HEADER LIGASE 25-FEB-20 6Y5P TITLE RING-DTC DOMAIN OF DELTEX1 BOUND TO NAD COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE DTX1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PROTEIN DELTEX-1,HDTX1,RING-TYPE E3 UBIQUITIN TRANSFERASE COMPND 5 DTX1; COMPND 6 EC: 2.3.2.27; COMPND 7 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: DTX1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS UBIQUITINATION, E3 RING LIGASE, NAD BINDING, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR M.GABRIELSEN,L.BUETOW,D.T.HUANG REVDAT 2 24-JAN-24 6Y5P 1 REMARK REVDAT 1 30-SEP-20 6Y5P 0 JRNL AUTH C.CHATRIN,M.GABRIELSEN,L.BUETOW,M.A.NAKASONE,S.F.AHMED, JRNL AUTH 2 D.SUMPTON,G.J.SIBBET,B.O.SMITH,D.T.HUANG JRNL TITL STRUCTURAL INSIGHTS INTO ADP-RIBOSYLATION OF UBIQUITIN BY JRNL TITL 2 DELTEX FAMILY E3 UBIQUITIN LIGASES. JRNL REF SCI ADV V. 6 2020 JRNL REFN ESSN 2375-2548 JRNL PMID 32948590 JRNL DOI 10.1126/SCIADV.ABC0418 REMARK 2 REMARK 2 RESOLUTION. 1.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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) : 1.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 65.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 148052 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.850 REMARK 3 FREE R VALUE TEST SET COUNT : 7180 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 65.4750 - 5.4052 1.00 4712 230 0.1938 0.2022 REMARK 3 2 5.4052 - 4.2905 1.00 4697 254 0.1426 0.1560 REMARK 3 3 4.2905 - 3.7483 1.00 4728 210 0.1450 0.1702 REMARK 3 4 3.7483 - 3.4056 1.00 4691 239 0.1640 0.1991 REMARK 3 5 3.4056 - 3.1615 1.00 4669 249 0.1613 0.2195 REMARK 3 6 3.1615 - 2.9751 1.00 4726 247 0.1727 0.1870 REMARK 3 7 2.9751 - 2.8261 1.00 4670 258 0.1745 0.2347 REMARK 3 8 2.8261 - 2.7031 1.00 4735 210 0.1759 0.2274 REMARK 3 9 2.7031 - 2.5990 1.00 4734 219 0.1734 0.1823 REMARK 3 10 2.5990 - 2.5093 1.00 4673 268 0.1789 0.2150 REMARK 3 11 2.5093 - 2.4309 1.00 4710 256 0.1862 0.2384 REMARK 3 12 2.4309 - 2.3614 1.00 4642 277 0.1889 0.2071 REMARK 3 13 2.3614 - 2.2992 1.00 4682 231 0.1945 0.2244 REMARK 3 14 2.2992 - 2.2431 1.00 4702 262 0.1937 0.2597 REMARK 3 15 2.2431 - 2.1921 1.00 4757 211 0.2070 0.2479 REMARK 3 16 2.1921 - 2.1454 1.00 4640 234 0.2051 0.2396 REMARK 3 17 2.1454 - 2.1025 1.00 4749 208 0.2011 0.2306 REMARK 3 18 2.1025 - 2.0629 1.00 4685 255 0.2109 0.2413 REMARK 3 19 2.0629 - 2.0260 1.00 4677 231 0.2124 0.2252 REMARK 3 20 2.0260 - 1.9917 1.00 4742 258 0.2205 0.2461 REMARK 3 21 1.9917 - 1.9595 1.00 4658 210 0.2379 0.2139 REMARK 3 22 1.9595 - 1.9294 1.00 4707 230 0.2433 0.2573 REMARK 3 23 1.9294 - 1.9010 1.00 4729 202 0.2605 0.2573 REMARK 3 24 1.9010 - 1.8742 1.00 4722 271 0.2765 0.3002 REMARK 3 25 1.8742 - 1.8489 1.00 4705 208 0.2914 0.3188 REMARK 3 26 1.8489 - 1.8249 1.00 4732 257 0.3008 0.2978 REMARK 3 27 1.8249 - 1.8021 1.00 4622 234 0.3073 0.3491 REMARK 3 28 1.8021 - 1.7804 1.00 4712 252 0.3133 0.3533 REMARK 3 29 1.7804 - 1.7597 0.99 4613 239 0.3248 0.3368 REMARK 3 30 1.7597 - 1.7400 0.98 4651 270 0.3412 0.3270 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.030 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.46 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 : 0.010 3812 REMARK 3 ANGLE : 1.103 5170 REMARK 3 CHIRALITY : 0.059 554 REMARK 3 PLANARITY : 0.008 665 REMARK 3 DIHEDRAL : 12.613 2244 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 72.0985 47.5040 11.2288 REMARK 3 T TENSOR REMARK 3 T11: 0.1985 T22: 0.1852 REMARK 3 T33: 0.1924 T12: 0.0027 REMARK 3 T13: 0.0072 T23: 0.0152 REMARK 3 L TENSOR REMARK 3 L11: 0.7301 L22: 0.2459 REMARK 3 L33: 0.8802 L12: 0.1556 REMARK 3 L13: -0.3682 L23: -0.2222 REMARK 3 S TENSOR REMARK 3 S11: -0.0918 S12: -0.0264 S13: -0.1477 REMARK 3 S21: -0.0927 S22: 0.0374 S23: -0.0606 REMARK 3 S31: 0.2148 S32: 0.0144 S33: 0.0433 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN A AND (RESID 388 THROUGH 535 OR REMARK 3 RESID 537 THROUGH 598 OR RESID 600 REMARK 3 THROUGH 615)) REMARK 3 SELECTION : (CHAIN B AND (RESID 388 THROUGH 535 OR REMARK 3 RESID 537 THROUGH 598 OR RESID 600 REMARK 3 THROUGH 615)) REMARK 3 ATOM PAIRS NUMBER : 2675 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6Y5P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1292106961. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-SEP-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91587 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 148052 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.740 REMARK 200 RESOLUTION RANGE LOW (A) : 66.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.74 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 1.33400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 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: 6Y5N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.16M CALCIUM ACETATE HYDRATE, REMARK 280 0.08MSODIUM CACODYLATE PH 6.5, 14.4% W/V PEG 8000, 20% V/V REMARK 280 GLYCEROL, PH 7.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K 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 33.42500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.47450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.62700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 65.47450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.42500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.62700 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 386 REMARK 465 SER A 387 REMARK 465 ALA A 616 REMARK 465 ALA A 617 REMARK 465 ALA A 618 REMARK 465 LYS A 619 REMARK 465 ALA A 620 REMARK 465 GLY B 386 REMARK 465 SER B 387 REMARK 465 ALA B 617 REMARK 465 ALA B 618 REMARK 465 LYS B 619 REMARK 465 ALA B 620 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 B 921 O HOH B 939 1.84 REMARK 500 O HOH A 993 O HOH A 1001 1.96 REMARK 500 O HOH B 932 O HOH B 945 1.97 REMARK 500 O HOH A 989 O HOH A 1017 2.00 REMARK 500 O HOH A 1021 O HOH B 941 2.01 REMARK 500 O HOH A 844 O HOH A 946 2.01 REMARK 500 O HOH B 924 O HOH B 925 2.05 REMARK 500 O HOH B 949 O HOH B 953 2.06 REMARK 500 O HOH A 825 O HOH A 964 2.07 REMARK 500 O HOH A 983 O HOH A 1034 2.07 REMARK 500 OE1 GLN B 611 O HOH B 801 2.08 REMARK 500 O HOH A 1005 O HOH A 1027 2.12 REMARK 500 O HOH A 954 O HOH A 992 2.13 REMARK 500 OE2 GLU B 556 O HOH B 802 2.17 REMARK 500 O2 EDO A 705 O HOH A 801 2.19 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 OD2 ASP B 501 H71N NAD B 701 4565 1.43 REMARK 500 OD2 ASP B 501 H72N NAD B 701 4565 1.60 REMARK 500 O HOH A 1023 O HOH B 876 4465 2.10 REMARK 500 O HOH A 1015 O HOH B 861 4465 2.11 REMARK 500 OD2 ASP B 501 C7N NAD B 701 4565 2.12 REMARK 500 O HOH A 813 O HOH A 966 4465 2.13 REMARK 500 O HOH B 933 O HOH B 942 4465 2.15 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 CYS B 411 CA - CB - SG ANGL. DEV. = 7.7 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 ASN A 578 -137.35 -90.44 REMARK 500 ASP A 597 95.13 -160.90 REMARK 500 HIS B 430 -74.37 -54.63 REMARK 500 ASN B 578 -131.96 -94.49 REMARK 500 ASP B 597 96.35 -160.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 708 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 411 SG REMARK 620 2 CYS A 414 SG 114.2 REMARK 620 3 HIS A 449 ND1 103.8 102.5 REMARK 620 4 CYS A 452 SG 120.3 100.9 114.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 709 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 444 SG REMARK 620 2 HIS A 446 ND1 104.6 REMARK 620 3 CYS A 468 SG 114.7 106.6 REMARK 620 4 CYS A 471 SG 107.3 114.6 109.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 705 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 411 SG REMARK 620 2 CYS B 414 SG 109.1 REMARK 620 3 HIS B 449 ND1 90.1 104.2 REMARK 620 4 CYS B 452 SG 121.7 106.7 123.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 704 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 444 SG REMARK 620 2 HIS B 446 ND1 100.5 REMARK 620 3 CYS B 468 SG 108.4 108.9 REMARK 620 4 CYS B 471 SG 115.2 113.1 110.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 706 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 707 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 708 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 709 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide NAD B 701 and ASP B REMARK 800 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6Y5N RELATED DB: PDB REMARK 900 APO STRUCTURE DBREF 6Y5P A 388 620 UNP Q86Y01 DTX1_HUMAN 388 620 DBREF 6Y5P B 388 620 UNP Q86Y01 DTX1_HUMAN 388 620 SEQADV 6Y5P GLY A 386 UNP Q86Y01 EXPRESSION TAG SEQADV 6Y5P SER A 387 UNP Q86Y01 EXPRESSION TAG SEQADV 6Y5P GLY B 386 UNP Q86Y01 EXPRESSION TAG SEQADV 6Y5P SER B 387 UNP Q86Y01 EXPRESSION TAG SEQRES 1 A 235 GLY SER LYS SER LYS ASN PRO GLU ASP VAL VAL ARG ARG SEQRES 2 A 235 TYR MET GLN LYS VAL LYS ASN PRO PRO ASP GLU ASP CYS SEQRES 3 A 235 THR ILE CYS MET GLU ARG LEU VAL THR ALA SER GLY TYR SEQRES 4 A 235 GLU GLY VAL LEU ARG HIS LYS GLY VAL ARG PRO GLU LEU SEQRES 5 A 235 VAL GLY ARG LEU GLY ARG CYS GLY HIS MET TYR HIS LEU SEQRES 6 A 235 LEU CYS LEU VAL ALA MET TYR SER ASN GLY ASN LYS ASP SEQRES 7 A 235 GLY SER LEU GLN CYS PRO THR CYS LYS ALA ILE TYR GLY SEQRES 8 A 235 GLU LYS THR GLY THR GLN PRO PRO GLY LYS MET GLU PHE SEQRES 9 A 235 HIS LEU ILE PRO HIS SER LEU PRO GLY PHE PRO ASP THR SEQRES 10 A 235 GLN THR ILE ARG ILE VAL TYR ASP ILE PRO THR GLY ILE SEQRES 11 A 235 GLN GLY PRO GLU HIS PRO ASN PRO GLY LYS LYS PHE THR SEQRES 12 A 235 ALA ARG GLY PHE PRO ARG HIS CYS TYR LEU PRO ASN ASN SEQRES 13 A 235 GLU LYS GLY ARG LYS VAL LEU ARG LEU LEU ILE THR ALA SEQRES 14 A 235 TRP GLU ARG ARG LEU ILE PHE THR ILE GLY THR SER ASN SEQRES 15 A 235 THR THR GLY GLU SER ASP THR VAL VAL TRP ASN GLU ILE SEQRES 16 A 235 HIS HIS LYS THR GLU PHE GLY SER ASN LEU THR GLY HIS SEQRES 17 A 235 GLY TYR PRO ASP ALA SER TYR LEU ASP ASN VAL LEU ALA SEQRES 18 A 235 GLU LEU THR ALA GLN GLY VAL SER GLU ALA ALA ALA LYS SEQRES 19 A 235 ALA SEQRES 1 B 235 GLY SER LYS SER LYS ASN PRO GLU ASP VAL VAL ARG ARG SEQRES 2 B 235 TYR MET GLN LYS VAL LYS ASN PRO PRO ASP GLU ASP CYS SEQRES 3 B 235 THR ILE CYS MET GLU ARG LEU VAL THR ALA SER GLY TYR SEQRES 4 B 235 GLU GLY VAL LEU ARG HIS LYS GLY VAL ARG PRO GLU LEU SEQRES 5 B 235 VAL GLY ARG LEU GLY ARG CYS GLY HIS MET TYR HIS LEU SEQRES 6 B 235 LEU CYS LEU VAL ALA MET TYR SER ASN GLY ASN LYS ASP SEQRES 7 B 235 GLY SER LEU GLN CYS PRO THR CYS LYS ALA ILE TYR GLY SEQRES 8 B 235 GLU LYS THR GLY THR GLN PRO PRO GLY LYS MET GLU PHE SEQRES 9 B 235 HIS LEU ILE PRO HIS SER LEU PRO GLY PHE PRO ASP THR SEQRES 10 B 235 GLN THR ILE ARG ILE VAL TYR ASP ILE PRO THR GLY ILE SEQRES 11 B 235 GLN GLY PRO GLU HIS PRO ASN PRO GLY LYS LYS PHE THR SEQRES 12 B 235 ALA ARG GLY PHE PRO ARG HIS CYS TYR LEU PRO ASN ASN SEQRES 13 B 235 GLU LYS GLY ARG LYS VAL LEU ARG LEU LEU ILE THR ALA SEQRES 14 B 235 TRP GLU ARG ARG LEU ILE PHE THR ILE GLY THR SER ASN SEQRES 15 B 235 THR THR GLY GLU SER ASP THR VAL VAL TRP ASN GLU ILE SEQRES 16 B 235 HIS HIS LYS THR GLU PHE GLY SER ASN LEU THR GLY HIS SEQRES 17 B 235 GLY TYR PRO ASP ALA SER TYR LEU ASP ASN VAL LEU ALA SEQRES 18 B 235 GLU LEU THR ALA GLN GLY VAL SER GLU ALA ALA ALA LYS SEQRES 19 B 235 ALA HET NAD A 701 70 HET EDO A 702 10 HET EDO A 703 10 HET EDO A 704 10 HET EDO A 705 10 HET EDO A 706 10 HET EDO A 707 10 HET ZN A 708 1 HET ZN A 709 1 HET NAD B 701 70 HET EDO B 702 10 HET EDO B 703 10 HET ZN B 704 1 HET ZN B 705 1 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM EDO 1,2-ETHANEDIOL HETNAM ZN ZINC ION HETSYN EDO ETHYLENE GLYCOL FORMUL 3 NAD 2(C21 H27 N7 O14 P2) FORMUL 4 EDO 8(C2 H6 O2) FORMUL 10 ZN 4(ZN 2+) FORMUL 17 HOH *420(H2 O) HELIX 1 AA1 ASN A 391 TYR A 399 1 9 HELIX 2 AA2 GLY A 426 HIS A 430 5 5 HELIX 3 AA3 LEU A 450 ASN A 459 1 10 HELIX 4 AA4 ASN A 541 ARG A 557 1 17 HELIX 5 AA5 SER A 599 GLN A 611 1 13 HELIX 6 AA6 ASN B 391 TYR B 399 1 9 HELIX 7 AA7 GLY B 426 HIS B 430 5 5 HELIX 8 AA8 LEU B 450 ASN B 459 1 10 HELIX 9 AA9 ASN B 541 ARG B 557 1 17 HELIX 10 AB1 SER B 599 GLN B 611 1 13 SHEET 1 AA1 3 MET A 400 LYS A 402 0 SHEET 2 AA1 3 VAL A 438 LEU A 441 -1 O ARG A 440 N GLN A 401 SHEET 3 AA1 3 HIS A 446 HIS A 449 -1 O HIS A 446 N LEU A 441 SHEET 1 AA2 2 LEU A 466 GLN A 467 0 SHEET 2 AA2 2 ILE A 474 TYR A 475 -1 O TYR A 475 N LEU A 466 SHEET 1 AA3 3 LYS A 486 ILE A 492 0 SHEET 2 AA3 3 THR A 504 ASP A 510 -1 O VAL A 508 N GLU A 488 SHEET 3 AA3 3 ARG A 534 PRO A 539 -1 O LEU A 538 N ILE A 505 SHEET 1 AA4 2 GLY A 514 ILE A 515 0 SHEET 2 AA4 2 LYS A 526 PHE A 527 -1 O PHE A 527 N GLY A 514 SHEET 1 AA5 2 PHE A 561 GLY A 564 0 SHEET 2 AA5 2 THR A 574 TRP A 577 -1 O VAL A 576 N THR A 562 SHEET 1 AA6 3 MET B 400 LYS B 402 0 SHEET 2 AA6 3 VAL B 438 LEU B 441 -1 O ARG B 440 N GLN B 401 SHEET 3 AA6 3 MET B 447 HIS B 449 -1 O TYR B 448 N GLY B 439 SHEET 1 AA7 2 LEU B 466 GLN B 467 0 SHEET 2 AA7 2 ILE B 474 TYR B 475 -1 O TYR B 475 N LEU B 466 SHEET 1 AA8 3 LYS B 486 ILE B 492 0 SHEET 2 AA8 3 THR B 504 ASP B 510 -1 O ARG B 506 N HIS B 490 SHEET 3 AA8 3 ARG B 534 PRO B 539 -1 O LEU B 538 N ILE B 505 SHEET 1 AA9 2 GLY B 514 ILE B 515 0 SHEET 2 AA9 2 LYS B 526 PHE B 527 -1 O PHE B 527 N GLY B 514 SHEET 1 AB1 2 PHE B 561 GLY B 564 0 SHEET 2 AB1 2 THR B 574 TRP B 577 -1 O THR B 574 N GLY B 564 LINK OD2 ASP B 501 N7N NAD B 701 1555 4565 1.30 LINK SG CYS A 411 ZN ZN A 708 1555 1555 2.30 LINK SG CYS A 414 ZN ZN A 708 1555 1555 2.34 LINK SG CYS A 444 ZN ZN A 709 1555 1555 2.27 LINK ND1 HIS A 446 ZN ZN A 709 1555 1555 1.96 LINK ND1 HIS A 449 ZN ZN A 708 1555 1555 2.03 LINK SG CYS A 452 ZN ZN A 708 1555 1555 2.30 LINK SG CYS A 468 ZN ZN A 709 1555 1555 2.32 LINK SG CYS A 471 ZN ZN A 709 1555 1555 2.36 LINK SG CYS B 411 ZN ZN B 705 1555 1555 1.99 LINK SG CYS B 414 ZN ZN B 705 1555 1555 2.40 LINK SG CYS B 444 ZN ZN B 704 1555 1555 2.31 LINK ND1 HIS B 446 ZN ZN B 704 1555 1555 2.05 LINK ND1 HIS B 449 ZN ZN B 705 1555 1555 2.25 LINK SG CYS B 452 ZN ZN B 705 1555 1555 2.33 LINK SG CYS B 468 ZN ZN B 704 1555 1555 2.37 LINK SG CYS B 471 ZN ZN B 704 1555 1555 2.15 CISPEP 1 PHE A 532 PRO A 533 0 -0.11 CISPEP 2 TYR A 595 PRO A 596 0 1.74 CISPEP 3 PHE B 532 PRO B 533 0 1.77 CISPEP 4 TYR B 595 PRO B 596 0 4.47 SITE 1 AC1 20 ARG A 530 GLY A 531 ARG A 534 SER A 566 SITE 2 AC1 20 ASN A 567 THR A 568 THR A 569 VAL A 576 SITE 3 AC1 20 TRP A 577 HIS A 581 HIS A 582 THR A 584 SITE 4 AC1 20 HIS A 593 HOH A 803 HOH A 817 HOH A 819 SITE 5 AC1 20 HOH A 863 HOH A 917 HOH A 947 HOH A 968 SITE 1 AC2 2 GLU A 416 LYS A 525 SITE 1 AC3 5 VAL A 403 LYS A 404 GLU A 436 LEU A 437 SITE 2 AC3 5 VAL A 438 SITE 1 AC4 3 GLY A 476 ASP A 501 HOH A 901 SITE 1 AC5 2 ILE A 492 HOH A 801 SITE 1 AC6 5 CYS A 414 GLY A 423 LYS A 525 HOH A 802 SITE 2 AC6 5 SER B 588 SITE 1 AC7 8 ASP A 410 CYS A 411 THR A 412 HIS A 446 SITE 2 AC7 8 MET A 447 TYR A 448 THR A 470 HOH A 826 SITE 1 AC8 4 CYS A 411 CYS A 414 HIS A 449 CYS A 452 SITE 1 AC9 4 CYS A 444 HIS A 446 CYS A 468 CYS A 471 SITE 1 AD1 3 LYS A 431 MET B 487 HOH B 802 SITE 1 AD2 2 LEU B 466 GLN B 467 SITE 1 AD3 4 CYS B 444 HIS B 446 CYS B 468 CYS B 471 SITE 1 AD4 4 CYS B 411 CYS B 414 HIS B 449 CYS B 452 SITE 1 AD5 26 SER B 495 PHE B 499 PRO B 500 THR B 502 SITE 2 AD5 26 ARG B 530 GLY B 531 ARG B 534 THR B 565 SITE 3 AD5 26 SER B 566 ASN B 567 THR B 568 VAL B 576 SITE 4 AD5 26 TRP B 577 HIS B 581 HIS B 582 THR B 584 SITE 5 AD5 26 HIS B 593 HOH B 805 HOH B 806 HOH B 811 SITE 6 AD5 26 HOH B 826 HOH B 838 HOH B 863 HOH B 868 SITE 7 AD5 26 HOH B 873 HOH B 883 CRYST1 66.850 85.254 130.949 90.00 90.00 90.00 P 21 21 21 8 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 0.014959 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011730 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007637 0.00000