HEADER DNA BINDING PROTEIN 29-JUL-22 8AK4 TITLE STRUCTURE OF THE C-TERMINALLY TRUNCATED NAD+-DEPENDENT DNA LIGASE FROM TITLE 2 THE POLY-EXTREMOPHILE DEINOCOCCUS RADIODURANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA LIGASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POLYDEOXYRIBONUCLEOTIDE SYNTHASE [NAD(+)]; COMPND 5 EC: 6.5.1.2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DEINOCOCCUS RADIODURANS; SOURCE 3 ORGANISM_TAXID: 1299; SOURCE 4 STRAIN: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / SOURCE 5 NCIMB 9279 / R1 / VKM B-1422; SOURCE 6 ATCC: 13939; SOURCE 7 GENE: LIGA, DR_2069; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 10 EXPRESSION_SYSTEM_VARIANT: DE3*; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PDEST14 KEYWDS DNA LIGASE A, BRCT, DNA NICK-JOINING, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.FERNANDES,A.K.WILLIAMSON,P.M.MATIAS,E.MOE REVDAT 1 27-SEP-23 8AK4 0 JRNL AUTH A.FERNANDES,A.WILLIAMSON,P.M.MATIAS,E.MOE JRNL TITL STRUCTURE/FUNCTION STUDIES OF THE NAD + -DEPENDENT DNA JRNL TITL 2 LIGASE FROM THE POLY-EXTREMOPHILE DEINOCOCCUS RADIODURANS JRNL TITL 3 REVEAL IMPORTANCE OF THE BRCT DOMAIN FOR DNA BINDING. JRNL REF EXTREMOPHILES V. 27 26 2023 JRNL REFN ESSN 1433-4909 JRNL PMID 37712998 JRNL DOI 10.1007/S00792-023-01309-Z REMARK 2 REMARK 2 RESOLUTION. 3.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 74.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 67.0 REMARK 3 NUMBER OF REFLECTIONS : 7813 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 393 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 74.9700 - 4.8500 0.89 3406 186 0.1932 0.2547 REMARK 3 2 4.8500 - 3.9100 0.89 2909 163 0.2380 0.2873 REMARK 3 3 3.8400 - 3.3600 0.31 1105 44 0.3030 0.4556 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) : 0.501 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.451 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 110.0 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 103.6 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 : 0.002 4002 REMARK 3 ANGLE : 0.487 5433 REMARK 3 CHIRALITY : 0.039 611 REMARK 3 PLANARITY : 0.004 722 REMARK 3 DIHEDRAL : 12.216 1486 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 81 THROUGH 328 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.4830 31.8330 30.6110 REMARK 3 T TENSOR REMARK 3 T11: 0.8172 T22: 0.7352 REMARK 3 T33: 0.7428 T12: 0.0588 REMARK 3 T13: -0.1296 T23: 0.0406 REMARK 3 L TENSOR REMARK 3 L11: 2.1499 L22: 3.6304 REMARK 3 L33: 1.4686 L12: 1.5490 REMARK 3 L13: -1.0791 L23: -0.1069 REMARK 3 S TENSOR REMARK 3 S11: -0.0192 S12: 0.3491 S13: 0.2256 REMARK 3 S21: -0.1217 S22: 0.0385 S23: 0.3424 REMARK 3 S31: -0.1680 S32: 0.1866 S33: 0.0147 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 329 THROUGH 436 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.3744 19.2525 63.5110 REMARK 3 T TENSOR REMARK 3 T11: 0.9023 T22: 1.0204 REMARK 3 T33: 0.8395 T12: -0.2399 REMARK 3 T13: -0.1387 T23: 0.0748 REMARK 3 L TENSOR REMARK 3 L11: 1.1189 L22: 2.1589 REMARK 3 L33: 1.8928 L12: -0.1449 REMARK 3 L13: -0.7028 L23: -1.6936 REMARK 3 S TENSOR REMARK 3 S11: 0.0748 S12: 0.0561 S13: -0.1660 REMARK 3 S21: 0.1959 S22: -0.7091 S23: -0.3049 REMARK 3 S31: -0.3210 S32: 0.7328 S33: 0.5033 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 437 THROUGH 593 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.4526 -6.5443 60.6277 REMARK 3 T TENSOR REMARK 3 T11: 1.0036 T22: 0.6386 REMARK 3 T33: 0.6733 T12: 0.0110 REMARK 3 T13: -0.0828 T23: -0.0086 REMARK 3 L TENSOR REMARK 3 L11: 2.6099 L22: 4.3660 REMARK 3 L33: 2.6899 L12: 1.7133 REMARK 3 L13: -0.2990 L23: -0.8941 REMARK 3 S TENSOR REMARK 3 S11: 0.0443 S12: -0.0403 S13: -0.5550 REMARK 3 S21: -0.2905 S22: -0.1282 S23: -0.0123 REMARK 3 S31: 0.4855 S32: 0.1383 S33: 0.0330 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGEN ATOMS WERE ADDED IN CALCULATED REMARK 3 POSITIONS WITH THE PHENIX.READYSET TOOL. ISOTROPIC DISPLACEMENT REMARK 3 PARAMETERS (ADPS) WERE REFINED FOR ALL NON-HYDROGEN ATOMS. TLS REMARK 3 RIGID BODY REFINEMENT OF ANISOTROPIC ADPS WAS PERFORMED IN THE REMARK 3 FINAL REFINEMENT CYCLES USING THREE RIGID BODY GROUPS FOR THE REMARK 3 PROTEIN CHAIN, ESTIMATED BY PHENIX FROM A PRIOR FULLY ISOTROPIC REMARK 3 REFINEMENT. RELATIVE X-RAY/STEREOCHEMISTRY AND X-RAY/ADP WEIGHTS REMARK 3 WERE OPTIMIZED TO REDUCE THE GAP BETWEEN R-WORK AND R-FREE. REMARK 4 REMARK 4 8AK4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1292124670. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUL-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979260 REMARK 200 MONOCHROMATOR : CHANNELL-CUT SI (111) REMARK 200 OPTICS : KB FOCUSING MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC 1.0.5 (20200918) REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.7 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7848 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.360 REMARK 200 RESOLUTION RANGE LOW (A) : 149.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 67.1 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.21800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 15.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 1.55200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: FROM ALPHAFOLD2 REMARK 200 REMARK 200 REMARK: THIN PLATES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M MAGNESIUM ACETATE TETRAHYDRATE, REMARK 280 0.1 M SODIUM CACODYLATE PH 6.5, 20 % PEG 8000, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,-Y,-Z+1/2 REMARK 290 4555 -X+1/2,-Y,Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 35.42200 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 74.97100 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.42200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 74.97100 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ARG A 2 REMARK 465 TYR A 3 REMARK 465 PRO A 4 REMARK 465 GLY A 5 REMARK 465 ARG A 6 REMARK 465 MET A 7 REMARK 465 THR A 8 REMARK 465 ASP A 9 REMARK 465 ALA A 10 REMARK 465 PRO A 11 REMARK 465 PRO A 12 REMARK 465 ASP A 13 REMARK 465 PRO A 14 REMARK 465 ARG A 15 REMARK 465 ALA A 16 REMARK 465 ARG A 17 REMARK 465 TYR A 18 REMARK 465 LEU A 19 REMARK 465 ALA A 20 REMARK 465 LEU A 21 REMARK 465 ARG A 22 REMARK 465 ASP A 23 REMARK 465 GLU A 24 REMARK 465 VAL A 25 REMARK 465 ALA A 26 REMARK 465 LEU A 27 REMARK 465 HIS A 28 REMARK 465 ASN A 29 REMARK 465 ARG A 30 REMARK 465 ALA A 31 REMARK 465 TYR A 32 REMARK 465 TYR A 33 REMARK 465 GLU A 34 REMARK 465 GLN A 35 REMARK 465 ASP A 36 REMARK 465 ALA A 37 REMARK 465 PRO A 38 REMARK 465 THR A 39 REMARK 465 ILE A 40 REMARK 465 PRO A 41 REMARK 465 ASP A 42 REMARK 465 ASP A 43 REMARK 465 GLU A 44 REMARK 465 TYR A 45 REMARK 465 ASP A 46 REMARK 465 ARG A 47 REMARK 465 LEU A 48 REMARK 465 ALA A 49 REMARK 465 ARG A 50 REMARK 465 GLU A 51 REMARK 465 LEU A 52 REMARK 465 ARG A 53 REMARK 465 GLU A 54 REMARK 465 LEU A 55 REMARK 465 GLU A 56 REMARK 465 ALA A 57 REMARK 465 ALA A 58 REMARK 465 HIS A 59 REMARK 465 PRO A 60 REMARK 465 GLU A 61 REMARK 465 PHE A 62 REMARK 465 ALA A 63 REMARK 465 ASP A 64 REMARK 465 ASP A 65 REMARK 465 HIS A 66 REMARK 465 SER A 67 REMARK 465 PRO A 68 REMARK 465 VAL A 69 REMARK 465 GLN A 70 REMARK 465 THR A 71 REMARK 465 VAL A 72 REMARK 465 GLY A 73 REMARK 465 GLY A 74 REMARK 465 ALA A 75 REMARK 465 PRO A 76 REMARK 465 SER A 77 REMARK 465 SER A 78 REMARK 465 ALA A 79 REMARK 465 PHE A 80 REMARK 465 ALA A 594 REMARK 465 GLU A 595 REMARK 465 GLU A 596 REMARK 465 VAL A 597 REMARK 465 THR A 598 REMARK 465 ARG A 599 REMARK 465 THR A 600 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 OD2 ASP A 97 OD2 ASP A 99 1.47 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 GLU A 126 -165.00 -100.42 REMARK 500 GLN A 144 -60.81 -105.70 REMARK 500 VAL A 158 56.07 -116.84 REMARK 500 PRO A 166 -86.59 -57.78 REMARK 500 PRO A 205 150.46 -49.09 REMARK 500 ASP A 289 49.68 -93.47 REMARK 500 ASP A 295 46.53 -102.15 REMARK 500 GLU A 308 34.10 -77.95 REMARK 500 GLU A 309 -44.18 -142.25 REMARK 500 THR A 313 -70.19 -74.84 REMARK 500 SER A 314 -51.49 -157.33 REMARK 500 GLU A 335 -75.81 -107.22 REMARK 500 GLU A 359 -74.60 57.73 REMARK 500 HIS A 369 -97.32 66.99 REMARK 500 VAL A 393 -73.53 -133.48 REMARK 500 MET A 398 -75.15 -108.96 REMARK 500 TYR A 435 -179.69 67.17 REMARK 500 PRO A 437 -96.24 -64.70 REMARK 500 ASN A 438 -150.47 -127.97 REMARK 500 ALA A 457 -101.83 -123.48 REMARK 500 ASP A 459 76.70 52.45 REMARK 500 HIS A 478 -63.05 -102.85 REMARK 500 ASP A 479 -165.37 -114.74 REMARK 500 LEU A 494 -141.07 -131.94 REMARK 500 HIS A 528 -31.05 67.20 REMARK 500 VAL A 529 95.75 -66.52 REMARK 500 PHE A 541 -55.02 -120.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN A 438 PRO A 439 -144.57 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 806 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 97 OD1 REMARK 620 2 ASP A 97 OD2 65.9 REMARK 620 3 ASP A 99 OD1 98.9 103.4 REMARK 620 4 ASP A 99 OD2 94.2 43.3 66.8 REMARK 620 5 ASP A 167 OD1 3.5 62.8 101.1 92.5 REMARK 620 6 ASP A 167 OD2 5.2 60.7 100.1 90.0 2.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 803 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 106 OE2 REMARK 620 2 ASP A 191 OD1 73.1 REMARK 620 3 ASP A 191 OD2 71.6 1.6 REMARK 620 4 HIS A 230 ND1 69.7 3.4 2.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 802 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 130 OD2 REMARK 620 2 ASP A 293 OD2 71.2 REMARK 620 3 ASP A 295 OD2 65.6 93.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 801 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 287 NE2 REMARK 620 2 ASP A 293 OD1 104.4 REMARK 620 3 ASP A 295 OD1 149.5 79.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 804 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 418 SG REMARK 620 2 CYS A 421 SG 87.1 REMARK 620 3 CYS A 436 SG 83.9 107.8 REMARK 620 4 CYS A 441 SG 104.4 143.5 107.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 805 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 423 NE2 REMARK 620 2 HIS A 423 NE2 0.0 REMARK 620 N 1 DBREF 8AK4 A 1 600 UNP Q9RSQ5 DNLJ_DEIRA 1 600 SEQRES 1 A 600 MET ARG TYR PRO GLY ARG MET THR ASP ALA PRO PRO ASP SEQRES 2 A 600 PRO ARG ALA ARG TYR LEU ALA LEU ARG ASP GLU VAL ALA SEQRES 3 A 600 LEU HIS ASN ARG ALA TYR TYR GLU GLN ASP ALA PRO THR SEQRES 4 A 600 ILE PRO ASP ASP GLU TYR ASP ARG LEU ALA ARG GLU LEU SEQRES 5 A 600 ARG GLU LEU GLU ALA ALA HIS PRO GLU PHE ALA ASP ASP SEQRES 6 A 600 HIS SER PRO VAL GLN THR VAL GLY GLY ALA PRO SER SER SEQRES 7 A 600 ALA PHE GLU PRO VAL THR HIS PRO THR GLN MET THR SER SEQRES 8 A 600 LEU ASP ASN VAL PHE ASP ASP ASP GLU LEU ARG ASP TRP SEQRES 9 A 600 GLN GLU LYS LEU ALA ARG SER LEU GLY LEU PRO LEU ASP SEQRES 10 A 600 THR ASP ASP PHE THR PHE THR GLY GLU LEU LYS ILE ASP SEQRES 11 A 600 GLY LEU SER VAL ASN LEU TYR TYR LEU ASP GLY GLU LEU SEQRES 12 A 600 GLN TRP ALA ALA THR ARG GLY ASN GLY ARG VAL GLY GLU SEQRES 13 A 600 ILE VAL THR ALA GLN VAL LEU THR ILE PRO ASP ILE PRO SEQRES 14 A 600 GLN LYS LEU GLU GLY LEU LYS GLY GLU LEU GLU VAL ARG SEQRES 15 A 600 GLY GLU VAL TYR LEU SER ARG ALA ASP PHE ALA ALA PHE SEQRES 16 A 600 ASN ALA GLN ALA GLU GLU LEU GLY THR PRO LEU LEU LYS SEQRES 17 A 600 ASN PRO ARG ASN GLY ALA ALA GLY ALA LEU ARG GLN LYS SEQRES 18 A 600 ASP PRO GLU VAL THR ARG THR ARG HIS LEU LYS ALA ILE SEQRES 19 A 600 LEU TYR ALA VAL GLY LYS ARG ASP GLY VAL PRO ALA ARG SEQRES 20 A 600 THR GLN TRP GLU VAL LEU GLU TRP LEU SER ALA GLN GLY SEQRES 21 A 600 PHE PRO THR SER ARG SER SER GLU HIS LEU ARG GLY ILE SEQRES 22 A 600 ALA ALA ALA ALA ASP TYR HIS ALA ARG MET ILE ARG ALA SEQRES 23 A 600 HIS ALA ASP PHE GLU PHE ASP ALA ASP GLY THR VAL LEU SEQRES 24 A 600 LYS LEU ASP SER LEU SER GLN GLN GLU GLU ALA GLY PHE SEQRES 25 A 600 THR SER ARG ALA PRO ARG TRP ALA ILE ALA TYR LYS PHE SEQRES 26 A 600 PRO VAL GLU GLU VAL GLU THR VAL LEU GLU SER ILE THR SEQRES 27 A 600 VAL ASN VAL GLY ARG THR GLY LYS LEU ALA PRO LEU ALA SEQRES 28 A 600 HIS LEU SER PRO ARG LEU ILE GLU GLY SER THR VAL SER SEQRES 29 A 600 LYS ALA THR LEU HIS ASN GLU ASP TYR ILE ARG ASP MET SEQRES 30 A 600 ASP LEU ARG VAL GLY ASP THR VAL LEU VAL ARG LYS SER SEQRES 31 A 600 GLY GLY VAL ILE PRO GLN ILE MET ARG VAL LEU PRO ASP SEQRES 32 A 600 LYS ARG PRO ALA ASP ALA ALA PRO PHE GLU PHE PRO THR SEQRES 33 A 600 HIS CYS PRO VAL CYS GLY HIS GLU ALA VAL ARG ALA GLU SEQRES 34 A 600 GLY ASP ALA ASN THR TYR CYS PRO ASN PRO ALA CYS PRO SEQRES 35 A 600 ALA GLN SER PHE GLU ARG ILE ARG TYR PHE VAL SER ARG SEQRES 36 A 600 GLY ALA MET ASP VAL ARG GLY ILE GLY GLU LYS LEU VAL SEQRES 37 A 600 THR GLN LEU LEU HIS GLU GLY LEU ILE HIS ASP ALA ALA SEQRES 38 A 600 GLY LEU TYR THR LEU SER ALA GLU GLN LEU ALA GLY LEU SEQRES 39 A 600 GLU ARG GLY GLY GLU LYS LYS ALA GLY ASN ILE LEU GLY SEQRES 40 A 600 GLN LEU GLU ALA SER LYS THR LYS PRO LEU TRP ARG LEU SEQRES 41 A 600 ILE ASN ALA LEU GLY MET SER HIS VAL GLY GLN ARG ASN SEQRES 42 A 600 ALA GLN ALA LEU ALA ARG ALA PHE GLY THR LEU GLU GLY SEQRES 43 A 600 LEU LEU ALA ALA THR PRO GLU GLN ILE GLU ALA VAL PRO SEQRES 44 A 600 GLY LEU GLY GLY ILE ILE ALA GLN SER VAL THR ALA SER SEQRES 45 A 600 LEU ALA ASP PRO ALA MET ARG ASP LEU ILE ALA ARG LEU SEQRES 46 A 600 GLN ALA SER GLY VAL ALA PRO GLN ALA GLU GLU VAL THR SEQRES 47 A 600 ARG THR HET MN A 801 1 HET MN A 802 1 HET ZN A 803 1 HET ZN A 804 1 HET ZN A 805 1 HET ZN A 806 1 HETNAM MN MANGANESE (II) ION HETNAM ZN ZINC ION FORMUL 2 MN 2(MN 2+) FORMUL 4 ZN 4(ZN 2+) HELIX 1 AA1 ASP A 97 LEU A 112 1 16 HELIX 2 AA2 VAL A 158 LEU A 163 1 6 HELIX 3 AA3 SER A 188 GLU A 201 1 14 HELIX 4 AA4 ASN A 209 ARG A 219 1 11 HELIX 5 AA5 ASP A 222 THR A 228 1 7 HELIX 6 AA6 THR A 248 GLN A 259 1 12 HELIX 7 AA7 GLY A 272 ARG A 285 1 14 HELIX 8 AA8 SER A 303 GLY A 311 1 9 HELIX 9 AA9 ASN A 370 ASP A 378 1 9 HELIX 10 AB1 GLY A 391 VAL A 393 5 3 HELIX 11 AB2 PRO A 402 ARG A 405 5 4 HELIX 12 AB3 CYS A 441 SER A 454 1 14 HELIX 13 AB4 GLY A 464 GLU A 474 1 11 HELIX 14 AB5 ALA A 480 THR A 485 1 6 HELIX 15 AB6 SER A 487 GLY A 493 1 7 HELIX 16 AB7 LEU A 494 GLY A 498 5 5 HELIX 17 AB8 GLU A 499 THR A 514 1 16 HELIX 18 AB9 LEU A 517 GLY A 525 1 9 HELIX 19 AC1 GLY A 530 GLY A 542 1 13 HELIX 20 AC2 THR A 543 ALA A 549 1 7 HELIX 21 AC3 THR A 551 ALA A 557 1 7 HELIX 22 AC4 ILE A 564 ALA A 574 1 11 HELIX 23 AC5 ASP A 575 GLY A 589 1 15 SHEET 1 AA1 2 PRO A 82 THR A 84 0 SHEET 2 AA1 2 VAL A 154 GLU A 156 -1 O GLY A 155 N VAL A 83 SHEET 1 AA2 5 ASP A 93 VAL A 95 0 SHEET 2 AA2 5 ALA A 320 TYR A 323 1 O ALA A 322 N VAL A 95 SHEET 3 AA2 5 ALA A 294 LEU A 301 -1 N THR A 297 O TYR A 323 SHEET 4 AA2 5 THR A 122 ILE A 129 -1 N THR A 124 O LYS A 300 SHEET 5 AA2 5 GLU A 268 ARG A 271 -1 O LEU A 270 N PHE A 123 SHEET 1 AA3 4 GLU A 142 THR A 148 0 SHEET 2 AA3 4 LEU A 132 LEU A 139 -1 N ASN A 135 O ALA A 147 SHEET 3 AA3 4 GLU A 178 TYR A 186 -1 O VAL A 181 N LEU A 136 SHEET 4 AA3 4 LYS A 232 ARG A 241 -1 O ILE A 234 N GLU A 184 SHEET 1 AA4 6 VAL A 330 VAL A 341 0 SHEET 2 AA4 6 LEU A 347 ILE A 358 -1 O ALA A 348 N ASN A 340 SHEET 3 AA4 6 SER A 361 THR A 367 -1 O SER A 364 N LEU A 353 SHEET 4 AA4 6 ILE A 394 VAL A 400 1 O PRO A 395 N THR A 367 SHEET 5 AA4 6 THR A 384 SER A 390 -1 N SER A 390 O ILE A 394 SHEET 6 AA4 6 VAL A 330 VAL A 341 -1 N THR A 332 O VAL A 385 LINK OD1 ASP A 97 ZN ZN A 806 1555 1555 2.03 LINK OD2 ASP A 97 ZN ZN A 806 1555 1555 2.00 LINK OD1 ASP A 99 ZN ZN A 806 1555 1555 2.00 LINK OD2 ASP A 99 ZN ZN A 806 1555 1555 1.99 LINK OE2 GLU A 106 ZN ZN A 803 1555 3565 1.90 LINK OD2 ASP A 130 MN MN A 802 1555 1555 2.16 LINK OD1 ASP A 167 ZN ZN A 806 1555 3465 2.45 LINK OD2 ASP A 167 ZN ZN A 806 1555 3465 2.22 LINK OD1 ASP A 191 ZN ZN A 803 1555 1555 2.02 LINK OD2 ASP A 191 ZN ZN A 803 1555 1555 1.99 LINK ND1 HIS A 230 ZN ZN A 803 1555 1555 2.04 LINK NE2 HIS A 287 MN MN A 801 1555 1555 2.17 LINK OD1 ASP A 293 MN MN A 801 1555 1555 2.17 LINK OD2 ASP A 293 MN MN A 802 1555 1555 2.14 LINK OD1 ASP A 295 MN MN A 801 1555 1555 2.11 LINK OD2 ASP A 295 MN MN A 802 1555 1555 2.17 LINK SG CYS A 418 ZN ZN A 804 1555 1555 2.30 LINK SG CYS A 421 ZN ZN A 804 1555 1555 2.23 LINK NE2 HIS A 423 ZN ZN A 805 1555 1555 2.03 LINK NE2 HIS A 423 ZN ZN A 805 1555 2556 2.09 LINK SG CYS A 436 ZN ZN A 804 1555 1555 2.39 LINK SG CYS A 441 ZN ZN A 804 1555 1555 2.31 CRYST1 70.844 73.434 149.942 90.00 90.00 90.00 P 21 2 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.014116 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013618 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006669 0.00000