HEADER TRANSFERASE 27-MAY-22 8A0G TITLE HUMAN DEOXYHYPUSINE SYNTHASE WITH TRAPPED TRANSITION STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEOXYHYPUSINE SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DHS; COMPND 5 EC: 2.5.1.46; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: K329 IS POSTTRANSLATIONALLY MODIFIED TO DEOXYHYPUSINE COMPND 8 I.E. 5GG. 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYPUSINATION, TRANSFERASE, POSTTRANSLATIONAL MODIFICATION EXPDTA X-RAY DIFFRACTION AUTHOR E.WATOR,P.WILK,P.GRUDNIK REVDAT 3 07-FEB-24 8A0G 1 LINK REVDAT 2 12-APR-23 8A0G 1 JRNL REVDAT 1 05-APR-23 8A0G 0 JRNL AUTH E.WATOR,P.WILK,A.BIELA,M.RAWSKI,K.M.ZAK,W.STEINCHEN,G.BANGE, JRNL AUTH 2 S.GLATT,P.GRUDNIK JRNL TITL CRYO-EM STRUCTURE OF HUMAN EIF5A-DHS COMPLEX REVEALS THE JRNL TITL 2 MOLECULAR BASIS OF HYPUSINATION-ASSOCIATED NEURODEGENERATIVE JRNL TITL 3 DISORDERS. JRNL REF NAT COMMUN V. 14 1698 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 36973244 JRNL DOI 10.1038/S41467-023-37305-2 REMARK 2 REMARK 2 RESOLUTION. 1.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 93096 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.148 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.164 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.57 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 : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 9 THROUGH 27 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.8838 15.7399 42.0633 REMARK 3 T TENSOR REMARK 3 T11: 0.8815 T22: 1.4088 REMARK 3 T33: 1.0298 T12: -0.1289 REMARK 3 T13: -0.0526 T23: -0.0385 REMARK 3 L TENSOR REMARK 3 L11: 0.0112 L22: 0.0044 REMARK 3 L33: 0.0039 L12: 0.0069 REMARK 3 L13: 0.0064 L23: 0.0038 REMARK 3 S TENSOR REMARK 3 S11: 0.1437 S12: 0.1353 S13: 0.1563 REMARK 3 S21: 0.1553 S22: -0.0772 S23: -0.1017 REMARK 3 S31: 0.0479 S32: 0.0305 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 28 THROUGH 53 ) REMARK 3 ORIGIN FOR THE GROUP (A): -33.9100 25.5372 20.1709 REMARK 3 T TENSOR REMARK 3 T11: 0.3471 T22: 0.2955 REMARK 3 T33: 0.3186 T12: -0.1095 REMARK 3 T13: 0.0175 T23: -0.0127 REMARK 3 L TENSOR REMARK 3 L11: 0.0230 L22: 0.0339 REMARK 3 L33: 0.0613 L12: -0.0214 REMARK 3 L13: -0.0268 L23: -0.0020 REMARK 3 S TENSOR REMARK 3 S11: -0.0138 S12: -0.0344 S13: 0.0005 REMARK 3 S21: -0.0308 S22: 0.1119 S23: -0.1536 REMARK 3 S31: -0.2937 S32: 0.3215 S33: 0.0014 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 54 THROUGH 97 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.9696 10.0258 3.6799 REMARK 3 T TENSOR REMARK 3 T11: 0.3022 T22: 0.3525 REMARK 3 T33: 0.2821 T12: -0.1327 REMARK 3 T13: 0.0821 T23: -0.0476 REMARK 3 L TENSOR REMARK 3 L11: 0.3417 L22: 0.3359 REMARK 3 L33: 0.0662 L12: -0.1886 REMARK 3 L13: 0.0193 L23: -0.0742 REMARK 3 S TENSOR REMARK 3 S11: -0.0829 S12: 0.1927 S13: -0.0328 REMARK 3 S21: -0.2246 S22: 0.0928 S23: -0.2210 REMARK 3 S31: -0.0136 S32: 0.1444 S33: -0.1220 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 98 THROUGH 307 ) REMARK 3 ORIGIN FOR THE GROUP (A): -46.4533 -3.3492 -0.1107 REMARK 3 T TENSOR REMARK 3 T11: 0.2751 T22: 0.2316 REMARK 3 T33: 0.2256 T12: -0.0597 REMARK 3 T13: 0.0083 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 0.4225 L22: 0.7515 REMARK 3 L33: 0.9478 L12: 0.1109 REMARK 3 L13: 0.0485 L23: 0.0522 REMARK 3 S TENSOR REMARK 3 S11: -0.0530 S12: 0.0706 S13: 0.0132 REMARK 3 S21: -0.1887 S22: 0.0804 S23: 0.0139 REMARK 3 S31: 0.0205 S32: 0.0397 S33: -0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 308 THROUGH 362 ) REMARK 3 ORIGIN FOR THE GROUP (A): -32.1396 4.7388 12.7216 REMARK 3 T TENSOR REMARK 3 T11: 0.2391 T22: 0.2947 REMARK 3 T33: 0.3071 T12: -0.0506 REMARK 3 T13: 0.0369 T23: -0.0189 REMARK 3 L TENSOR REMARK 3 L11: 0.0067 L22: 0.2130 REMARK 3 L33: 0.1940 L12: -0.0439 REMARK 3 L13: -0.0235 L23: 0.1381 REMARK 3 S TENSOR REMARK 3 S11: -0.0575 S12: -0.0258 S13: 0.0905 REMARK 3 S21: -0.0714 S22: 0.1004 S23: -0.2557 REMARK 3 S31: -0.0412 S32: 0.2459 S33: 0.0071 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 363 THROUGH 363 ) REMARK 3 ORIGIN FOR THE GROUP (A): -36.0550 18.6704 -9.3289 REMARK 3 T TENSOR REMARK 3 T11: 0.9156 T22: 0.9487 REMARK 3 T33: 0.9416 T12: -0.0153 REMARK 3 T13: -0.0913 T23: -0.0768 REMARK 3 L TENSOR REMARK 3 L11: 9.5025 L22: 2.0000 REMARK 3 L33: 6.7279 L12: 7.1219 REMARK 3 L13: -4.8106 L23: -9.3556 REMARK 3 S TENSOR REMARK 3 S11: 0.0449 S12: 1.8690 S13: 0.2860 REMARK 3 S21: 0.2386 S22: -0.2667 S23: -0.0420 REMARK 3 S31: 0.1468 S32: -0.7541 S33: 0.1987 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 28 THROUGH 53 ) REMARK 3 ORIGIN FOR THE GROUP (A): -49.7366 -18.1398 46.4851 REMARK 3 T TENSOR REMARK 3 T11: 0.3576 T22: 0.2555 REMARK 3 T33: 0.3015 T12: 0.0441 REMARK 3 T13: 0.0071 T23: 0.0231 REMARK 3 L TENSOR REMARK 3 L11: 0.0213 L22: 0.0387 REMARK 3 L33: 0.0434 L12: -0.0065 REMARK 3 L13: 0.0084 L23: -0.0406 REMARK 3 S TENSOR REMARK 3 S11: -0.0006 S12: -0.0597 S13: -0.1110 REMARK 3 S21: 0.2835 S22: 0.0073 S23: 0.1354 REMARK 3 S31: 0.2222 S32: -0.0944 S33: -0.0001 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 54 THROUGH 97 ) REMARK 3 ORIGIN FOR THE GROUP (A): -58.2756 -27.5237 21.7163 REMARK 3 T TENSOR REMARK 3 T11: 0.3282 T22: 0.2278 REMARK 3 T33: 0.2556 T12: -0.0776 REMARK 3 T13: -0.0326 T23: 0.0267 REMARK 3 L TENSOR REMARK 3 L11: 0.4457 L22: 0.3028 REMARK 3 L33: 0.1575 L12: -0.1831 REMARK 3 L13: -0.0653 L23: 0.0062 REMARK 3 S TENSOR REMARK 3 S11: 0.0188 S12: 0.0699 S13: -0.0190 REMARK 3 S21: -0.0104 S22: 0.0218 S23: 0.1367 REMARK 3 S31: 0.2563 S32: -0.2363 S33: 0.0419 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 98 THROUGH 363 ) REMARK 3 ORIGIN FOR THE GROUP (A): -40.5111 -20.9581 13.9032 REMARK 3 T TENSOR REMARK 3 T11: 0.2532 T22: 0.1680 REMARK 3 T33: 0.2047 T12: 0.0270 REMARK 3 T13: 0.0106 T23: -0.0257 REMARK 3 L TENSOR REMARK 3 L11: 0.4996 L22: 0.5737 REMARK 3 L33: 1.0809 L12: 0.0390 REMARK 3 L13: 0.0132 L23: -0.1304 REMARK 3 S TENSOR REMARK 3 S11: -0.0213 S12: 0.0216 S13: -0.0282 REMARK 3 S21: -0.1193 S22: 0.0744 S23: -0.0411 REMARK 3 S31: 0.2443 S32: 0.1000 S33: 0.0005 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 8A0G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1292123384. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-21 REMARK 200 TEMPERATURE (KELVIN) : 293 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 : 14.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.895 REMARK 200 MONOCHROMATOR : CCM SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 93129 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.840 REMARK 200 RESOLUTION RANGE LOW (A) : 46.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.905 REMARK 200 R MERGE (I) : 0.19200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 10.10 REMARK 200 R MERGE FOR SHELL (I) : 1.96700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.970 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: 6XXJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MG/ML PROTEIN SOLUTION WAS MIXED REMARK 280 WITH EQUAL VOLUME OF MOTHER LIQUOR CONSISTING OF 0.025-0.125 MM REMARK 280 CARBOXYLIC ACID MIX, 30-60% PRECIPITANT MIX, PEG 1000, PEG 3350 REMARK 280 AND 100 MM TRIS-BICINE PH 8.5., VAPOR DIFFUSION, SITTING 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 107.58667 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 53.79333 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 53.79333 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 107.58667 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 32750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -165.0 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 53.79333 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 -1 REMARK 465 SER A 0 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 GLU A 8 REMARK 465 ALA A 9 REMARK 465 PRO A 10 REMARK 465 ALA A 11 REMARK 465 GLY A 12 REMARK 465 ALA A 13 REMARK 465 LEU A 14 REMARK 465 ALA A 15 REMARK 465 ALA A 16 REMARK 465 VAL A 17 REMARK 465 LEU A 18 REMARK 465 LYS A 19 REMARK 465 HIS A 20 REMARK 465 SER A 21 REMARK 465 SER A 22 REMARK 465 THR A 23 REMARK 465 LEU A 24 REMARK 465 PRO A 25 REMARK 465 PRO A 26 REMARK 465 GLU A 27 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 GLY B -1 REMARK 465 SER B 0 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 SER B 78 REMARK 465 GLN B 79 REMARK 465 ASP B 80 REMARK 465 GLU B 81 REMARK 465 ASP B 82 REMARK 465 GLN B 83 REMARK 465 HIS B 84 REMARK 465 ALA B 85 REMARK 465 ASP B 86 REMARK 465 LEU B 87 REMARK 465 THR B 88 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 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 GLN A 89 CG CD OE1 NE2 REMARK 470 LYS A 226 NZ REMARK 470 LYS A 251 CG CD CE NZ REMARK 470 ARG B 91 NE CZ NH1 NH2 REMARK 470 LYS B 274 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 NH2 ARG A 331 OD2 ASP A 333 2.16 REMARK 500 O HOH A 520 O HOH A 607 2.17 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 MET A 278 CG - SD - CE ANGL. DEV. = 11.5 DEGREES REMARK 500 MET B 69 CG - SD - CE ANGL. DEV. = 11.9 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 -137.60 52.37 REMARK 500 ASP A 86 -16.03 141.46 REMARK 500 SER A 233 83.10 -157.54 REMARK 500 ALA A 235 54.26 -103.83 REMARK 500 THR A 354 -89.54 -126.89 REMARK 500 GLU B 27 5.42 -69.79 REMARK 500 PHE B 54 -138.85 51.77 REMARK 500 SER B 233 80.16 -160.80 REMARK 500 ALA B 235 56.93 -103.09 REMARK 500 ASN B 252 79.79 -155.50 REMARK 500 THR B 354 -92.02 -125.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 VAL B 286 -13.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6XXJ RELATED DB: PDB REMARK 900 DHS WTILD TYPE REMARK 900 RELATED ID: 7A6T RELATED DB: PDB REMARK 900 DHS N173S REMARK 900 RELATED ID: 7A6S RELATED DB: PDB REMARK 900 DHS N173S REMARK 900 RELATED ID: 8A0E RELATED DB: PDB REMARK 900 CRYOEM DHS-EIF5A REMARK 900 RELATED ID: 8A0F RELATED DB: PDB REMARK 900 DHS K329A DBREF 8A0G A 1 369 UNP P49366 DHYS_HUMAN 1 369 DBREF 8A0G B 1 369 UNP P49366 DHYS_HUMAN 1 369 SEQADV 8A0G GLY A -1 UNP P49366 EXPRESSION TAG SEQADV 8A0G SER A 0 UNP P49366 EXPRESSION TAG SEQADV 8A0G GLY B -1 UNP P49366 EXPRESSION TAG SEQADV 8A0G SER B 0 UNP P49366 EXPRESSION TAG SEQRES 1 A 371 GLY SER MET GLU GLY SER LEU GLU ARG GLU ALA PRO ALA SEQRES 2 A 371 GLY ALA LEU ALA ALA VAL LEU LYS HIS SER SER THR LEU SEQRES 3 A 371 PRO PRO GLU SER THR GLN VAL ARG GLY TYR ASP PHE ASN SEQRES 4 A 371 ARG GLY VAL ASN TYR ARG ALA LEU LEU GLU ALA PHE GLY SEQRES 5 A 371 THR THR GLY PHE GLN ALA THR ASN PHE GLY ARG ALA VAL SEQRES 6 A 371 GLN GLN VAL ASN ALA MET ILE GLU LYS LYS LEU GLU PRO SEQRES 7 A 371 LEU SER GLN ASP GLU ASP GLN HIS ALA ASP LEU THR GLN SEQRES 8 A 371 SER ARG ARG PRO LEU THR SER CYS THR ILE PHE LEU GLY SEQRES 9 A 371 TYR THR SER ASN LEU ILE SER SER GLY ILE ARG GLU THR SEQRES 10 A 371 ILE ARG TYR LEU VAL GLN HIS ASN MET VAL ASP VAL LEU SEQRES 11 A 371 VAL THR THR ALA GLY GLY VAL GLU GLU ASP LEU ILE LYS SEQRES 12 A 371 CYS LEU ALA PRO THR TYR LEU GLY GLU PHE SER LEU ARG SEQRES 13 A 371 GLY LYS GLU LEU ARG GLU ASN GLY ILE ASN ARG ILE GLY SEQRES 14 A 371 ASN LEU LEU VAL PRO ASN GLU ASN TYR CSS LYS PHE GLU SEQRES 15 A 371 ASP TRP LEU MET PRO ILE LEU ASP GLN MET VAL MET GLU SEQRES 16 A 371 GLN ASN THR GLU GLY VAL LYS TRP THR PRO SER LYS MET SEQRES 17 A 371 ILE ALA ARG LEU GLY LYS GLU ILE ASN ASN PRO GLU SER SEQRES 18 A 371 VAL TYR TYR TRP ALA GLN LYS ASN HIS ILE PRO VAL PHE SEQRES 19 A 371 SER PRO ALA LEU THR ASP GLY SER LEU GLY ASP MET ILE SEQRES 20 A 371 PHE PHE HIS SER TYR LYS ASN PRO GLY LEU VAL LEU ASP SEQRES 21 A 371 ILE VAL GLU ASP LEU ARG LEU ILE ASN THR GLN ALA ILE SEQRES 22 A 371 PHE ALA LYS CYS THR GLY MET ILE ILE LEU GLY GLY GLY SEQRES 23 A 371 VAL VAL LYS HIS HIS ILE ALA ASN ALA ASN LEU MET ARG SEQRES 24 A 371 ASN GLY ALA ASP TYR ALA VAL TYR ILE ASN THR ALA GLN SEQRES 25 A 371 GLU PHE ASP GLY SER ASP SER GLY ALA ARG PRO ASP GLU SEQRES 26 A 371 ALA VAL SER TRP GLY 5GG ILE ARG VAL ASP ALA GLN PRO SEQRES 27 A 371 VAL LYS VAL TYR ALA ASP ALA SER LEU VAL PHE PRO LEU SEQRES 28 A 371 LEU VAL ALA GLU THR PHE ALA GLN LYS MET ASP ALA PHE SEQRES 29 A 371 MET HIS GLU LYS ASN GLU ASP SEQRES 1 B 371 GLY SER MET GLU GLY SER LEU GLU ARG GLU ALA PRO ALA SEQRES 2 B 371 GLY ALA LEU ALA ALA VAL LEU LYS HIS SER SER THR LEU SEQRES 3 B 371 PRO PRO GLU SER THR GLN VAL ARG GLY TYR ASP PHE ASN SEQRES 4 B 371 ARG GLY VAL ASN TYR ARG ALA LEU LEU GLU ALA PHE GLY SEQRES 5 B 371 THR THR GLY PHE GLN ALA THR ASN PHE GLY ARG ALA VAL SEQRES 6 B 371 GLN GLN VAL ASN ALA MET ILE GLU LYS LYS LEU GLU PRO SEQRES 7 B 371 LEU SER GLN ASP GLU ASP GLN HIS ALA ASP LEU THR GLN SEQRES 8 B 371 SER ARG ARG PRO LEU THR SER CYS THR ILE PHE LEU GLY SEQRES 9 B 371 TYR THR SER ASN LEU ILE SER SER GLY ILE ARG GLU THR SEQRES 10 B 371 ILE ARG TYR LEU VAL GLN HIS ASN MET VAL ASP VAL LEU SEQRES 11 B 371 VAL THR THR ALA GLY GLY VAL GLU GLU ASP LEU ILE LYS SEQRES 12 B 371 CYS LEU ALA PRO THR TYR LEU GLY GLU PHE SER LEU ARG SEQRES 13 B 371 GLY LYS GLU LEU ARG GLU ASN GLY ILE ASN ARG ILE GLY SEQRES 14 B 371 ASN LEU LEU VAL PRO ASN GLU ASN TYR CSS LYS PHE GLU SEQRES 15 B 371 ASP TRP LEU MET PRO ILE LEU ASP GLN MET VAL MET GLU SEQRES 16 B 371 GLN ASN THR GLU GLY VAL LYS TRP THR PRO SER LYS MET SEQRES 17 B 371 ILE ALA ARG LEU GLY LYS GLU ILE ASN ASN PRO GLU SER SEQRES 18 B 371 VAL TYR TYR TRP ALA GLN LYS ASN HIS ILE PRO VAL PHE SEQRES 19 B 371 SER PRO ALA LEU THR ASP GLY SER LEU GLY ASP MET ILE SEQRES 20 B 371 PHE PHE HIS SER TYR LYS ASN PRO GLY LEU VAL LEU ASP SEQRES 21 B 371 ILE VAL GLU ASP LEU ARG LEU ILE ASN THR GLN ALA ILE SEQRES 22 B 371 PHE ALA LYS CYS THR GLY MET ILE ILE LEU GLY GLY GLY SEQRES 23 B 371 VAL VAL LYS HIS HIS ILE ALA ASN ALA ASN LEU MET ARG SEQRES 24 B 371 ASN GLY ALA ASP TYR ALA VAL TYR ILE ASN THR ALA GLN SEQRES 25 B 371 GLU PHE ASP GLY SER ASP SER GLY ALA ARG PRO ASP GLU SEQRES 26 B 371 ALA VAL SER TRP GLY 5GG ILE ARG VAL ASP ALA GLN PRO SEQRES 27 B 371 VAL LYS VAL TYR ALA ASP ALA SER LEU VAL PHE PRO LEU SEQRES 28 B 371 LEU VAL ALA GLU THR PHE ALA GLN LYS MET ASP ALA PHE SEQRES 29 B 371 MET HIS GLU LYS ASN GLU ASP MODRES 8A0G CSS A 177 CYS MODIFIED RESIDUE MODRES 8A0G 5GG A 329 LYS MODIFIED RESIDUE MODRES 8A0G CSS B 177 CYS MODIFIED RESIDUE MODRES 8A0G 5GG B 329 LYS MODIFIED RESIDUE HET CSS A 177 11 HET 5GG A 329 14 HET CSS B 177 7 HET 5GG B 329 14 HET 13D A 401 5 HET MRD A 402 8 HET NAD A 403 44 HET SPD B 401 10 HET NAD B 402 44 HETNAM CSS S-MERCAPTOCYSTEINE HETNAM 5GG DEOXYHYPUSINE HETNAM 13D 1,3-DIAMINOPROPANE HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM SPD SPERMIDINE HETSYN SPD N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34) FORMUL 1 CSS 2(C3 H7 N O2 S2) FORMUL 1 5GG 2(C10 H23 N3 O2) FORMUL 3 13D C3 H10 N2 FORMUL 4 MRD C6 H14 O2 FORMUL 5 NAD 2(C21 H27 N7 O14 P2) FORMUL 6 SPD C7 H19 N3 FORMUL 8 HOH *305(H2 O) HELIX 1 AA1 ASP A 35 GLY A 39 5 5 HELIX 2 AA2 ASN A 41 ALA A 48 1 8 HELIX 3 AA3 PHE A 49 THR A 52 5 4 HELIX 4 AA4 GLY A 53 GLU A 75 1 23 HELIX 5 AA5 SER A 78 ALA A 85 1 8 HELIX 6 AA6 THR A 104 SER A 110 1 7 HELIX 7 AA7 GLY A 111 HIS A 122 1 12 HELIX 8 AA8 THR A 131 CYS A 142 1 12 HELIX 9 AA9 ARG A 154 ASN A 161 1 8 HELIX 10 AB1 ASN A 173 GLY A 198 1 26 HELIX 11 AB2 THR A 202 ASN A 215 1 14 HELIX 12 AB3 SER A 219 ASN A 227 1 9 HELIX 13 AB4 GLY A 239 ASN A 252 1 14 HELIX 14 AB5 ILE A 259 PHE A 272 1 14 HELIX 15 AB6 GLY A 284 MET A 296 1 13 HELIX 16 AB7 GLN A 310 GLY A 314 5 5 HELIX 17 AB8 ARG A 320 GLY A 328 1 9 HELIX 18 AB9 ASP A 342 THR A 354 1 13 HELIX 19 AC1 PHE A 355 MET A 363 5 9 HELIX 20 AC2 PRO B 10 LEU B 18 1 9 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 THR B 104 SER B 110 1 7 HELIX 26 AC8 GLY B 111 HIS B 122 1 12 HELIX 27 AC9 THR B 131 CYS B 142 1 12 HELIX 28 AD1 ARG B 154 ASN B 161 1 8 HELIX 29 AD2 ASN B 173 GLY B 198 1 26 HELIX 30 AD3 THR B 202 ASN B 215 1 14 HELIX 31 AD4 SER B 219 ASN B 227 1 9 HELIX 32 AD5 GLY B 239 ASN B 252 1 14 HELIX 33 AD6 ILE B 259 PHE B 272 1 14 HELIX 34 AD7 GLY B 284 MET B 296 1 13 HELIX 35 AD8 GLN B 310 GLY B 314 5 5 HELIX 36 AD9 ARG B 320 GLY B 328 1 9 HELIX 37 AE1 ASP B 342 THR B 354 1 13 HELIX 38 AE2 PHE B 355 GLN B 357 5 3 HELIX 39 AE3 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 MET A 278 SHEET 6 AA1 6 VAL A 337 TYR A 340 1 O VAL A 337 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 LEU B 281 N GLY B 102 SHEET 5 AA3 6 TYR B 302 ASN B 307 1 O ILE B 306 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 SSBOND 1 CYS A 97 CYS A 275 1555 1555 2.36 SSBOND 2 CYS B 97 CYS B 275 1555 1555 2.08 LINK C TYR A 176 N CSS A 177 1555 1555 1.33 LINK C CSS A 177 N LYS A 178 1555 1555 1.33 LINK C GLY A 328 N 5GG A 329 1555 1555 1.40 LINK C 5GG A 329 N ILE A 330 1555 1555 1.30 LINK C TYR B 176 N CSS B 177 1555 1555 1.34 LINK C CSS B 177 N LYS B 178 1555 1555 1.33 LINK C GLY B 328 N 5GG B 329 1555 1555 1.41 LINK C 5GG B 329 N ILE B 330 1555 1555 1.32 CRYST1 106.950 106.950 161.380 90.00 90.00 120.00 P 32 2 1 12 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 0.009350 0.005398 0.000000 0.00000 SCALE2 0.000000 0.010797 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006197 0.00000