33: 0.6433 T12: -0.1047 REMARK 3 T13: -0.2813 T23: 0.0241 REMARK 3 L TENSOR REMARK 3 L11: 1.5122 L22: 7.8521 REMARK 3 L33: 2.5326 L12: -0.2754 REMARK 3 L13: -0.3298 L23: -1.4977 REMARK 3 S TENSOR REMARK 3 S11: 0.2575 S12: 0.0816 S13: -0.4949 REMARK 3 S21: -1.0273 S22: 0.0865 S23: 0.3807 REMARK 3 S31: 0.8403 S32: -0.1249 S33: -0.3582 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN G AND RESID 397:412) REMARK 3 ORIGIN FOR THE GROUP (A): 71.5015 -40.2250 -37.7009 REMARK 3 T TENSOR REMARK 3 T11: 2.1035 T22: 1.5575 REMARK 3 T33: 1.5656 T12: 0.0625 REMARK 3 T13: 0.6960 T23: -0.4550 REMARK 3 L TENSOR REMARK 3 L11: 3.5874 L22: 0.1368 REMARK 3 L33: 4.7013 L12: 0.6104 REMARK 3 L13: -0.3386 L23: -0.6037 REMARK 3 S TENSOR REMARK 3 S11: -0.9186 S12: 0.2872 S13: -1.2123 REMARK 3 S21: 0.3690 S22: -0.6606 S23: -0.0714 REMARK 3 S31: 1.5262 S32: 1.3424 S33: 1.2078 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN G AND RESID 413:421) REMARK 3 ORIGIN FOR THE GROUP (A): 70.8701 -49.2780 -17.1153 REMARK 3 T TENSOR REMARK 3 T11: 1.7849 T22: 0.5416 REMARK 3 T33: 0.8946 T12: -0.1328 REMARK 3 T13: -0.3714 T23: -0.0486 REMARK 3 L TENSOR REMARK 3 L11: 8.6899 L22: 2.1521 REMARK 3 L33: 9.1584 L12: -1.7955 REMARK 3 L13: -0.3237 L23: -4.3001 REMARK 3 S TENSOR REMARK 3 S11: -0.4709 S12: 0.0439 S13: -0.7580 REMARK 3 S21: -1.1751 S22: 0.5278 S23: -0.0115 REMARK 3 S31: 0.2052 S32: 0.6182 S33: -0.3918 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN G AND RESID 422:441) REMARK 3 ORIGIN FOR THE GROUP (A): 69.3692 -60.0448 -2.9310 REMARK 3 T TENSOR REMARK 3 T11: 2.3569 T22: 1.1514 REMARK 3 T33: 1.4903 T12: -0.0776 REMARK 3 T13: -0.3543 T23: 0.2978 REMARK 3 L TENSOR REMARK 3 L11: 7.5228 L22: 1.5241 REMARK 3 L33: 4.9144 L12: 3.3999 REMARK 3 L13: 6.1164 L23: 2.7093 REMARK 3 S TENSOR REMARK 3 S11: 1.2067 S12: -0.5410 S13: -0.6791 REMARK 3 S21: 2.6408 S22: 0.6800 S23: -2.1366 REMARK 3 S31: -0.0453 S32: -0.0657 S33: -1.6914 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN G AND RESID 442:470) REMARK 3 ORIGIN FOR THE GROUP (A): 63.7623 -35.4022 -21.7967 REMARK 3 T TENSOR REMARK 3 T11: 0.8867 T22: 0.4469 REMARK 3 T33: 0.4202 T12: -0.0260 REMARK 3 T13: -0.1877 T23: -0.0341 REMARK 3 L TENSOR REMARK 3 L11: 4.0619 L22: 7.1883 REMARK 3 L33: 4.7952 L12: -6.2165 REMARK 3 L13: 1.9796 L23: -5.0409 REMARK 3 S TENSOR REMARK 3 S11: -0.0566 S12: 0.1853 S13: 0.1751 REMARK 3 S21: -1.1093 S22: 0.5696 S23: 0.5035 REMARK 3 S31: 0.3705 S32: -0.5336 S33: -0.4863 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN G AND RESID 471:484) REMARK 3 ORIGIN FOR THE GROUP (A): 51.1789 -31.4962 -11.4577 REMARK 3 T TENSOR REMARK 3 T11: 1.2738 T22: 1.3038 REMARK 3 T33: 1.4560 T12: -0.1696 REMARK 3 T13: -0.3504 T23: 0.1871 REMARK 3 L TENSOR REMARK 3 L11: 1.9134 L22: 9.3595 REMARK 3 L33: 2.0213 L12: -9.3517 REMARK 3 L13: 2.7386 L23: 0.8892 REMARK 3 S TENSOR REMARK 3 S11: 1.1784 S12: 2.0863 S13: -1.0173 REMARK 3 S21: -1.0515 S22: -0.2416 S23: 4.0833 REMARK 3 S31: 0.5988 S32: -1.2323 S33: -0.8404 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN H AND RESID 1:9) REMARK 3 ORIGIN FOR THE GROUP (A): 71.6704 -12.6534 4.2473 REMARK 3 T TENSOR REMARK 3 T11: 1.8532 T22: 0.8566 REMARK 3 T33: 1.0421 T12: -0.4754 REMARK 3 T13: -0.1603 T23: -0.1534 REMARK 3 L TENSOR REMARK 3 L11: 5.0198 L22: 4.8207 REMARK 3 L33: 2.1040 L12: 2.5491 REMARK 3 L13: 6.7157 L23: 1.1067 REMARK 3 S TENSOR REMARK 3 S11: 0.7170 S12: -2.2192 S13: 3.7617 REMARK 3 S21: 1.5796 S22: -0.8827 S23: -0.7040 REMARK 3 S31: -1.4473 S32: 0.4014 S33: 0.0696 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN H AND RESID 10:126) REMARK 3 ORIGIN FOR THE GROUP (A): 74.7770 -15.9269 -6.2527 REMARK 3 T TENSOR REMARK 3 T11: 0.8042 T22: 0.4880 REMARK 3 T33: 0.6848 T12: -0.1531 REMARK 3 T13: -0.2016 T23: 0.1523 REMARK 3 L TENSOR REMARK 3 L11: 2.3941 L22: 5.8425 REMARK 3 L33: 2.6908 L12: 2.7884 REMARK 3 L13: 1.2592 L23: 1.4976 REMARK 3 S TENSOR REMARK 3 S11: 0.4912 S12: -0.3619 S13: -0.5380 REMARK 3 S21: 1.0370 S22: -0.2050 S23: -0.9245 REMARK 3 S31: 0.1047 S32: 0.3050 S33: -0.2817 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN H AND RESID 127:134) REMARK 3 ORIGIN FOR THE GROUP (A): 93.0183 29.6381 -4.3366 REMARK 3 T TENSOR REMARK 3 T11: 3.4149 T22: 1.2071 REMARK 3 T33: 1.2183 T12: -0.1950 REMARK 3 T13: 0.0216 T23: 0.0187 REMARK 3 L TENSOR REMARK 3 L11: -0.0003 L22: -0.0342 REMARK 3 L33: 0.0007 L12: -0.0033 REMARK 3 L13: -0.0052 L23: 0.0131 REMARK 3 S TENSOR REMARK 3 S11: -1.5586 S12: -0.0722 S13: -0.2801 REMARK 3 S21: -2.5574 S22: 0.2200 S23: -2.4025 REMARK 3 S31: -0.1355 S32: -1.2193 S33: 0.8311 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN H AND RESID 135:215) REMARK 3 ORIGIN FOR THE GROUP (A): 92.1692 11.7697 2.3806 REMARK 3 T TENSOR REMARK 3 T11: 1.0861 T22: 0.7998 REMARK 3 T33: 0.9853 T12: -0.3577 REMARK 3 T13: -0.2870 T23: 0.1927 REMARK 3 L TENSOR REMARK 3 L11: 5.7450 L22: 3.4313 REMARK 3 L33: 6.7337 L12: -0.6643 REMARK 3 L13: 1.8491 L23: 6.6880 REMARK 3 S TENSOR REMARK 3 S11: 0.1137 S12: -0.5066 S13: -0.4377 REMARK 3 S21: 0.9114 S22: 0.1736 S23: -1.0819 REMARK 3 S31: 0.0991 S32: 0.6552 S33: -0.3226 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: (CHAIN L AND RESID 1:104) REMARK 3 ORIGIN FOR THE GROUP (A): 60.1723 0.2492 -12.1805 REMARK 3 T TENSOR REMARK 3 T11: 0.7519 T22: 0.3791 REMARK 3 T33: 0.5656 T12: -0.1085 REMARK 3 T13: 0.0975 T23: 0.0639 REMARK 3 L TENSOR REMARK 3 L11: 5.1241 L22: 6.4003 REMARK 3 L33: 5.5137 L12: -0.4120 REMARK 3 L13: 1.7778 L23: -0.6939 REMARK 3 S TENSOR REMARK 3 S11: 0.0666 S12: -0.2254 S13: 0.6677 REMARK 3 S21: 0.5536 S22: -0.2026 S23: 0.4944 REMARK 3 S31: -0.5237 S32: -0.0671 S33: 0.1366 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: (CHAIN L AND RESID 105:214) REMARK 3 ORIGIN FOR THE GROUP (A): 91.1177 18.2558 -13.0073 REMARK 3 T TENSOR REMARK 3 T11: 1.0597 T22: 0.7802 REMARK 3 T33: 0.7743 T12: -0.3507 REMARK 3 T13: 0.0459 T23: 0.0300 REMARK 3 L TENSOR REMARK 3 L11: 8.3423 L22: 4.6244 REMARK 3 L33: 2.0360 L12: -2.3955 REMARK 3 L13: -0.5544 L23: 0.2702 REMARK 3 S TENSOR REMARK 3 S11: 0.1569 S12: 0.3718 S13: 0.3209 REMARK 3 S21: -0.3643 S22: -0.1072 S23: -0.9651 REMARK 3 S31: -0.5244 S32: 0.7370 S33: -0.0727 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 4I3R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1000076266. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22975 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.14600 REMARK 200 R SYM (I) : 0.14600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.8200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.610 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: PDB ENTRY 3SE9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG400, 20% PEG8000, 100 MM NA REMARK 280 -ACETATE PH5.5, 500 MM NACL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.51333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.75667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 26.75667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 53.51333 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 300 REMARK: THE BIOLOGICAL UNIT IS IDENTICAL TO THAT FOUND IN THE REMARK 300 ASYMMETRIC UNIT. 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS H 129 CG CD CE NZ 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 GLN G 258 -61.04 -106.57 REMARK 500 ASP G 276 118.44 -163.57 REMARK 500 ASN G 392 79.80 -151.96 REMARK 500 ALA G 400 -134.93 65.78 REMARK 500 SER G 432 43.98 -96.90 REMARK 500 GLN G 440 49.91 -90.80 REMARK 500 SER G 460 -46.70 -140.09 REMARK 500 PRO G 470 21.44 -75.59 REMARK 500 MET G 475 61.05 -111.38 REMARK 500 MET G 475 68.28 -111.38 REMARK 500 ASP G 477 80.96 69.21 REMARK 500 ASP G 477 80.96 108.33 REMARK 500 ASN G 478 -6.95 -143.75 REMARK 500 PRO H 126 112.26 -32.44 REMARK 500 ASP H 144 69.62 63.93 REMARK 500 ALA L 50 -121.64 50.28 REMARK 500 PRO L 59 154.60 -46.41 REMARK 500 LEU L 91 -124.54 40.57 REMARK 500 ARG L 108 -168.85 -121.83 REMARK 500 LYS L 190 -67.30 -96.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 NAG G 903 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3SE9 RELATED DB: PDB REMARK 900 RELATED ID: 3NGB RELATED DB: PDB REMARK 900 RELATED ID: 3SE8 RELATED DB: PDB REMARK 900 RELATED ID: 3TYG RELATED DB: PDB REMARK 900 RELATED ID: 4I3S RELATED DB: PDB DBREF 4I3R G 252 481 PDB 4I3R 4I3R 252 481 DBREF 4I3R H 1 216 PDB 4I3R 4I3R 1 216 DBREF 4I3R L 1 214 PDB 4I3R 4I3R 1 214 SEQRES 1 G 190 LYS PRO VAL VAL SER THR GLN LEU LEU LEU ASN GLY SER SEQRES 2 G 190 LEU ALA GLU LYS GLU ILE ARG ILE LYS SER GLU ASP ILE SEQRES 3 G 190 SER ASP ASN ALA LYS ASN ILE ILE VAL GLN LEU THR LYS SEQRES 4 G 190 PRO VAL LEU ILE ASN CYS ALA ARG PRO SER ASN ASN THR SEQRES 5 G 190 GLN TYR CYS VAL VAL ASN ARG THR GLN TRP ASN ASP THR SEQRES 6 G 190 LEU GLY GLN VAL ALA ILE GLN LEU ARG LYS HIS TRP ASN SEQRES 7 G 190 THR CYS ILE ILE PHE ASN GLU PRO SER GLY GLY ASP LEU SEQRES 8 G 190 GLU ILE THR THR HIS SER PHE ASN CYS GLY GLY GLU PHE SEQRES 9 G 190 PHE TYR CYS ASN THR SER ASP LEU PHE ASN SER THR TRP SEQRES 10 G 190 ASN ILE GLU GLY THR ALA SER ILE ASP GLY THR GLU SER SEQRES 11 G 190 ASN ASP ASP ILE THR LEU PRO CYS ARG ILE LYS GLY SER SEQRES 12 G 190 GLY ALA PRO PRO ILE GLN GLY VAL ILE ARG CYS GLN SER SEQRES 13 G 190 ASN ILE THR GLY ILE LEU LEU THR ARG ASP GLY GLY SER SEQRES 14 G 190 GLY SER GLY THR CYS GLU THR PHE ARG PRO GLY GLY GLY SEQRES 15 G 190 ASP MET ARG ASP ASN TRP ARG SER SEQRES 1 H 228 GLN VAL GLN LEU VAL GLN SER GLY SER GLY VAL LYS LYS SEQRES 2 H 228 PRO GLY ALA SER VAL ARG VAL SER CYS TRP THR SER GLU SEQRES 3 H 228 ASP ILE PHE GLU ARG THR GLU LEU ILE HIS TRP VAL ARG SEQRES 4 H 228 GLN ALA PRO GLY GLN GLY LEU GLU TRP ILE GLY TRP VAL SEQRES 5 H 228 LYS THR VAL THR GLY ALA VAL ASN PHE GLY SER PRO ASP SEQRES 6 H 228 PHE ARG GLN ARG VAL SER LEU THR ARG ASP ARG ASP LEU SEQRES 7 H 228 PHE THR ALA HIS MET ASP ILE ARG GLY LEU THR GLN GLY SEQRES 8 H 228 ASP THR ALA THR TYR PHE CYS ALA ARG GLN LYS PHE TYR SEQRES 9 H 228 THR GLY GLY GLN GLY TRP TYR PHE ASP LEU TRP GLY ARG SEQRES 10 H 228 GLY THR LEU ILE VAL VAL SER SER ALA SER THR LYS GLY SEQRES 11 H 228 PRO SER VAL PHE PRO LEU ALA PRO SER SER LYS SER THR SEQRES 12 H 228 SER GLY GLY THR ALA ALA LEU GLY CYS LEU VAL LYS ASP SEQRES 13 H 228 TYR PHE PRO GLU PRO VAL THR VAL SER TRP ASN SER GLY SEQRES 14 H 228 ALA LEU THR SER GLY VAL HIS THR PHE PRO ALA VAL LEU SEQRES 15 H 228 GLN SER SER GLY LEU TYR SER LEU SER SER VAL VAL THR SEQRES 16 H 228 VAL PRO SER SER SER LEU GLY THR GLN THR TYR ILE CYS SEQRES 17 H 228 ASN VAL ASN HIS LYS PRO SER ASN THR LYS VAL ASP LYS SEQRES 18 H 228 LYS VAL GLU PRO LYS SER CYS SEQRES 1 L 208 GLU ILE VAL LEU THR GLN SER PRO GLY THR LEU SER LEU SEQRES 2 L 208 SER PRO GLY GLU THR ALA SER LEU SER CYS THR ALA ALA SEQRES 3 L 208 SER TYR GLY HIS MET THR TRP TYR GLN LYS LYS PRO GLY SEQRES 4 L 208 GLN PRO PRO LYS LEU LEU ILE PHE ALA THR SER LYS ARG SEQRES 5 L 208 ALA SER GLY ILE PRO ASP ARG PHE SER GLY SER GLN PHE SEQRES 6 L 208 GLY LYS GLN TYR THR LEU THR ILE THR ARG MET GLU PRO SEQRES 7 L 208 GLU ASP PHE ALA ARG TYR TYR CYS GLN GLN LEU GLU PHE SEQRES 8 L 208 PHE GLY GLN GLY THR ARG LEU GLU ILE ARG ARG THR VAL SEQRES 9 L 208 ALA ALA PRO SER VAL PHE ILE PHE PRO PRO SER ASP GLU SEQRES 10 L 208 GLN LEU LYS SER GLY THR ALA SER VAL VAL CYS LEU LEU SEQRES 11 L 208 ASN ASN PHE TYR PRO ARG GLU ALA LYS VAL GLN TRP LYS SEQRES 12 L 208 VAL ASP ASN ALA LEU GLN SER GLY ASN SER GLN GLU SER SEQRES 13 L 208 VAL THR GLU GLN ASP SER LYS ASP SER THR TYR SER LEU SEQRES 14 L 208 SER SER THR LEU THR LEU SER LYS ALA ASP TYR GLU LYS SEQRES 15 L 208 HIS LYS VAL TYR ALA CYS GLU VAL THR HIS GLN GLY LEU SEQRES 16 L 208 SER SER PRO VAL THR LYS SER PHE ASN ARG GLY GLU CYS MODRES 4I3R ASN G 448 ASN GLYCOSYLATION SITE MODRES 4I3R ASN G 334 ASN GLYCOSYLATION SITE MODRES 4I3R ASN G 301 ASN GLYCOSYLATION SITE MODRES 4I3R ASN G 339 ASN GLYCOSYLATION SITE HET NAG G 900 14 HET NAG G 901 14 HET NAG G 902 14 HET NAG G 903 11 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 4 NAG 4(C8 H15 N O6) FORMUL 8 HOH *4(H2 O) HELIX 1 1 ASN G 334 LYS G 351 1 18 HELIX 2 2 ASP G 368 THR G 373 1 6 HELIX 3 3 SER H 25 ARG H 31 1 7 HELIX 4 4 SER H 60 ARG H 66 1 7 HELIX 5 5 THR H 83 THR H 87 5 5 HELIX 6 6 SER H 156 ALA H 158 5 3 HELIX 7 7 SER H 187 LEU H 189 5 3 HELIX 8 8 LYS H 201 ASN H 204 5 4 HELIX 9 9 GLU L 79 PHE L 83 5 5 HELIX 10 10 SER L 121 GLY L 128 1 8 HELIX 11 11 LYS L 183 HIS L 189 1 7 SHEET 1 A 7 LEU G 259 LEU G 261 0 SHEET 2 A 7 ILE G 443 ARG G 456 -1 O GLY G 451 N LEU G 260 SHEET 3 A 7 ILE G 284 SER G 300 -1 N VAL G 286 O ILE G 452 SHEET 4 A 7 THR G 303 VAL G 333 -1 O VAL G 332 N ASN G 295 SHEET 5 A 7 ILE G 414 ILE G 420 -1 O ILE G 414 N VAL G 333 SHEET 6 A 7 GLU G 381 CYS G 385 -1 N TYR G 384 O ARG G 419 SHEET 7 A 7 HIS G 374 CYS G 378 -1 N PHE G 376 O PHE G 383 SHEET 1 B 6 ARG G 271 LYS G 273 0 SHEET 2 B 6 ILE G 284 SER G 300 -1 O ILE G 285 N LYS G 273 SHEET 3 B 6 ILE G 443 ARG G 456 -1 O ILE G 452 N VAL G 286 SHEET 4 B 6 GLU G 466 ARG G 469 -1 O ARG G 469 N THR G 455 SHEET 5 B 6 ILE G 359 PHE G 361 1 N ILE G 360 O PHE G 468 SHEET 6 B 6 SER G 393 TRP G 395 -1 O TRP G 395 N ILE G 359 SHEET 1 C 4 VAL H 5 GLN H 6 0 SHEET 2 C 4 VAL H 18 TRP H 23 -1 O TRP H 23 N VAL H 5 SHEET 3 C 4 THR H 77 ILE H 82 -1 O ILE H 82 N VAL H 18 SHEET 4 C 4 VAL H 67 ASP H 72 -1 N SER H 68 O ASP H 81 SHEET 1 D 6 GLY H 10 LYS H 12 0 SHEET 2 D 6 THR H 107 VAL H 111 1 O VAL H 110 N LYS H 12 SHEET 3 D 6 ALA H 88 LYS H 96 -1 N TYR H 90 O THR H 107 SHEET 4 D 6 THR H 32 GLN H 39 -1 N VAL H 37 O PHE H 91 SHEET 5 D 6 GLU H 46 LYS H 52 -1 O GLU H 46 N ARG H 38 SHEET 6 D 6 VAL H 56 PHE H 58 -1 O ASN H 57 N TRP H 50 SHEET 1 E 4 SER H 120 LEU H 124 0 SHEET 2 E 4 THR H 135 TYR H 145 -1 O LEU H 141 N PHE H 122 SHEET 3 E 4 TYR H 176 PRO H 185 -1 O LEU H 178 N VAL H 142 SHEET 4 E 4 VAL H 163 THR H 165 -1 N HIS H 164 O VAL H 181 SHEET 1 F 4 SER H 120 LEU H 124 0 SHEET 2 F 4 THR H 135 TYR H 145 -1 O LEU H 141 N PHE H 122 SHEET 3 F 4 TYR H 176 PRO H 185 -1 O LEU H 178 N VAL H 142 SHEET 4 F 4 VAL H 169 LEU H 170 -1 N VAL H 169 O SER H 177 SHEET 1 G 3 THR H 151 TRP H 154 0 SHEET 2 G 3 TYR H 194 HIS H 200 -1 O ASN H 197 N SER H 153 SHEET 3 G 3 THR H 205 VAL H 211 -1 O VAL H 207 N VAL H 198 SHEET 1 H 4 LEU L 4 SER L 7 0 SHEET 2 H 4 ALA L 19 ALA L 25 -1 O THR L 24 N THR L 5 SHEET 3 H 4 GLN L 70 ILE L 75 -1 O TYR L 71 N CYS L 23 SHEET 4 H 4 PHE L 62 PHE L 67 -1 N SER L 63 O THR L 74 SHEET 1 I 6 THR L 10 LEU L 13 0 SHEET 2 I 6 THR L 102 ILE L 106 1 O ARG L 103 N LEU L 11 SHEET 3 I 6 ARG L 85 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 I 6 THR L 34 LYS L 38 -1 N THR L 34 O GLN L 89 SHEET 5 I 6 LYS L 45 PHE L 49 -1 O LYS L 45 N GLN L 37 SHEET 6 I 6 LYS L 53 ARG L 54 -1 O LYS L 53 N PHE L 49 SHEET 1 J 4 THR L 10 LEU L 13 0 SHEET 2 J 4 THR L 102 ILE L 106 1 O ARG L 103 N LEU L 11 SHEET 3 J 4 ARG L 85 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 J 4 PHE L 97 PHE L 98 -1 O PHE L 97 N GLN L 90 SHEET 1 K 4 SER L 114 PHE L 118 0 SHEET 2 K 4 THR L 129 PHE L 139 -1 O ASN L 137 N SER L 114 SHEET 3 K 4 TYR L 173 SER L 182 -1 O LEU L 175 N LEU L 136 SHEET 4 K 4 SER L 159 VAL L 163 -1 N GLN L 160 O THR L 178 SHEET 1 L 3 ALA L 144 VAL L 150 0 SHEET 2 L 3 VAL L 191 HIS L 198 -1 O GLU L 195 N GLN L 147 SHEET 3 L 3 VAL L 205 ASN L 210 -1 O VAL L 205 N VAL L 196 SSBOND 1 CYS G 296 CYS G 331 1555 1555 2.03 SSBOND 2 CYS G 358 CYS G 465 1555 1555 2.04 SSBOND 3 CYS G 378 CYS G 445 1555 1555 2.05 SSBOND 4 CYS G 385 CYS G 418 1555 1555 2.03 SSBOND 5 CYS H 22 CYS H 92 1555 1555 2.04 SSBOND 6 CYS H 140 CYS H 196 1555 1555 2.03 SSBOND 7 CYS H 216 CYS L 214 1555 1555 1.96 SSBOND 8 CYS L 23 CYS L 88 1555 1555 2.04 SSBOND 9 CYS L 134 CYS L 194 1555 1555 2.04 LINK ND2 ASN G 301 C1 NAG G 900 1555 1555 1.58 LINK ND2 ASN G 334 C1 NAG G 902 1555 1555 1.54 LINK ND2 ASN G 339 C1 NAG G 903 1555 1555 1.78 LINK ND2 ASN G 448 C1 NAG G 901 1555 1555 1.48 CISPEP 1 GLY G 431 SER G 432 0 -7.84 CISPEP 2 SER H 128 LYS H 129 0 -21.26 CISPEP 3 SER H 130 THR H 131 0 -0.59 CISPEP 4 PHE H 146 PRO H 147 0 -5.00 CISPEP 5 GLU H 148 PRO H 149 0 -2.34 CISPEP 6 SER L 7 PRO L 8 0 -7.58 CISPEP 7 TYR L 140 PRO L 141 0 6.73 CRYST1 158.910 158.910 80.270 90.00 90.00 120.00 P 32 2 1 6 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 0.006293 0.003633 0.000000 0.00000 SCALE2 0.000000 0.007266 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012458 0.00000