HEADER TRANSFERASE 07-JAN-17 5WXK TITLE EARP BOUND WITH DOMAIN I OF EF-P COMPND MOL_ID: 1; COMPND 2 MOLECULE: EARP; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ELONGATION FACTOR P; COMPND 7 CHAIN: B; COMPND 8 FRAGMENT: UNP RESIDUES 1-63; COMPND 9 SYNONYM: EF-P; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS SEROGROUP B / SEROTYPE SOURCE 3 15 (STRAIN H44/76); SOURCE 4 ORGANISM_TAXID: 909420; SOURCE 5 STRAIN: H44/76; SOURCE 6 GENE: NMH_0797; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS SEROGROUP B / SEROTYPE SOURCE 12 15 (STRAIN H44/76); SOURCE 13 ORGANISM_TAXID: 909420; SOURCE 14 STRAIN: H44/76; SOURCE 15 GENE: EFP, NMH_0798; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS GLYCOSYLTRANSFERASE, GT-B, EF-P, RHAMNOSYLATION, TRANSLATION KEYWDS 2 ELONGATION, DTDP-RHAMNOSE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR T.SENGOKU,S.YOKOYAMA,T.YANAGISAWA REVDAT 3 03-APR-24 5WXK 1 LINK REVDAT 2 04-APR-18 5WXK 1 JRNL REVDAT 1 28-FEB-18 5WXK 0 JRNL AUTH T.SENGOKU,T.SUZUKI,N.DOHMAE,C.WATANABE,T.HONMA,Y.HIKIDA, JRNL AUTH 2 Y.YAMAGUCHI,H.TAKAHASHI,S.YOKOYAMA,T.YANAGISAWA JRNL TITL STRUCTURAL BASIS OF PROTEIN ARGININE RHAMNOSYLATION BY JRNL TITL 2 GLYCOSYLTRANSFERASE EARP JRNL REF NAT. CHEM. BIOL. V. 14 368 2018 JRNL REFN ESSN 1552-4469 JRNL PMID 29440735 JRNL DOI 10.1038/S41589-018-0002-Y REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 45715 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 2282 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 41.9764 - 4.5358 0.99 2787 155 0.1515 0.1676 REMARK 3 2 4.5358 - 3.6008 1.00 2759 137 0.1240 0.1664 REMARK 3 3 3.6008 - 3.1458 1.00 2732 150 0.1366 0.1765 REMARK 3 4 3.1458 - 2.8583 1.00 2722 145 0.1555 0.2143 REMARK 3 5 2.8583 - 2.6534 1.00 2727 126 0.1522 0.2090 REMARK 3 6 2.6534 - 2.4970 1.00 2671 159 0.1506 0.2189 REMARK 3 7 2.4970 - 2.3720 1.00 2741 142 0.1538 0.2219 REMARK 3 8 2.3720 - 2.2687 1.00 2715 145 0.1556 0.2087 REMARK 3 9 2.2687 - 2.1814 1.00 2700 141 0.1591 0.1984 REMARK 3 10 2.1814 - 2.1061 1.00 2674 142 0.1649 0.2018 REMARK 3 11 2.1061 - 2.0403 1.00 2709 144 0.1704 0.2229 REMARK 3 12 2.0403 - 1.9819 1.00 2713 141 0.1858 0.2272 REMARK 3 13 1.9819 - 1.9298 1.00 2710 121 0.1888 0.2452 REMARK 3 14 1.9298 - 1.8827 1.00 2715 150 0.2074 0.2349 REMARK 3 15 1.8827 - 1.8399 1.00 2703 152 0.2220 0.2885 REMARK 3 16 1.8399 - 1.8007 0.98 2655 132 0.2502 0.2939 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.340 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 : 0.007 3783 REMARK 3 ANGLE : 0.901 5152 REMARK 3 CHIRALITY : 0.053 539 REMARK 3 PLANARITY : 0.005 660 REMARK 3 DIHEDRAL : 17.941 2223 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 13 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 4 THROUGH 70 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.4564 -15.2775 12.2057 REMARK 3 T TENSOR REMARK 3 T11: 0.2035 T22: 0.1292 REMARK 3 T33: 0.2488 T12: -0.0057 REMARK 3 T13: 0.0956 T23: -0.0296 REMARK 3 L TENSOR REMARK 3 L11: 1.3526 L22: 1.4660 REMARK 3 L33: 0.8089 L12: 0.3857 REMARK 3 L13: -0.4406 L23: -0.1127 REMARK 3 S TENSOR REMARK 3 S11: -0.1510 S12: 0.1482 S13: -0.3264 REMARK 3 S21: 0.0212 S22: 0.0063 S23: 0.0262 REMARK 3 S31: 0.2412 S32: 0.0066 S33: 0.1222 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 71 THROUGH 96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.5311 -15.8140 11.0781 REMARK 3 T TENSOR REMARK 3 T11: 0.2904 T22: 0.1902 REMARK 3 T33: 0.3335 T12: -0.0460 REMARK 3 T13: 0.1007 T23: -0.1073 REMARK 3 L TENSOR REMARK 3 L11: 1.3584 L22: 3.6701 REMARK 3 L33: 0.1406 L12: -0.3761 REMARK 3 L13: -0.1859 L23: -0.4478 REMARK 3 S TENSOR REMARK 3 S11: -0.1868 S12: 0.4896 S13: -0.5872 REMARK 3 S21: -0.4270 S22: -0.1535 S23: 0.2201 REMARK 3 S31: 0.2687 S32: -0.2442 S33: 0.1757 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 97 THROUGH 179 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.0945 -6.3321 20.8562 REMARK 3 T TENSOR REMARK 3 T11: 0.1468 T22: 0.0901 REMARK 3 T33: 0.1647 T12: 0.0090 REMARK 3 T13: 0.0471 T23: 0.0002 REMARK 3 L TENSOR REMARK 3 L11: 2.0600 L22: 0.8836 REMARK 3 L33: 0.9523 L12: 0.2462 REMARK 3 L13: -0.8443 L23: -0.1877 REMARK 3 S TENSOR REMARK 3 S11: -0.0882 S12: -0.0907 S13: -0.2902 REMARK 3 S21: 0.0449 S22: -0.0457 S23: 0.0048 REMARK 3 S31: 0.1117 S32: 0.0094 S33: 0.1063 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 180 THROUGH 202 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.1063 15.4230 8.7496 REMARK 3 T TENSOR REMARK 3 T11: 0.1310 T22: 0.1070 REMARK 3 T33: 0.1273 T12: -0.0145 REMARK 3 T13: 0.0670 T23: -0.0181 REMARK 3 L TENSOR REMARK 3 L11: 3.6411 L22: 2.9657 REMARK 3 L33: 1.0828 L12: 1.4085 REMARK 3 L13: 0.5456 L23: 0.1296 REMARK 3 S TENSOR REMARK 3 S11: 0.0663 S12: -0.0356 S13: 0.3620 REMARK 3 S21: -0.0275 S22: 0.0216 S23: 0.0853 REMARK 3 S31: -0.2182 S32: 0.0615 S33: -0.0835 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 203 THROUGH 235 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.5229 10.9946 0.6004 REMARK 3 T TENSOR REMARK 3 T11: 0.1621 T22: 0.1292 REMARK 3 T33: 0.1179 T12: 0.0018 REMARK 3 T13: 0.0551 T23: 0.0079 REMARK 3 L TENSOR REMARK 3 L11: 4.0214 L22: 2.4606 REMARK 3 L33: 0.1280 L12: -0.1495 REMARK 3 L13: -0.0448 L23: -0.5388 REMARK 3 S TENSOR REMARK 3 S11: 0.0795 S12: 0.2557 S13: 0.1579 REMARK 3 S21: -0.2398 S22: -0.0934 S23: -0.0731 REMARK 3 S31: 0.1067 S32: -0.0204 S33: 0.0256 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 236 THROUGH 290 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.0983 4.3714 13.1635 REMARK 3 T TENSOR REMARK 3 T11: 0.0924 T22: 0.0937 REMARK 3 T33: 0.1183 T12: -0.0087 REMARK 3 T13: 0.0173 T23: 0.0028 REMARK 3 L TENSOR REMARK 3 L11: 1.3797 L22: 1.2382 REMARK 3 L33: 1.5298 L12: 0.2228 REMARK 3 L13: -1.2403 L23: -0.3242 REMARK 3 S TENSOR REMARK 3 S11: -0.0268 S12: -0.0516 S13: -0.0731 REMARK 3 S21: -0.0572 S22: -0.0475 S23: -0.1126 REMARK 3 S31: 0.0037 S32: 0.1237 S33: 0.0781 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 291 THROUGH 346 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.4897 18.4156 20.9723 REMARK 3 T TENSOR REMARK 3 T11: 0.1885 T22: 0.1205 REMARK 3 T33: 0.2007 T12: -0.0273 REMARK 3 T13: 0.0883 T23: -0.0532 REMARK 3 L TENSOR REMARK 3 L11: 1.8335 L22: 2.4343 REMARK 3 L33: 1.2934 L12: 1.0275 REMARK 3 L13: -0.5376 L23: -0.4319 REMARK 3 S TENSOR REMARK 3 S11: 0.2119 S12: -0.2132 S13: 0.3372 REMARK 3 S21: 0.1054 S22: -0.0645 S23: 0.1069 REMARK 3 S31: -0.2655 S32: 0.1124 S33: -0.1158 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 347 THROUGH 378 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.0099 -0.9038 30.3456 REMARK 3 T TENSOR REMARK 3 T11: 0.1271 T22: 0.1848 REMARK 3 T33: 0.1136 T12: 0.0316 REMARK 3 T13: -0.0079 T23: 0.0205 REMARK 3 L TENSOR REMARK 3 L11: 3.3448 L22: 6.6530 REMARK 3 L33: 1.6053 L12: 3.6329 REMARK 3 L13: -1.1491 L23: -0.4996 REMARK 3 S TENSOR REMARK 3 S11: 0.1024 S12: -0.4374 S13: -0.3170 REMARK 3 S21: 0.3804 S22: -0.2066 S23: -0.2094 REMARK 3 S31: 0.0537 S32: 0.2881 S33: 0.0572 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.7509 2.1130 17.9747 REMARK 3 T TENSOR REMARK 3 T11: 0.1696 T22: 0.2135 REMARK 3 T33: 0.2193 T12: 0.0196 REMARK 3 T13: 0.0045 T23: 0.0503 REMARK 3 L TENSOR REMARK 3 L11: 8.1349 L22: 6.5485 REMARK 3 L33: 6.6756 L12: -0.3701 REMARK 3 L13: -4.6213 L23: 0.4171 REMARK 3 S TENSOR REMARK 3 S11: 0.0532 S12: 0.1124 S13: 0.3848 REMARK 3 S21: -0.1825 S22: 0.1451 S23: 0.3852 REMARK 3 S31: -0.3236 S32: -0.5785 S33: -0.1914 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 12 THROUGH 17 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.8373 -9.4419 24.6311 REMARK 3 T TENSOR REMARK 3 T11: 0.2235 T22: 0.3502 REMARK 3 T33: 0.2172 T12: -0.0971 REMARK 3 T13: 0.0042 T23: -0.0921 REMARK 3 L TENSOR REMARK 3 L11: 8.6756 L22: 2.6190 REMARK 3 L33: 5.3418 L12: -1.0441 REMARK 3 L13: -1.8908 L23: 0.5634 REMARK 3 S TENSOR REMARK 3 S11: -0.0076 S12: 0.2951 S13: -0.6105 REMARK 3 S21: 0.1440 S22: -0.0221 S23: 0.3387 REMARK 3 S31: 0.5867 S32: -0.4876 S33: 0.2035 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 18 THROUGH 34 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.9178 2.1641 22.0987 REMARK 3 T TENSOR REMARK 3 T11: 0.1337 T22: 0.1848 REMARK 3 T33: 0.1593 T12: 0.0002 REMARK 3 T13: 0.0032 T23: 0.0073 REMARK 3 L TENSOR REMARK 3 L11: 6.5120 L22: 2.6680 REMARK 3 L33: 3.0219 L12: 1.7792 REMARK 3 L13: -3.6890 L23: -0.6557 REMARK 3 S TENSOR REMARK 3 S11: 0.3348 S12: -0.0619 S13: 0.4523 REMARK 3 S21: 0.1344 S22: -0.0721 S23: 0.1722 REMARK 3 S31: -0.1508 S32: -0.0912 S33: -0.3019 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 35 THROUGH 55 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.3300 -2.3628 27.9203 REMARK 3 T TENSOR REMARK 3 T11: 0.1402 T22: 0.1737 REMARK 3 T33: 0.1839 T12: -0.0170 REMARK 3 T13: 0.0344 T23: -0.0279 REMARK 3 L TENSOR REMARK 3 L11: 7.9510 L22: 1.9496 REMARK 3 L33: 9.2731 L12: 3.9358 REMARK 3 L13: -8.5859 L23: -4.2458 REMARK 3 S TENSOR REMARK 3 S11: 0.3348 S12: -0.1870 S13: 0.2565 REMARK 3 S21: 0.2501 S22: -0.1211 S23: 0.1081 REMARK 3 S31: -0.3625 S32: 0.2146 S33: -0.2001 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 56 THROUGH 66 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.7304 -2.1767 18.9166 REMARK 3 T TENSOR REMARK 3 T11: 0.1628 T22: 0.1984 REMARK 3 T33: 0.2083 T12: -0.0120 REMARK 3 T13: -0.0133 T23: 0.0260 REMARK 3 L TENSOR REMARK 3 L11: 4.6496 L22: 5.2329 REMARK 3 L33: 7.3287 L12: 2.0966 REMARK 3 L13: -3.6127 L23: -2.1998 REMARK 3 S TENSOR REMARK 3 S11: 0.1817 S12: 0.5389 S13: 0.1997 REMARK 3 S21: 0.1181 S22: 0.0616 S23: 0.6976 REMARK 3 S31: -0.1964 S32: -0.6761 S33: -0.1973 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 5WXK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1300002547. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45727 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 43.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: APO EARP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES-NAOH BUFFER (PH 7.0) AND REMARK 280 1.8 M AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 61.10200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.62700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 61.10200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 28.62700 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: 4460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -86.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 783 LIES ON A SPECIAL POSITION. 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 A 1 REMARK 465 ASN A 2 REMARK 465 THR A 3 REMARK 465 GLN A 379 REMARK 465 LYS A 380 REMARK 465 ILE A 381 REMARK 465 ARG A 382 REMARK 465 HIS B 67 REMARK 465 HIS B 68 REMARK 465 HIS B 69 REMARK 465 HIS B 70 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 GLU A 159 CG CD OE1 OE2 REMARK 470 ARG A 162 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 170 CG CD OE1 OE2 REMARK 470 LYS A 377 CG CD CE NZ REMARK 470 LYS B 2 CG CD CE NZ REMARK 470 LYS B 24 CG CD CE NZ 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 701 O HOH A 730 2.11 REMARK 500 O HOH A 823 O HOH B 259 2.15 REMARK 500 O HOH A 802 O HOH A 909 2.15 REMARK 500 O HOH A 812 O HOH A 872 2.19 REMARK 500 O HOH A 744 O HOH A 855 2.19 REMARK 500 O HOH B 212 O HOH B 257 2.19 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 ASN A 17 -154.20 62.34 REMARK 500 SER A 189 143.43 -171.14 REMARK 500 ALA A 240 -133.47 56.95 REMARK 500 GLU A 270 -34.10 -134.74 REMARK 500 ARG B 32 -120.06 46.72 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 NI A 410 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 346 NE2 REMARK 620 2 HIS B 66 NE2 57.5 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TYD A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BME A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BME A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BME A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5WXJ RELATED DB: PDB REMARK 900 RELATED ID: 5WXI RELATED DB: PDB DBREF 5WXK A 1 382 UNP E6MVV9 E6MVV9_NEIMH 1 382 DBREF 5WXK B 1 63 UNP E6MVW0 E6MVW0_NEIMH 1 63 SEQADV 5WXK GLY B 64 UNP E6MVW0 EXPRESSION TAG SEQADV 5WXK HIS B 65 UNP E6MVW0 EXPRESSION TAG SEQADV 5WXK HIS B 66 UNP E6MVW0 EXPRESSION TAG SEQADV 5WXK HIS B 67 UNP E6MVW0 EXPRESSION TAG SEQADV 5WXK HIS B 68 UNP E6MVW0 EXPRESSION TAG SEQADV 5WXK HIS B 69 UNP E6MVW0 EXPRESSION TAG SEQADV 5WXK HIS B 70 UNP E6MVW0 EXPRESSION TAG SEQRES 1 A 382 MET ASN THR PRO PRO PHE VAL CYS TRP ILE PHE CYS LYS SEQRES 2 A 382 VAL ILE ASP ASN PHE GLY ASP ILE GLY VAL SER TRP ARG SEQRES 3 A 382 LEU ALA ARG VAL LEU HIS ARG GLU LEU GLY TRP GLN VAL SEQRES 4 A 382 HIS LEU TRP THR ASP ASP VAL SER ALA LEU ARG ALA LEU SEQRES 5 A 382 CYS PRO ASP LEU PRO ASP VAL PRO CYS VAL HIS GLN ASP SEQRES 6 A 382 ILE HIS VAL ARG THR TRP HIS SER ASP ALA ALA ASP ILE SEQRES 7 A 382 ASP THR ALA PRO VAL PRO ASP VAL VAL ILE GLU THR PHE SEQRES 8 A 382 ALA CYS ASP LEU PRO GLU ASN VAL LEU HIS ILE ILE ARG SEQRES 9 A 382 ARG HIS LYS PRO LEU TRP LEU ASN TRP GLU TYR LEU SER SEQRES 10 A 382 ALA GLU GLU SER ASN GLU ARG LEU HIS LEU MET PRO SER SEQRES 11 A 382 PRO GLN GLU GLY VAL GLN LYS TYR PHE TRP PHE MET GLY SEQRES 12 A 382 PHE SER GLU LYS SER GLY GLY LEU ILE ARG GLU ARG ASP SEQRES 13 A 382 TYR CYS GLU ALA VAL ARG PHE ASP THR GLU ALA LEU ARG SEQRES 14 A 382 GLU ARG LEU MET LEU PRO GLU LYS ASN ALA SER GLU TRP SEQRES 15 A 382 LEU LEU PHE GLY TYR ARG SER ASP VAL TRP ALA LYS TRP SEQRES 16 A 382 LEU GLU MET TRP ARG GLN ALA GLY SER PRO MET THR LEU SEQRES 17 A 382 LEU LEU ALA GLY THR GLN ILE ILE ASP SER LEU LYS GLN SEQRES 18 A 382 SER GLY VAL ILE PRO GLN ASP ALA LEU GLN ASN ASP GLY SEQRES 19 A 382 ASP VAL PHE GLN THR ALA SER VAL ARG LEU VAL LYS ILE SEQRES 20 A 382 PRO PHE VAL PRO GLN GLN ASP PHE ASP GLN LEU LEU HIS SEQRES 21 A 382 LEU ALA ASP CYS ALA VAL ILE ARG GLY GLU ASP SER PHE SEQRES 22 A 382 VAL ARG ALA GLN LEU ALA GLY LYS PRO PHE PHE TRP HIS SEQRES 23 A 382 ILE TYR PRO GLN ASP GLU ASN VAL HIS LEU ASP LYS LEU SEQRES 24 A 382 HIS ALA PHE TRP ASP LYS ALA HIS GLY PHE TYR THR PRO SEQRES 25 A 382 GLU THR VAL SER ALA HIS ARG ARG LEU SER ASP ASP LEU SEQRES 26 A 382 ASN GLY GLY GLU ALA LEU SER ALA THR GLN ARG LEU GLU SEQRES 27 A 382 CYS TRP GLN THR LEU GLN GLN HIS GLN ASN GLY TRP ARG SEQRES 28 A 382 GLN GLY ALA GLU ASP TRP SER ARG TYR LEU PHE GLY GLN SEQRES 29 A 382 PRO SER ALA PRO GLU LYS LEU ALA ALA PHE VAL SER LYS SEQRES 30 A 382 HIS GLN LYS ILE ARG SEQRES 1 B 70 MET LYS THR ALA GLN GLU LEU ARG ALA GLY ASN VAL PHE SEQRES 2 B 70 MET VAL GLY ASN ASP PRO MET VAL VAL GLN LYS THR GLU SEQRES 3 B 70 TYR ILE LYS GLY GLY ARG SER SER ALA LYS VAL SER MET SEQRES 4 B 70 LYS LEU LYS ASN LEU LEU THR GLY ALA ALA SER GLU THR SEQRES 5 B 70 ILE TYR LYS ALA ASP ASP LYS PHE ASP VAL VAL GLY HIS SEQRES 6 B 70 HIS HIS HIS HIS HIS HET TYD A 401 25 HET SO4 A 402 5 HET SO4 A 403 5 HET SO4 A 404 5 HET SO4 A 405 5 HET BME A 406 4 HET BME A 407 4 HET BME A 408 4 HET GOL A 409 6 HET NI A 410 1 HET GOL B 101 6 HETNAM TYD THYMIDINE-5'-DIPHOSPHATE HETNAM SO4 SULFATE ION HETNAM BME BETA-MERCAPTOETHANOL HETNAM GOL GLYCEROL HETNAM NI NICKEL (II) ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 TYD C10 H16 N2 O11 P2 FORMUL 4 SO4 4(O4 S 2-) FORMUL 8 BME 3(C2 H6 O S) FORMUL 11 GOL 2(C3 H8 O3) FORMUL 12 NI NI 2+ FORMUL 14 HOH *477(H2 O) HELIX 1 AA1 PHE A 18 GLY A 36 1 19 HELIX 2 AA2 ASP A 45 CYS A 53 1 9 HELIX 3 AA3 PRO A 96 LYS A 107 1 12 HELIX 4 AA4 GLU A 119 HIS A 126 1 8 HELIX 5 AA5 ASP A 156 VAL A 161 1 6 HELIX 6 AA6 ASP A 164 LEU A 172 1 9 HELIX 7 AA7 ASP A 190 GLY A 203 1 14 HELIX 8 AA8 THR A 213 SER A 222 1 10 HELIX 9 AA9 PRO A 251 GLN A 253 5 3 HELIX 10 AB1 ASP A 254 ALA A 262 1 9 HELIX 11 AB2 GLU A 270 GLY A 280 1 11 HELIX 12 AB3 GLN A 290 ASN A 293 5 4 HELIX 13 AB4 VAL A 294 HIS A 307 1 14 HELIX 14 AB5 GLY A 308 TYR A 310 5 3 HELIX 15 AB6 THR A 311 ASN A 326 1 16 HELIX 16 AB7 SER A 332 HIS A 346 1 15 HELIX 17 AB8 HIS A 346 GLY A 363 1 18 HELIX 18 AB9 SER A 366 HIS A 378 1 13 HELIX 19 AC1 GLN B 5 LEU B 7 5 3 SHEET 1 AA1 7 CYS A 61 HIS A 63 0 SHEET 2 AA1 7 ILE A 66 THR A 70 -1 O VAL A 68 N CYS A 61 SHEET 3 AA1 7 GLN A 38 THR A 43 1 N LEU A 41 O HIS A 67 SHEET 4 AA1 7 VAL A 7 CYS A 12 1 N CYS A 8 O HIS A 40 SHEET 5 AA1 7 VAL A 86 THR A 90 1 O ILE A 88 N TRP A 9 SHEET 6 AA1 7 LEU A 109 TRP A 113 1 O LEU A 109 N VAL A 87 SHEET 7 AA1 7 TYR A 138 TRP A 140 1 O TRP A 140 N ASN A 112 SHEET 1 AA2 6 VAL A 236 THR A 239 0 SHEET 2 AA2 6 VAL A 242 LYS A 246 -1 O LEU A 244 N PHE A 237 SHEET 3 AA2 6 MET A 206 LEU A 210 1 N LEU A 208 O ARG A 243 SHEET 4 AA2 6 SER A 180 LEU A 184 1 N TRP A 182 O LEU A 209 SHEET 5 AA2 6 CYS A 264 ARG A 268 1 O VAL A 266 N LEU A 183 SHEET 6 AA2 6 PHE A 283 HIS A 286 1 O HIS A 286 N ILE A 267 SHEET 1 AA3 2 LYS B 2 THR B 3 0 SHEET 2 AA3 2 LYS B 59 PHE B 60 -1 O PHE B 60 N LYS B 2 SHEET 1 AA4 5 ALA B 49 LYS B 55 0 SHEET 2 AA4 5 ALA B 35 ASN B 43 -1 N LEU B 41 O SER B 50 SHEET 3 AA4 5 ASP B 18 LYS B 29 -1 N GLN B 23 O LYS B 40 SHEET 4 AA4 5 ASN B 11 VAL B 15 -1 N PHE B 13 O MET B 20 SHEET 5 AA4 5 VAL B 62 HIS B 65 -1 O VAL B 63 N VAL B 12 LINK SG ACYS A 53 S2 BME A 408 1555 1555 1.97 LINK SG CYS A 158 S2 BME A 407 1555 1555 1.98 LINK SG CYS A 339 S2 BME A 406 1555 1555 1.96 LINK NE2 HIS A 346 NI NI A 410 1555 1555 1.93 LINK NI NI A 410 NE2 HIS B 66 3445 1555 2.16 CISPEP 1 VAL A 59 PRO A 60 0 6.30 SITE 1 AC1 19 ASN A 17 PHE A 18 GLY A 19 LEU A 52 SITE 2 AC1 19 PHE A 185 TYR A 187 ALA A 211 PHE A 249 SITE 3 AC1 19 VAL A 250 GLN A 252 PHE A 255 ARG A 268 SITE 4 AC1 19 GLY A 269 GLU A 270 ASP A 271 SER A 272 SITE 5 AC1 19 HOH A 665 HOH A 671 HOH B 209 SITE 1 AC2 5 GLY A 212 THR A 213 GLN A 214 ARG A 268 SITE 2 AC2 5 HOH A 528 SITE 1 AC3 4 SER A 145 GLU A 146 TYR A 360 HOH A 726 SITE 1 AC4 9 HIS A 32 TRP A 37 GLN A 38 HIS A 67 SITE 2 AC4 9 ARG A 320 GLN A 335 HOH A 520 HOH A 704 SITE 3 AC4 9 HOH A 751 SITE 1 AC5 6 VAL A 46 ARG A 50 ASP A 58 VAL A 59 SITE 2 AC5 6 HOH A 502 HOH A 521 SITE 1 AC6 3 ARG A 320 GLU A 338 CYS A 339 SITE 1 AC7 1 CYS A 158 SITE 1 AC8 8 CYS A 53 PRO A 54 ASP A 55 GLN A 64 SITE 2 AC8 8 PRO A 251 GLN A 253 HOH A 583 HOH A 639 SITE 1 AC9 5 ARG A 171 GLY A 223 VAL A 224 PRO A 251 SITE 2 AC9 5 HOH A 533 SITE 1 AD1 2 HIS A 346 HIS B 66 SITE 1 AD2 5 LEU B 7 ARG B 8 ALA B 9 LYS B 24 SITE 2 AD2 5 THR B 25 CRYST1 122.204 57.254 72.831 90.00 101.44 90.00 C 1 2 1 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 0.008183 0.000000 0.001656 0.00000 SCALE2 0.000000 0.017466 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014009 0.00000