HEADER TRANSLATION 20-MAY-16 5K4C TITLE STRUCTURE OF EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT D TITLE 2 (EIF3D) CAP BINDING DOMAIN FROM NASONIA VITRIPENNIS, CRYSTAL FORM 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT D; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 172-537; COMPND 5 SYNONYM: EIF3D,EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 7; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NASONIA VITRIPENNIS; SOURCE 3 ORGANISM_COMMON: PARASITIC WASP; SOURCE 4 ORGANISM_TAXID: 7425; SOURCE 5 GENE: LOC100122367; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS EUKARYOTIC TRANSLATION INITIATION FACTOR 3, CAP-BINDING DOMAIN, KEYWDS 2 TRANSLATION EXPDTA X-RAY DIFFRACTION AUTHOR P.J.KRANZUSCH,A.S.Y.LEE,J.A.DOUDNA,J.H.D.CATE REVDAT 6 06-MAR-24 5K4C 1 REMARK REVDAT 5 20-NOV-19 5K4C 1 REMARK REVDAT 4 20-SEP-17 5K4C 1 JRNL REMARK REVDAT 3 17-AUG-16 5K4C 1 JRNL REVDAT 2 10-AUG-16 5K4C 1 JRNL REVDAT 1 27-JUL-16 5K4C 0 JRNL AUTH A.S.LEE,P.J.KRANZUSCH,J.A.DOUDNA,J.H.CATE JRNL TITL EIF3D IS AN MRNA CAP-BINDING PROTEIN THAT IS REQUIRED FOR JRNL TITL 2 SPECIALIZED TRANSLATION INITIATION. JRNL REF NATURE V. 536 96 2016 JRNL REFN ESSN 1476-4687 JRNL PMID 27462815 JRNL DOI 10.1038/NATURE18954 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 47026 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.250 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 46.1163 - 4.0910 1.00 3455 154 0.1619 0.2039 REMARK 3 2 4.0910 - 3.2474 1.00 3306 146 0.1411 0.1476 REMARK 3 3 3.2474 - 2.8370 1.00 3279 146 0.1559 0.2034 REMARK 3 4 2.8370 - 2.5776 1.00 3229 143 0.1598 0.1969 REMARK 3 5 2.5776 - 2.3929 1.00 3251 144 0.1565 0.1812 REMARK 3 6 2.3929 - 2.2518 1.00 3211 143 0.1525 0.1979 REMARK 3 7 2.2518 - 2.1390 1.00 3212 143 0.1471 0.1854 REMARK 3 8 2.1390 - 2.0459 1.00 3204 142 0.1545 0.2060 REMARK 3 9 2.0459 - 1.9672 1.00 3187 142 0.1577 0.2032 REMARK 3 10 1.9672 - 1.8993 1.00 3201 142 0.1806 0.2230 REMARK 3 11 1.8993 - 1.8399 1.00 3186 142 0.1868 0.2177 REMARK 3 12 1.8399 - 1.7873 1.00 3193 142 0.2014 0.2447 REMARK 3 13 1.7873 - 1.7402 1.00 3192 141 0.2234 0.2531 REMARK 3 14 1.7402 - 1.6978 0.92 2920 130 0.2720 0.3183 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.480 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 : 0.012 3026 REMARK 3 ANGLE : 1.359 4098 REMARK 3 CHIRALITY : 0.071 452 REMARK 3 PLANARITY : 0.007 536 REMARK 3 DIHEDRAL : 13.306 1145 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 10 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 172 THROUGH 192 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.8894 -3.7124 -32.6390 REMARK 3 T TENSOR REMARK 3 T11: 0.1469 T22: 0.2247 REMARK 3 T33: 0.2190 T12: 0.0049 REMARK 3 T13: 0.0070 T23: 0.0125 REMARK 3 L TENSOR REMARK 3 L11: 0.0918 L22: 0.3425 REMARK 3 L33: 0.1665 L12: -0.1847 REMARK 3 L13: 0.1081 L23: -0.2379 REMARK 3 S TENSOR REMARK 3 S11: 0.0078 S12: -0.0287 S13: -0.0333 REMARK 3 S21: -0.0690 S22: 0.0473 S23: 0.2466 REMARK 3 S31: 0.0769 S32: -0.2616 S33: 0.0010 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 193 THROUGH 224 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.9946 -10.6853 -14.5551 REMARK 3 T TENSOR REMARK 3 T11: 0.1369 T22: 0.2069 REMARK 3 T33: 0.1526 T12: 0.0422 REMARK 3 T13: -0.0055 T23: -0.0128 REMARK 3 L TENSOR REMARK 3 L11: 0.4781 L22: 0.4362 REMARK 3 L33: 0.6105 L12: 0.2680 REMARK 3 L13: 0.3215 L23: -0.2273 REMARK 3 S TENSOR REMARK 3 S11: 0.0635 S12: 0.0652 S13: 0.0014 REMARK 3 S21: 0.0808 S22: -0.1512 S23: -0.1575 REMARK 3 S31: -0.0326 S32: 0.3204 S33: 0.0050 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 225 THROUGH 290 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.2887 -2.0281 -16.4465 REMARK 3 T TENSOR REMARK 3 T11: 0.1479 T22: 0.1094 REMARK 3 T33: 0.1358 T12: -0.0017 REMARK 3 T13: -0.0069 T23: -0.0044 REMARK 3 L TENSOR REMARK 3 L11: 0.3632 L22: 0.2763 REMARK 3 L33: 0.6268 L12: -0.2236 REMARK 3 L13: 0.0829 L23: 0.0035 REMARK 3 S TENSOR REMARK 3 S11: 0.0087 S12: -0.0501 S13: 0.0580 REMARK 3 S21: 0.0803 S22: 0.0301 S23: 0.0728 REMARK 3 S31: -0.1397 S32: -0.0354 S33: 0.0026 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 291 THROUGH 319 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.1531 -19.0152 -17.9035 REMARK 3 T TENSOR REMARK 3 T11: 0.1281 T22: 0.1318 REMARK 3 T33: 0.1363 T12: -0.0359 REMARK 3 T13: 0.0210 T23: -0.0192 REMARK 3 L TENSOR REMARK 3 L11: 0.3686 L22: 0.1351 REMARK 3 L33: 0.3457 L12: 0.0894 REMARK 3 L13: -0.3398 L23: -0.1607 REMARK 3 S TENSOR REMARK 3 S11: 0.0303 S12: -0.0032 S13: 0.0081 REMARK 3 S21: 0.0657 S22: -0.0313 S23: 0.1085 REMARK 3 S31: 0.0336 S32: -0.1505 S33: 0.0392 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 320 THROUGH 359 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.3675 -10.6073 -4.4465 REMARK 3 T TENSOR REMARK 3 T11: 0.1615 T22: 0.1349 REMARK 3 T33: 0.1007 T12: -0.0172 REMARK 3 T13: -0.0082 T23: -0.0086 REMARK 3 L TENSOR REMARK 3 L11: 0.3806 L22: 0.3589 REMARK 3 L33: 0.3629 L12: -0.2312 REMARK 3 L13: 0.0196 L23: -0.1574 REMARK 3 S TENSOR REMARK 3 S11: 0.0510 S12: -0.1060 S13: -0.0101 REMARK 3 S21: 0.2153 S22: -0.0573 S23: -0.0805 REMARK 3 S31: -0.0751 S32: -0.0463 S33: 0.0048 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 360 THROUGH 408 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.9325 -4.6956 -14.5080 REMARK 3 T TENSOR REMARK 3 T11: 0.1178 T22: 0.1465 REMARK 3 T33: 0.1381 T12: -0.0253 REMARK 3 T13: -0.0139 T23: 0.0161 REMARK 3 L TENSOR REMARK 3 L11: 0.4995 L22: 0.4099 REMARK 3 L33: 0.6924 L12: -0.0118 REMARK 3 L13: 0.0818 L23: 0.2207 REMARK 3 S TENSOR REMARK 3 S11: -0.0209 S12: -0.0094 S13: 0.0370 REMARK 3 S21: 0.1108 S22: 0.0163 S23: -0.1138 REMARK 3 S31: -0.0965 S32: 0.1102 S33: 0.0081 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 409 THROUGH 426 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.4578 -34.4956 -19.2242 REMARK 3 T TENSOR REMARK 3 T11: 0.2112 T22: 0.1441 REMARK 3 T33: 0.1538 T12: 0.0467 REMARK 3 T13: 0.0068 T23: -0.0091 REMARK 3 L TENSOR REMARK 3 L11: 0.0716 L22: 0.1159 REMARK 3 L33: 0.3172 L12: -0.0701 REMARK 3 L13: -0.0387 L23: -0.0155 REMARK 3 S TENSOR REMARK 3 S11: 0.0005 S12: 0.1050 S13: -0.1361 REMARK 3 S21: 0.0063 S22: -0.0150 S23: 0.0165 REMARK 3 S31: 0.5555 S32: 0.0344 S33: 0.0049 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 427 THROUGH 452 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.1515 -18.3667 -23.2919 REMARK 3 T TENSOR REMARK 3 T11: 0.1211 T22: 0.1321 REMARK 3 T33: 0.1499 T12: 0.0083 REMARK 3 T13: -0.0092 T23: -0.0037 REMARK 3 L TENSOR REMARK 3 L11: 0.0444 L22: 0.0883 REMARK 3 L33: 0.1315 L12: -0.0159 REMARK 3 L13: -0.0666 L23: 0.0063 REMARK 3 S TENSOR REMARK 3 S11: -0.0054 S12: 0.0785 S13: -0.0766 REMARK 3 S21: 0.0278 S22: 0.0368 S23: -0.0715 REMARK 3 S31: 0.0530 S32: 0.0949 S33: 0.0000 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 453 THROUGH 481 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.6993 -24.5520 -12.4941 REMARK 3 T TENSOR REMARK 3 T11: 0.1489 T22: 0.1345 REMARK 3 T33: 0.1340 T12: 0.0018 REMARK 3 T13: 0.0057 T23: 0.0133 REMARK 3 L TENSOR REMARK 3 L11: 0.2058 L22: 0.0553 REMARK 3 L33: 0.4873 L12: 0.1112 REMARK 3 L13: 0.0484 L23: 0.0232 REMARK 3 S TENSOR REMARK 3 S11: -0.0626 S12: -0.0025 S13: -0.0776 REMARK 3 S21: -0.0132 S22: 0.0157 S23: -0.0705 REMARK 3 S31: 0.1486 S32: 0.0965 S33: -0.0033 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 482 THROUGH 537 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.9919 -2.3891 -28.9880 REMARK 3 T TENSOR REMARK 3 T11: 0.1264 T22: 0.1493 REMARK 3 T33: 0.1527 T12: 0.0094 REMARK 3 T13: 0.0103 T23: -0.0052 REMARK 3 L TENSOR REMARK 3 L11: 0.2511 L22: 0.4528 REMARK 3 L33: 0.6993 L12: 0.0933 REMARK 3 L13: 0.1292 L23: -0.2140 REMARK 3 S TENSOR REMARK 3 S11: 0.0221 S12: 0.0519 S13: -0.0019 REMARK 3 S21: 0.0158 S22: -0.0604 S23: 0.1100 REMARK 3 S31: -0.0456 S32: -0.0272 S33: -0.0107 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 5K4C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1000221706. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.11586 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47123 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.698 REMARK 200 RESOLUTION RANGE LOW (A) : 46.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.45000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6-1.8 M AMMONIUM CITRATE PH 7.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 24.50550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 69.15550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.92200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 69.15550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.50550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.92200 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 GLY A 170 REMARK 465 SER A 171 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 855 O HOH A 966 1.90 REMARK 500 OE1 GLU A 200 O HOH A 701 1.91 REMARK 500 O HOH A 1068 O HOH A 1084 1.95 REMARK 500 OD2 ASP A 349 O HOH A 702 1.99 REMARK 500 O HOH A 1006 O HOH A 1064 1.99 REMARK 500 O HOH A 926 O HOH A 1041 2.03 REMARK 500 OG SER A 275 O HOH A 703 2.09 REMARK 500 O HOH A 1010 O HOH A 1029 2.10 REMARK 500 O HOH A 785 O HOH A 1003 2.11 REMARK 500 O HOH A 927 O HOH A 1063 2.15 REMARK 500 O HOH A 706 O HOH A 959 2.17 REMARK 500 O HOH A 934 O HOH A 1059 2.17 REMARK 500 O HOH A 957 O HOH A 986 2.18 REMARK 500 OD1 ASP A 298 O HOH A 704 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 A 744 O HOH A 957 3554 2.05 REMARK 500 O HOH A 800 O HOH A 938 3554 2.11 REMARK 500 O HOH A 907 O HOH A 998 3544 2.13 REMARK 500 O HOH A 1023 O HOH A 1037 3554 2.16 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 224 59.67 -142.63 REMARK 500 ASN A 255 -2.05 -142.44 REMARK 500 ASN A 376 177.99 61.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1085 DISTANCE = 6.06 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 603 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5K4B RELATED DB: PDB REMARK 900 RELATED ID: 5K4D RELATED DB: PDB DBREF 5K4C A 172 537 UNP K7IM66 K7IM66_NASVI 172 537 SEQADV 5K4C GLY A 170 UNP K7IM66 EXPRESSION TAG SEQADV 5K4C SER A 171 UNP K7IM66 EXPRESSION TAG SEQRES 1 A 368 GLY SER SER VAL THR VAL ARG PRO ASP TRP VAL THR ILE SEQRES 2 A 368 GLU GLU MET ASP PHE PRO ARG LEU SER LYS LEU THR LEU SEQRES 3 A 368 PRO GLY VAL LYS GLU GLY GLU ASP VAL LEU CYS CYS GLY SEQRES 4 A 368 ALA VAL GLU TYR TYR ASP LYS SER TYR ASP ARG VAL ASN SEQRES 5 A 368 VAL LYS ASN GLU LYS PRO LEU GLN ARG ILE ASP ARG ILE SEQRES 6 A 368 PHE HIS THR VAL THR THR THR ASP ASP PRO VAL ILE ARG SEQRES 7 A 368 LYS LEU SER LYS THR GLU GLY ASN VAL TYR ALA THR ASP SEQRES 8 A 368 ALA ILE LEU ALA THR ILE MET CYS CYS THR ARG SER ASN SEQRES 9 A 368 TYR SER TRP ASP ILE VAL ILE GLU LYS ILE GLY ASN LYS SEQRES 10 A 368 LEU PHE PHE ASP LYS ARG ASP ASN THR GLU PHE ASP LEU SEQRES 11 A 368 LEU THR VAL ASN GLU THR SER VAL GLU PRO PRO GLN ASP SEQRES 12 A 368 ASP GLY ASN SER LEU ASN SER PRO ARG ASN LEU ALA LEU SEQRES 13 A 368 GLU ALA THR PHE ILE ASN HIS ASN PHE SER GLN GLN VAL SEQRES 14 A 368 LEU LYS SER ASN GLU PRO ARG TYR LYS PHE ASP GLU PRO SEQRES 15 A 368 ASN PRO PHE ILE SER GLU GLU GLU GLU GLY GLU VAL ALA SEQRES 16 A 368 SER VAL ALA TYR ARG TYR ARG LYS TRP ASP LEU ASN ASN SEQRES 17 A 368 GLY ILE THR LEU ILE ALA ARG CYS GLU HIS ASP ALA VAL SEQRES 18 A 368 MET GLN GLY PRO ASN ASN GLU THR GLN PHE LEU THR ILE SEQRES 19 A 368 LYS ALA LEU ASN GLU TRP ASP SER LYS LEU ALA ASN GLY SEQRES 20 A 368 VAL GLU TRP ARG ARG LYS LEU ASP THR GLN ARG GLY ALA SEQRES 21 A 368 VAL LEU ALA ASN GLU LEU ARG ASN ASN ALA CYS LYS LEU SEQRES 22 A 368 ALA LYS TRP THR VAL GLN ALA LEU LEU ALA GLY SER ASP SEQRES 23 A 368 GLN LEU LYS PHE GLY TYR VAL SER ARG ALA SER VAL ARG SEQRES 24 A 368 ASP SER SER LYS HIS VAL ILE LEU GLU THR GLN GLN TYR SEQRES 25 A 368 LYS PRO ASN GLU PHE ALA THR GLN ILE ASN LEU ASN MET SEQRES 26 A 368 ASP ASN ALA TRP GLY ILE LEU ARG CYS ILE ILE ASP ILE SEQRES 27 A 368 CYS MET ASN GLN LYS ASP GLY LYS TYR LEU ILE MET LYS SEQRES 28 A 368 ASP PRO ASN LYS PRO MET ILE ARG LEU TYR ASP ILE PRO SEQRES 29 A 368 ASP ASN THR PHE HET GOL A 601 6 HET GOL A 602 6 HET GOL A 603 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 3(C3 H8 O3) FORMUL 5 HOH *385(H2 O) HELIX 1 AA1 PHE A 187 SER A 191 1 5 HELIX 2 AA2 ASP A 214 VAL A 220 5 7 HELIX 3 AA3 ASN A 221 GLU A 225 5 5 HELIX 4 AA4 THR A 239 ASP A 242 5 4 HELIX 5 AA5 ASP A 243 SER A 250 1 8 HELIX 6 AA6 ASP A 260 CYS A 268 1 9 HELIX 7 AA7 CYS A 269 SER A 272 5 4 HELIX 8 AA8 SER A 319 VAL A 338 1 20 HELIX 9 AA9 SER A 356 GLU A 360 5 5 HELIX 10 AB1 ASP A 410 ASN A 415 1 6 HELIX 11 AB2 GLU A 418 LEU A 423 1 6 HELIX 12 AB3 GLN A 426 ASN A 438 1 13 HELIX 13 AB4 ASN A 438 GLY A 453 1 16 HELIX 14 AB5 LYS A 482 ILE A 490 1 9 HELIX 15 AB6 ASN A 493 ASN A 510 1 18 SHEET 1 AA110 VAL A 180 ASP A 186 0 SHEET 2 AA110 MET A 526 ASP A 531 -1 O LEU A 529 N ILE A 182 SHEET 3 AA110 GLY A 514 LYS A 520 -1 N LEU A 517 O TYR A 530 SHEET 4 AA110 TRP A 276 ILE A 283 -1 N ILE A 280 O TYR A 516 SHEET 5 AA110 LYS A 286 ASP A 290 -1 O ASP A 290 N VAL A 279 SHEET 6 AA110 VAL A 256 THR A 259 1 N TYR A 257 O PHE A 289 SHEET 7 AA110 THR A 380 HIS A 387 1 O ILE A 382 N VAL A 256 SHEET 8 AA110 VAL A 366 ASP A 374 -1 N ARG A 369 O CYS A 385 SHEET 9 AA110 GLU A 202 VAL A 210 -1 N VAL A 204 O TYR A 370 SHEET 10 AA110 TYR A 346 LYS A 347 -1 O TYR A 346 N VAL A 210 SHEET 1 AA2 5 LYS A 226 PRO A 227 0 SHEET 2 AA2 5 ASP A 469 TYR A 481 -1 O ILE A 475 N LYS A 226 SHEET 3 AA2 5 GLN A 456 SER A 466 -1 N TYR A 461 O LEU A 476 SHEET 4 AA2 5 THR A 398 GLU A 408 1 N LEU A 406 O GLY A 460 SHEET 5 AA2 5 ALA A 389 GLN A 392 -1 N MET A 391 O GLN A 399 SITE 1 AC1 10 ARG A 189 SER A 306 VAL A 307 GLU A 308 SITE 2 AC1 10 ASN A 415 ASN A 433 ARG A 436 ASN A 437 SITE 3 AC1 10 HOH A 773 HOH A 862 SITE 1 AC2 7 PRO A 310 GLN A 311 ASP A 312 ASN A 318 SITE 2 AC2 7 HOH A 782 HOH A 839 HOH A 884 SITE 1 AC3 10 LYS A 199 GLU A 200 GLY A 201 ARG A 371 SITE 2 AC3 10 TRP A 373 LEU A 450 LEU A 451 TRP A 498 SITE 3 AC3 10 HOH A 701 HOH A 705 CRYST1 49.011 61.844 138.311 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 0.020404 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016170 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007230 0.00000