HEADER TRANSFERASE 26-AUG-20 7A6T TITLE CRYSTAL STRUCTURE OF ASN173SER VARIANT OF HUMAN DEOXYHYPUSINE SYNTHASE TITLE 2 IN COMPLEX WITH NAD AND SPERMIDINE 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 MUTATION: 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS DEOXYHYPUSINE SYNTHASE, HYPUSINATION, HYPUSINE, TRANSLATION, KEYWDS 2 NEURODEGENERATION, SPERMIDINE DHPS DEFICIENCY, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR E.WATOR,P.WILK,P.GRUDNIK REVDAT 3 07-FEB-24 7A6T 1 REMARK REVDAT 2 05-APR-23 7A6T 1 JRNL REVDAT 1 23-MAR-22 7A6T 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. 1.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.320 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 120517 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.740 REMARK 3 FREE R VALUE TEST SET COUNT : 2096 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 46.0100 - 4.0900 1.00 8301 148 0.1555 0.1733 REMARK 3 2 4.0900 - 3.2500 1.00 8039 142 0.1341 0.1515 REMARK 3 3 3.2500 - 2.8400 1.00 7960 141 0.1351 0.1449 REMARK 3 4 2.8400 - 2.5800 1.00 7957 141 0.1308 0.1498 REMARK 3 5 2.5800 - 2.3900 1.00 7868 139 0.1342 0.1783 REMARK 3 6 2.3900 - 2.2500 1.00 7935 140 0.1516 0.1637 REMARK 3 7 2.2500 - 2.1400 1.00 7845 139 0.1647 0.1989 REMARK 3 8 2.1400 - 2.0500 1.00 7880 139 0.1867 0.2247 REMARK 3 9 2.0500 - 1.9700 1.00 7855 139 0.2119 0.2529 REMARK 3 10 1.9700 - 1.9000 1.00 7821 139 0.2418 0.2931 REMARK 3 11 1.9000 - 1.8400 1.00 7794 138 0.2846 0.2964 REMARK 3 12 1.8400 - 1.7900 1.00 7857 138 0.3164 0.3217 REMARK 3 13 1.7900 - 1.7400 1.00 7827 138 0.3507 0.3878 REMARK 3 14 1.7400 - 1.7000 0.99 7791 139 0.3863 0.4162 REMARK 3 15 1.7000 - 1.6600 0.98 7691 136 0.4558 0.4795 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.83 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 : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 28 THROUGH 53 ) REMARK 3 ORIGIN FOR THE GROUP (A): -38.4861 -16.0068 -6.7440 REMARK 3 T TENSOR REMARK 3 T11: 0.4901 T22: 0.2332 REMARK 3 T33: 0.2583 T12: 0.1033 REMARK 3 T13: 0.0223 T23: 0.0521 REMARK 3 L TENSOR REMARK 3 L11: 6.9645 L22: 4.0260 REMARK 3 L33: 3.1285 L12: 2.5157 REMARK 3 L13: 1.4936 L23: 0.5490 REMARK 3 S TENSOR REMARK 3 S11: 0.0062 S12: 0.1606 S13: 0.3589 REMARK 3 S21: -0.2345 S22: 0.0366 S23: -0.2305 REMARK 3 S31: -0.6485 S32: -0.1136 S33: 0.0205 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 54 THROUGH 88 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.7210 -17.7766 -24.6430 REMARK 3 T TENSOR REMARK 3 T11: 0.6052 T22: 0.3216 REMARK 3 T33: 0.3403 T12: 0.0281 REMARK 3 T13: 0.1183 T23: 0.0789 REMARK 3 L TENSOR REMARK 3 L11: 2.3784 L22: 1.5637 REMARK 3 L33: 1.4409 L12: 0.2706 REMARK 3 L13: 0.3452 L23: -0.4819 REMARK 3 S TENSOR REMARK 3 S11: 0.1510 S12: 0.6193 S13: 0.3042 REMARK 3 S21: -0.5444 S22: -0.0974 S23: -0.3417 REMARK 3 S31: -0.4866 S32: 0.2431 S33: -0.1789 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 89 THROUGH 110 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.2973 -29.2939 -27.9772 REMARK 3 T TENSOR REMARK 3 T11: 0.5289 T22: 0.3451 REMARK 3 T33: 0.2479 T12: 0.0380 REMARK 3 T13: 0.0681 T23: 0.0238 REMARK 3 L TENSOR REMARK 3 L11: 2.3696 L22: 1.1893 REMARK 3 L33: 1.6763 L12: -0.0178 REMARK 3 L13: 0.2636 L23: 0.2913 REMARK 3 S TENSOR REMARK 3 S11: -0.0007 S12: 0.4361 S13: 0.2123 REMARK 3 S21: -0.5279 S22: 0.0067 S23: -0.3573 REMARK 3 S31: -0.3710 S32: 0.1812 S33: -0.0252 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 111 THROUGH 307 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.6708 -41.2086 -27.2109 REMARK 3 T TENSOR REMARK 3 T11: 0.4110 T22: 0.3001 REMARK 3 T33: 0.2035 T12: 0.0687 REMARK 3 T13: 0.0009 T23: 0.0075 REMARK 3 L TENSOR REMARK 3 L11: 0.7159 L22: 0.8096 REMARK 3 L33: 0.9397 L12: -0.2980 REMARK 3 L13: -0.0066 L23: 0.0614 REMARK 3 S TENSOR REMARK 3 S11: 0.1510 S12: 0.1806 S13: -0.0113 REMARK 3 S21: -0.2615 S22: -0.1423 S23: -0.0150 REMARK 3 S31: -0.0344 S32: 0.0362 S33: -0.0001 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 308 THROUGH 342 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.7385 -24.8569 -9.7508 REMARK 3 T TENSOR REMARK 3 T11: 0.4032 T22: 0.2715 REMARK 3 T33: 0.3069 T12: -0.0369 REMARK 3 T13: 0.0275 T23: 0.0074 REMARK 3 L TENSOR REMARK 3 L11: 1.9245 L22: 0.9015 REMARK 3 L33: 1.3795 L12: -0.3770 REMARK 3 L13: -0.0126 L23: 0.2891 REMARK 3 S TENSOR REMARK 3 S11: 0.0386 S12: -0.1052 S13: 0.3639 REMARK 3 S21: -0.0830 S22: -0.0490 S23: -0.1648 REMARK 3 S31: -0.3040 S32: 0.2005 S33: -0.0319 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 343 THROUGH 363 ) REMARK 3 ORIGIN FOR THE GROUP (A): -31.8225 -23.1058 -22.4698 REMARK 3 T TENSOR REMARK 3 T11: 0.4468 T22: 0.2974 REMARK 3 T33: 0.2661 T12: 0.0994 REMARK 3 T13: 0.0049 T23: 0.0456 REMARK 3 L TENSOR REMARK 3 L11: 4.0878 L22: 2.1576 REMARK 3 L33: 7.6050 L12: 1.6873 REMARK 3 L13: -0.4178 L23: -3.4756 REMARK 3 S TENSOR REMARK 3 S11: 0.1584 S12: 0.4915 S13: 0.4961 REMARK 3 S21: -0.0056 S22: 0.0205 S23: 0.4595 REMARK 3 S31: -0.3406 S32: -0.5108 S33: -0.1093 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 28 THROUGH 97 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.9785 -57.3998 6.8132 REMARK 3 T TENSOR REMARK 3 T11: 0.2751 T22: 0.2877 REMARK 3 T33: 0.2188 T12: 0.0230 REMARK 3 T13: -0.0337 T23: 0.0527 REMARK 3 L TENSOR REMARK 3 L11: 2.0517 L22: 3.0219 REMARK 3 L33: 4.0672 L12: -0.5779 REMARK 3 L13: -0.3930 L23: 1.7819 REMARK 3 S TENSOR REMARK 3 S11: 0.1242 S12: -0.0862 S13: -0.2271 REMARK 3 S21: -0.1242 S22: 0.0636 S23: -0.1266 REMARK 3 S31: 0.4051 S32: 0.2974 S33: -0.1835 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 98 THROUGH 364 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.6254 -44.4683 -12.6604 REMARK 3 T TENSOR REMARK 3 T11: 0.2647 T22: 0.3383 REMARK 3 T33: 0.2241 T12: 0.0213 REMARK 3 T13: 0.0341 T23: 0.0135 REMARK 3 L TENSOR REMARK 3 L11: 0.6971 L22: 0.7204 REMARK 3 L33: 1.3328 L12: -0.1217 REMARK 3 L13: 0.1409 L23: -0.0339 REMARK 3 S TENSOR REMARK 3 S11: 0.1180 S12: 0.0893 S13: 0.0661 REMARK 3 S21: -0.1548 S22: -0.0720 S23: -0.1609 REMARK 3 S31: -0.0059 S32: 0.3842 S33: -0.0423 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 7A6T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1292110948. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-OCT-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 PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 120759 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 46.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.08 REMARK 200 R MERGE (I) : 0.16200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.4700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.66 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 10.07 REMARK 200 R MERGE FOR SHELL (I) : 3.61500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.550 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: 6XXJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.11 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 106.66467 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 53.33233 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 53.33233 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 106.66467 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: 32970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 39650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 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 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 B1861 LIES ON A SPECIAL POSITION. REMARK 375 HOH B1870 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 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 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 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 GLN B 89 REMARK 465 SER B 90 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 SER A 78 OG REMARK 470 GLN A 79 CG CD OE1 NE2 REMARK 470 GLU A 81 CG CD OE1 OE2 REMARK 470 ASP A 82 CG OD1 OD2 REMARK 470 LYS A 200 CE NZ REMARK 470 LYS A 274 CG CD CE NZ REMARK 470 LYS B 251 CG CD CE NZ REMARK 470 HIS B 364 CG ND1 CD2 CE1 NE2 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 1.46 REMARK 500 O HOH B 1712 O HOH B 1854 2.04 REMARK 500 O HOH A 663 O HOH A 691 2.08 REMARK 500 OE1 GLU B 137 O HOH B 1701 2.12 REMARK 500 O HOH B 1759 O HOH B 1774 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLY A 284 C VAL A 285 N -0.191 REMARK 500 VAL A 285 CA VAL A 285 C 0.157 REMARK 500 VAL B 40 CB VAL B 40 CG1 -0.238 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 ASP A 243 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 VAL B 40 CA - CB - CG1 ANGL. DEV. = -17.4 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 -138.26 50.10 REMARK 500 SER A 233 77.62 -160.91 REMARK 500 ALA A 235 51.63 -102.81 REMARK 500 ASN A 252 79.84 -153.34 REMARK 500 THR A 354 -93.60 -127.67 REMARK 500 PHE A 362 26.07 -76.59 REMARK 500 PHE B 54 -132.62 45.11 REMARK 500 SER B 233 79.78 -162.52 REMARK 500 ALA B 235 54.73 -99.29 REMARK 500 THR B 354 -93.93 -128.89 REMARK 500 REMARK 500 REMARK: NULL DBREF 7A6T A 1 369 UNP P49366 DHYS_HUMAN 1 369 DBREF 7A6T B 1 369 UNP P49366 DHYS_HUMAN 1 369 SEQADV 7A6T SER A 173 UNP P49366 ASN 173 ENGINEERED MUTATION SEQADV 7A6T SER B 173 UNP P49366 ASN 173 ENGINEERED MUTATION 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 SER 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 SER 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 CYS 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 7A6T CSS A 177 CYS MODIFIED RESIDUE MODRES 7A6T CSS B 177 CYS MODIFIED RESIDUE HET CSS A 177 10 HET CSS B 177 10 HET NAD A 401 70 HET SPD A 402 29 HET EDO A 403 10 HET EDO A 404 10 HET EDO A 405 10 HET BME A 406 10 HET EDO A 407 10 HET EDO A 408 10 HET NAD B1601 70 HET SPD B1602 29 HET OXM B1603 8 HET EDO B1604 10 HETNAM CSS S-MERCAPTOCYSTEINE HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM SPD SPERMIDINE HETNAM EDO 1,2-ETHANEDIOL HETNAM BME BETA-MERCAPTOETHANOL HETNAM OXM OXAMIC ACID HETSYN SPD N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34) HETSYN EDO ETHYLENE GLYCOL FORMUL 1 CSS 2(C3 H7 N O2 S2) FORMUL 3 NAD 2(C21 H27 N7 O14 P2) FORMUL 4 SPD 2(C7 H19 N3) FORMUL 5 EDO 6(C2 H6 O2) FORMUL 8 BME C2 H6 O S FORMUL 13 OXM C2 H3 N O3 FORMUL 15 HOH *380(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 ASP A 80 GLN A 89 1 10 HELIX 6 AA6 SER A 105 SER A 110 1 6 HELIX 7 AA7 GLY A 111 HIS A 122 1 12 HELIX 8 AA8 THR A 131 LYS A 141 1 11 HELIX 9 AA9 ARG A 154 ASN A 161 1 8 HELIX 10 AB1 SER A 173 GLU A 197 1 25 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 283 MET A 296 1 14 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 359 5 5 HELIX 20 AC2 ASP B 35 GLY B 39 5 5 HELIX 21 AC3 ASN B 41 ALA B 48 1 8 HELIX 22 AC4 PHE B 49 THR B 52 5 4 HELIX 23 AC5 GLY B 53 GLU B 75 1 23 HELIX 24 AC6 THR B 104 SER B 110 1 7 HELIX 25 AC7 GLY B 111 HIS B 122 1 12 HELIX 26 AC8 ALA B 132 LYS B 141 1 10 HELIX 27 AC9 ARG B 154 ASN B 161 1 8 HELIX 28 AD1 SER B 173 GLY B 198 1 26 HELIX 29 AD2 THR B 202 ASN B 215 1 14 HELIX 30 AD3 SER B 219 ASN B 227 1 9 HELIX 31 AD4 GLY B 239 ASN B 252 1 14 HELIX 32 AD5 ILE B 259 PHE B 272 1 14 HELIX 33 AD6 GLY B 283 MET B 296 1 14 HELIX 34 AD7 GLN B 310 GLY B 314 5 5 HELIX 35 AD8 ARG B 320 GLY B 328 1 9 HELIX 36 AD9 ASP B 342 THR B 354 1 13 HELIX 37 AE1 PHE B 355 MET B 363 5 9 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 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 2.09 SSBOND 2 CYS B 97 CYS B 275 1555 1555 2.12 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 TYR B 176 N CSS B 177 1555 1555 1.33 LINK C CSS B 177 N LYS B 178 1555 1555 1.33 CRYST1 105.032 105.032 159.997 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 0.009521 0.005497 0.000000 0.00000 SCALE2 0.000000 0.010994 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006250 0.00000