HEADER TRANSFERASE 27-JAN-20 6XXM TITLE CRYSTAL STRUCTURE OF HUMAN DEOXYHYPUSINE SYNTHASE IN COMPLEX WITH TITLE 2 PUTRESCINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEOXYHYPUSINE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DHS; COMPND 5 EC: 2.5.1.46; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DEOXYHYPUSINE SYNTHASE; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: DHS; COMPND 11 EC: 2.5.1.46; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: DHPS, DS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: DHPS, DS; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS HYPUSINATION, DEOXYHYPUSINE SYNTHASE, EIF5A, TRANSLATION, HYPUSINE, KEYWDS 2 POSTTRANSLATIONAL MODIFICATION, POLYAMINES, DEOXYHYPUSINE, KEYWDS 3 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR E.WATOR,P.WILK,P.GRUDNIK REVDAT 2 24-JAN-24 6XXM 1 LINK REVDAT 1 15-APR-20 6XXM 0 JRNL AUTH E.WATOR,P.WILK,P.GRUDNIK JRNL TITL HALF WAY TO HYPUSINE-STRUCTURAL BASIS FOR SUBSTRATE JRNL TITL 2 RECOGNITION BY HUMAN DEOXYHYPUSINE SYNTHASE. JRNL REF BIOMOLECULES V. 10 2020 JRNL REFN ESSN 2218-273X JRNL PMID 32235505 JRNL DOI 10.3390/BIOM10040522 REMARK 2 REMARK 2 RESOLUTION. 1.67 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX V.1.17.1 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) : 1.67 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.12 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 118314 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.175 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.770 REMARK 3 FREE R VALUE TEST SET COUNT : 2099 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 46.1200 - 4.1200 1.00 8127 147 0.1571 0.1705 REMARK 3 2 4.1200 - 3.2700 1.00 7869 142 0.1335 0.1511 REMARK 3 3 3.2700 - 2.8500 1.00 7828 142 0.1392 0.1466 REMARK 3 4 2.8500 - 2.5900 1.00 7779 140 0.1344 0.1383 REMARK 3 5 2.5900 - 2.4100 1.00 7774 141 0.1347 0.1413 REMARK 3 6 2.4100 - 2.2700 1.00 7739 140 0.1425 0.1519 REMARK 3 7 2.2700 - 2.1500 1.00 7748 140 0.1509 0.1732 REMARK 3 8 2.1500 - 2.0600 1.00 7689 139 0.1680 0.1869 REMARK 3 9 2.0600 - 1.9800 1.00 7736 139 0.1744 0.1899 REMARK 3 10 1.9800 - 1.9100 1.00 7665 139 0.1967 0.2091 REMARK 3 11 1.9100 - 1.8500 1.00 7699 139 0.2344 0.2587 REMARK 3 12 1.8500 - 1.8000 1.00 7682 139 0.2563 0.3213 REMARK 3 13 1.8000 - 1.7500 1.00 7673 138 0.2817 0.3209 REMARK 3 14 1.7500 - 1.7100 1.00 7651 138 0.3062 0.3204 REMARK 3 15 1.7100 - 1.6700 0.98 7556 136 0.3517 0.3824 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.830 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.97 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.21 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 8 THROUGH 27 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.8171 -15.4464 43.6618 REMARK 3 T TENSOR REMARK 3 T11: 0.8450 T22: 1.4965 REMARK 3 T33: 0.9934 T12: -0.2163 REMARK 3 T13: 0.0721 T23: 0.0348 REMARK 3 L TENSOR REMARK 3 L11: 0.0676 L22: 0.6121 REMARK 3 L33: 0.0161 L12: 0.0063 REMARK 3 L13: -0.0357 L23: -0.0170 REMARK 3 S TENSOR REMARK 3 S11: -0.0712 S12: 0.0575 S13: -0.5052 REMARK 3 S21: -0.1431 S22: 0.1275 S23: 0.2830 REMARK 3 S31: -0.0772 S32: 1.2669 S33: -0.0789 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 28 THROUGH 53 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.4752 -25.5269 20.2545 REMARK 3 T TENSOR REMARK 3 T11: 0.2916 T22: 0.2530 REMARK 3 T33: 0.2429 T12: -0.1456 REMARK 3 T13: -0.0215 T23: -0.0001 REMARK 3 L TENSOR REMARK 3 L11: 1.4730 L22: 1.7465 REMARK 3 L33: 0.7336 L12: -1.3585 REMARK 3 L13: -0.4682 L23: 0.7066 REMARK 3 S TENSOR REMARK 3 S11: -0.0066 S12: 0.0311 S13: -0.0447 REMARK 3 S21: -0.1636 S22: 0.0973 S23: 0.1715 REMARK 3 S31: 0.2677 S32: -0.3734 S33: 0.0830 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 54 THROUGH 197 ) REMARK 3 ORIGIN FOR THE GROUP (A): 43.4547 -1.7389 1.1402 REMARK 3 T TENSOR REMARK 3 T11: 0.2392 T22: 0.1585 REMARK 3 T33: 0.1475 T12: -0.0896 REMARK 3 T13: -0.0123 T23: -0.0100 REMARK 3 L TENSOR REMARK 3 L11: 0.6607 L22: 1.1080 REMARK 3 L33: 1.3226 L12: 0.1978 REMARK 3 L13: -0.4567 L23: -0.2501 REMARK 3 S TENSOR REMARK 3 S11: -0.1118 S12: 0.1417 S13: 0.0239 REMARK 3 S21: -0.3078 S22: 0.1403 S23: 0.0725 REMARK 3 S31: 0.0022 S32: -0.1569 S33: 0.0470 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 198 THROUGH 239 ) REMARK 3 ORIGIN FOR THE GROUP (A): 44.0314 2.1933 -7.3760 REMARK 3 T TENSOR REMARK 3 T11: 0.3612 T22: 0.2533 REMARK 3 T33: 0.1982 T12: -0.1026 REMARK 3 T13: -0.0047 T23: 0.0014 REMARK 3 L TENSOR REMARK 3 L11: 0.3194 L22: 1.9085 REMARK 3 L33: 0.2602 L12: 0.2560 REMARK 3 L13: -0.2216 L23: -0.4580 REMARK 3 S TENSOR REMARK 3 S11: -0.0705 S12: 0.0925 S13: 0.1303 REMARK 3 S21: -0.3280 S22: 0.0867 S23: 0.0547 REMARK 3 S31: -0.0506 S32: -0.1841 S33: 0.0465 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 240 THROUGH 363 ) REMARK 3 ORIGIN FOR THE GROUP (A): 33.5134 1.4807 5.8811 REMARK 3 T TENSOR REMARK 3 T11: 0.2500 T22: 0.2769 REMARK 3 T33: 0.2381 T12: -0.0621 REMARK 3 T13: -0.0457 T23: 0.0187 REMARK 3 L TENSOR REMARK 3 L11: 0.2528 L22: 0.8027 REMARK 3 L33: 0.5566 L12: -0.1378 REMARK 3 L13: 0.1718 L23: 0.0286 REMARK 3 S TENSOR REMARK 3 S11: -0.0565 S12: -0.0041 S13: 0.0519 REMARK 3 S21: -0.1370 S22: 0.0825 S23: 0.1955 REMARK 3 S31: -0.0688 S32: -0.2101 S33: 0.0582 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 28 THROUGH 110 ) REMARK 3 ORIGIN FOR THE GROUP (A): 51.8577 23.5854 28.1744 REMARK 3 T TENSOR REMARK 3 T11: 0.2560 T22: 0.1634 REMARK 3 T33: 0.2158 T12: -0.0091 REMARK 3 T13: 0.0083 T23: -0.0209 REMARK 3 L TENSOR REMARK 3 L11: 0.7797 L22: 0.6648 REMARK 3 L33: 0.6512 L12: -0.0656 REMARK 3 L13: -0.1346 L23: 0.3166 REMARK 3 S TENSOR REMARK 3 S11: -0.0306 S12: 0.0852 S13: 0.0790 REMARK 3 S21: -0.0241 S22: 0.1557 S23: -0.1036 REMARK 3 S31: -0.2472 S32: 0.1128 S33: 0.0274 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 111 THROUGH 363 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.6531 20.6642 13.5898 REMARK 3 T TENSOR REMARK 3 T11: 0.2438 T22: 0.1666 REMARK 3 T33: 0.1898 T12: 0.0117 REMARK 3 T13: -0.0206 T23: 0.0192 REMARK 3 L TENSOR REMARK 3 L11: 0.6477 L22: 0.7507 REMARK 3 L33: 1.0642 L12: 0.0019 REMARK 3 L13: -0.0308 L23: 0.1255 REMARK 3 S TENSOR REMARK 3 S11: -0.0433 S12: 0.0330 S13: 0.0235 REMARK 3 S21: -0.1681 S22: 0.0850 S23: 0.0398 REMARK 3 S31: -0.2136 S32: -0.0892 S33: -0.0001 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 6XXM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1292106494. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 118364 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.670 REMARK 200 RESOLUTION RANGE LOW (A) : 46.120 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 10.06 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.2800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.67 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 9.71 REMARK 200 R MERGE FOR SHELL (I) : 2.58600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.950 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX V.1.17.1 REMARK 200 STARTING MODEL: 1DHS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.025-0.125 MM CARBOXYLIC ACID MIX, 30 REMARK 280 -60% PRECIPITANT MIX (MPD, PEG 3350, PEG 1000), 100 MM TRIS- REMARK 280 BICINE PH = 8.5, VAPOR DIFFUSION, SITTING DROP, 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 107.11467 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 53.55733 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 53.55733 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 107.11467 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 28280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 42780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -157.0 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 53.55733 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 GLU A 2 REMARK 465 GLY A 3 REMARK 465 SER A 4 REMARK 465 LEU A 5 REMARK 465 GLU A 6 REMARK 465 ARG A 7 REMARK 465 HIS A 364 REMARK 465 GLU A 365 REMARK 465 LYS A 366 REMARK 465 ASN A 367 REMARK 465 GLU A 368 REMARK 465 ASP A 369 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 GLY B 3 REMARK 465 SER B 4 REMARK 465 LEU B 5 REMARK 465 GLU B 6 REMARK 465 ARG B 7 REMARK 465 GLU B 8 REMARK 465 ALA B 9 REMARK 465 PRO B 10 REMARK 465 ALA B 11 REMARK 465 GLY B 12 REMARK 465 ALA B 13 REMARK 465 LEU B 14 REMARK 465 ALA B 15 REMARK 465 ALA B 16 REMARK 465 VAL B 17 REMARK 465 LEU B 18 REMARK 465 LYS B 19 REMARK 465 HIS B 20 REMARK 465 SER B 21 REMARK 465 SER B 22 REMARK 465 THR B 23 REMARK 465 LEU B 24 REMARK 465 PRO B 25 REMARK 465 PRO B 26 REMARK 465 GLU B 27 REMARK 465 HIS B 364 REMARK 465 GLU B 365 REMARK 465 LYS B 366 REMARK 465 ASN B 367 REMARK 465 GLU B 368 REMARK 465 ASP B 369 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 HH12 ARG B 92 OD1 ASN B 123 1.51 REMARK 500 HH21 ARG A 43 OE1 GLU A 353 1.58 REMARK 500 OE1 GLU B 71 O HOH B 501 1.76 REMARK 500 O HOH A 745 O HOH A 751 1.98 REMARK 500 O HOH B 769 O HOH B 776 2.00 REMARK 500 O HOH B 752 O HOH B 766 2.03 REMARK 500 NH2 ARG A 43 OE1 GLU A 353 2.06 REMARK 500 OE2 GLU A 261 O HOH A 501 2.08 REMARK 500 O HOH B 509 O HOH B 779 2.08 REMARK 500 O HOH A 581 O HOH A 715 2.10 REMARK 500 OE2 GLU A 71 NZ LYS A 358 2.10 REMARK 500 OG1 THR B 88 O HOH B 502 2.10 REMARK 500 O HOH A 777 O HOH A 779 2.14 REMARK 500 OG SER A 105 OG1 THR A 131 2.15 REMARK 500 O HOH B 513 O HOH B 749 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLN A 310 CA - CB - CG ANGL. DEV. = -14.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHE A 54 -138.66 49.64 REMARK 500 SER A 233 76.35 -160.23 REMARK 500 ALA A 235 54.50 -109.53 REMARK 500 ASN A 252 80.37 -153.62 REMARK 500 THR A 354 -92.57 -127.08 REMARK 500 PHE B 54 -135.93 48.78 REMARK 500 GLN B 89 35.76 -91.48 REMARK 500 SER B 233 77.77 -161.63 REMARK 500 ALA B 235 54.15 -105.08 REMARK 500 THR B 354 -92.15 -127.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 GLN A 310 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PUT A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PUT B 402 DBREF 6XXM A 1 369 UNP P49366 DHYS_HUMAN 1 369 DBREF 6XXM B 1 369 UNP P49366 DHYS_HUMAN 1 369 SEQRES 1 A 369 MET GLU GLY SER LEU GLU ARG GLU ALA PRO ALA GLY ALA SEQRES 2 A 369 LEU ALA ALA VAL LEU LYS HIS SER SER THR LEU PRO PRO SEQRES 3 A 369 GLU SER THR GLN VAL ARG GLY TYR ASP PHE ASN ARG GLY SEQRES 4 A 369 VAL ASN TYR ARG ALA LEU LEU GLU ALA PHE GLY THR THR SEQRES 5 A 369 GLY PHE GLN ALA THR ASN PHE GLY ARG ALA VAL GLN GLN SEQRES 6 A 369 VAL ASN ALA MET ILE GLU LYS LYS LEU GLU PRO LEU SER SEQRES 7 A 369 GLN ASP GLU ASP GLN HIS ALA ASP LEU THR GLN SER ARG SEQRES 8 A 369 ARG PRO LEU THR SER CYS THR ILE PHE LEU GLY TYR THR SEQRES 9 A 369 SER ASN LEU ILE SER SER GLY ILE ARG GLU THR ILE ARG SEQRES 10 A 369 TYR LEU VAL GLN HIS ASN MET VAL ASP VAL LEU VAL THR SEQRES 11 A 369 THR ALA GLY GLY VAL GLU GLU ASP LEU ILE LYS CYS LEU SEQRES 12 A 369 ALA PRO THR TYR LEU GLY GLU PHE SER LEU ARG GLY LYS SEQRES 13 A 369 GLU LEU ARG GLU ASN GLY ILE ASN ARG ILE GLY ASN LEU SEQRES 14 A 369 LEU VAL PRO ASN GLU ASN TYR CSS LYS PHE GLU ASP TRP SEQRES 15 A 369 LEU MET PRO ILE LEU ASP GLN MET VAL MET GLU GLN ASN SEQRES 16 A 369 THR GLU GLY VAL LYS TRP THR PRO SER LYS MET ILE ALA SEQRES 17 A 369 ARG LEU GLY LYS GLU ILE ASN ASN PRO GLU SER VAL TYR SEQRES 18 A 369 TYR TRP ALA GLN LYS ASN HIS ILE PRO VAL PHE SER PRO SEQRES 19 A 369 ALA LEU THR ASP GLY SER LEU GLY ASP MET ILE PHE PHE SEQRES 20 A 369 HIS SER TYR LYS ASN PRO GLY LEU VAL LEU ASP ILE VAL SEQRES 21 A 369 GLU ASP LEU ARG LEU ILE ASN THR GLN ALA ILE PHE ALA SEQRES 22 A 369 LYS CYS THR GLY MET ILE ILE LEU GLY GLY GLY VAL VAL SEQRES 23 A 369 LYS HIS HIS ILE ALA ASN ALA ASN LEU MET ARG ASN GLY SEQRES 24 A 369 ALA ASP TYR ALA VAL TYR ILE ASN THR ALA GLN GLU PHE SEQRES 25 A 369 ASP GLY SER ASP SER GLY ALA ARG PRO ASP GLU ALA VAL SEQRES 26 A 369 SER TRP GLY LYS ILE ARG VAL ASP ALA GLN PRO VAL LYS SEQRES 27 A 369 VAL TYR ALA ASP ALA SER LEU VAL PHE PRO LEU LEU VAL SEQRES 28 A 369 ALA GLU THR PHE ALA GLN LYS MET ASP ALA PHE MET HIS SEQRES 29 A 369 GLU LYS ASN GLU ASP SEQRES 1 B 369 MET GLU GLY SER LEU GLU ARG GLU ALA PRO ALA GLY ALA SEQRES 2 B 369 LEU ALA ALA VAL LEU LYS HIS SER SER THR LEU PRO PRO SEQRES 3 B 369 GLU SER THR GLN VAL ARG GLY TYR ASP PHE ASN ARG GLY SEQRES 4 B 369 VAL ASN TYR ARG ALA LEU LEU GLU ALA PHE GLY THR THR SEQRES 5 B 369 GLY PHE GLN ALA THR ASN PHE GLY ARG ALA VAL GLN GLN SEQRES 6 B 369 VAL ASN ALA MET ILE GLU LYS LYS LEU GLU PRO LEU SER SEQRES 7 B 369 GLN ASP GLU ASP GLN HIS ALA ASP LEU THR GLN SER ARG SEQRES 8 B 369 ARG PRO LEU THR SER CYS THR ILE PHE LEU GLY TYR THR SEQRES 9 B 369 SER ASN LEU ILE SER SER GLY ILE ARG GLU THR ILE ARG SEQRES 10 B 369 TYR LEU VAL GLN HIS ASN MET VAL ASP VAL LEU VAL THR SEQRES 11 B 369 THR ALA GLY GLY VAL GLU GLU ASP LEU ILE LYS CYS LEU SEQRES 12 B 369 ALA PRO THR TYR LEU GLY GLU PHE SER LEU ARG GLY LYS SEQRES 13 B 369 GLU LEU ARG GLU ASN GLY ILE ASN ARG ILE GLY ASN LEU SEQRES 14 B 369 LEU VAL PRO ASN GLU ASN TYR CSS LYS PHE GLU ASP TRP SEQRES 15 B 369 LEU MET PRO ILE LEU ASP GLN MET VAL MET GLU GLN ASN SEQRES 16 B 369 THR GLU GLY VAL LYS TRP THR PRO SER LYS MET ILE ALA SEQRES 17 B 369 ARG LEU GLY LYS GLU ILE ASN ASN PRO GLU SER VAL TYR SEQRES 18 B 369 TYR TRP ALA GLN LYS ASN HIS ILE PRO VAL PHE SER PRO SEQRES 19 B 369 ALA LEU THR ASP GLY SER LEU GLY ASP MET ILE PHE PHE SEQRES 20 B 369 HIS SER TYR LYS ASN PRO GLY LEU VAL LEU ASP ILE VAL SEQRES 21 B 369 GLU ASP LEU ARG LEU ILE ASN THR GLN ALA ILE PHE ALA SEQRES 22 B 369 LYS CSS THR GLY MET ILE ILE LEU GLY GLY GLY VAL VAL SEQRES 23 B 369 LYS HIS HIS ILE ALA ASN ALA ASN LEU MET ARG ASN GLY SEQRES 24 B 369 ALA ASP TYR ALA VAL TYR ILE ASN THR ALA GLN GLU PHE SEQRES 25 B 369 ASP GLY SER ASP SER GLY ALA ARG PRO ASP GLU ALA VAL SEQRES 26 B 369 SER TRP GLY LYS ILE ARG VAL ASP ALA GLN PRO VAL LYS SEQRES 27 B 369 VAL TYR ALA ASP ALA SER LEU VAL PHE PRO LEU LEU VAL SEQRES 28 B 369 ALA GLU THR PHE ALA GLN LYS MET ASP ALA PHE MET HIS SEQRES 29 B 369 GLU LYS ASN GLU ASP MODRES 6XXM CSS A 177 CYS MODIFIED RESIDUE MODRES 6XXM CSS B 177 CYS MODIFIED RESIDUE MODRES 6XXM CSS B 275 CYS MODIFIED RESIDUE HET CSS A 177 10 HET CSS B 177 17 HET CSS B 275 10 HET PUT A 401 18 HET MPD B 401 22 HET PUT B 402 18 HETNAM CSS S-MERCAPTOCYSTEINE HETNAM PUT 1,4-DIAMINOBUTANE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETSYN PUT PUTRESCINE FORMUL 1 CSS 3(C3 H7 N O2 S2) FORMUL 3 PUT 2(C4 H12 N2) FORMUL 4 MPD C6 H14 O2 FORMUL 6 HOH *569(H2 O) HELIX 1 AA1 PRO A 10 LEU A 18 1 9 HELIX 2 AA2 ASP A 35 GLY A 39 5 5 HELIX 3 AA3 ASN A 41 ALA A 48 1 8 HELIX 4 AA4 PHE A 49 THR A 52 5 4 HELIX 5 AA5 GLY A 53 LEU A 74 1 22 HELIX 6 AA6 ASP A 80 GLN A 89 1 10 HELIX 7 AA7 THR A 104 SER A 110 1 7 HELIX 8 AA8 GLY A 111 HIS A 122 1 12 HELIX 9 AA9 THR A 131 LYS A 141 1 11 HELIX 10 AB1 ARG A 154 ASN A 161 1 8 HELIX 11 AB2 ASN A 173 GLY A 198 1 26 HELIX 12 AB3 THR A 202 ASN A 215 1 14 HELIX 13 AB4 SER A 219 ASN A 227 1 9 HELIX 14 AB5 GLY A 239 ASN A 252 1 14 HELIX 15 AB6 ILE A 259 PHE A 272 1 14 HELIX 16 AB7 GLY A 284 MET A 296 1 13 HELIX 17 AB8 GLN A 310 GLY A 314 5 5 HELIX 18 AB9 ARG A 320 GLY A 328 1 9 HELIX 19 AC1 ASP A 342 THR A 354 1 13 HELIX 20 AC2 PHE A 355 MET A 359 5 5 HELIX 21 AC3 ASP B 35 GLY B 39 5 5 HELIX 22 AC4 ASN B 41 ALA B 48 1 8 HELIX 23 AC5 PHE B 49 THR B 52 5 4 HELIX 24 AC6 GLY B 53 LEU B 74 1 22 HELIX 25 AC7 SER B 78 ASP B 86 1 9 HELIX 26 AC8 THR B 104 SER B 110 1 7 HELIX 27 AC9 GLY B 111 HIS B 122 1 12 HELIX 28 AD1 THR B 131 LYS B 141 1 11 HELIX 29 AD2 ARG B 154 ASN B 161 1 8 HELIX 30 AD3 ASN B 173 GLY B 198 1 26 HELIX 31 AD4 THR B 202 ASN B 215 1 14 HELIX 32 AD5 SER B 219 ASN B 227 1 9 HELIX 33 AD6 GLY B 239 ASN B 252 1 14 HELIX 34 AD7 ILE B 259 PHE B 272 1 14 HELIX 35 AD8 GLY B 284 MET B 296 1 13 HELIX 36 AD9 GLN B 310 GLY B 314 5 5 HELIX 37 AE1 ARG B 320 GLY B 328 1 9 HELIX 38 AE2 ASP B 342 THR B 354 1 13 HELIX 39 AE3 PHE B 355 GLN B 357 5 3 HELIX 40 AE4 LYS B 358 MET B 363 1 6 SHEET 1 AA1 6 VAL A 231 PHE A 232 0 SHEET 2 AA1 6 VAL A 127 THR A 130 1 N LEU A 128 O PHE A 232 SHEET 3 AA1 6 THR A 98 TYR A 103 1 N LEU A 101 O VAL A 127 SHEET 4 AA1 6 THR A 276 LEU A 281 1 O GLY A 277 N PHE A 100 SHEET 5 AA1 6 TYR A 302 ASN A 307 1 O VAL A 304 N ILE A 280 SHEET 6 AA1 6 VAL A 337 TYR A 340 1 O VAL A 339 N TYR A 305 SHEET 1 AA2 3 TYR A 147 LEU A 148 0 SHEET 2 AA2 3 LEU A 169 PRO A 172 -1 O LEU A 170 N TYR A 147 SHEET 3 AA2 3 ILE A 163 ILE A 166 -1 N ASN A 164 O VAL A 171 SHEET 1 AA3 6 VAL B 231 PHE B 232 0 SHEET 2 AA3 6 VAL B 127 THR B 130 1 N LEU B 128 O PHE B 232 SHEET 3 AA3 6 THR B 98 TYR B 103 1 N LEU B 101 O VAL B 127 SHEET 4 AA3 6 THR B 276 LEU B 281 1 O GLY B 277 N PHE B 100 SHEET 5 AA3 6 TYR B 302 ASN B 307 1 O VAL B 304 N ILE B 280 SHEET 6 AA3 6 VAL B 337 TYR B 340 1 O VAL B 339 N TYR B 305 SHEET 1 AA4 3 TYR B 147 LEU B 148 0 SHEET 2 AA4 3 LEU B 169 PRO B 172 -1 O LEU B 170 N TYR B 147 SHEET 3 AA4 3 ILE B 163 ILE B 166 -1 N ASN B 164 O VAL B 171 LINK C TYR A 176 N CSS A 177 1555 1555 1.34 LINK C CSS A 177 N LYS A 178 1555 1555 1.33 LINK C TYR B 176 N CSS B 177 1555 1555 1.33 LINK C CSS B 177 N LYS B 178 1555 1555 1.33 LINK C LYS B 274 N CSS B 275 1555 1555 1.33 LINK C CSS B 275 N THR B 276 1555 1555 1.33 SITE 1 AC1 10 GLU A 136 GLU A 137 SER A 240 ASP A 243 SITE 2 AC1 10 HOH A 605 HOH A 700 HIS B 288 ASN B 292 SITE 3 AC1 10 LEU B 295 HOH B 514 SITE 1 AC2 4 TYR A 250 ARG B 38 VAL B 40 HOH B 674 SITE 1 AC3 11 ASN A 292 LEU A 295 TRP A 327 GLU B 136 SITE 2 AC3 11 GLU B 137 TYR B 176 GLY B 239 SER B 240 SITE 3 AC3 11 ASP B 243 HOH B 576 HOH B 666 CRYST1 104.734 104.734 160.672 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 0.009548 0.005513 0.000000 0.00000 SCALE2 0.000000 0.011025 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006224 0.00000