HEADER HYDROLASE/DNA 10-SEP-20 7K33 TITLE CRYSTAL STRUCTURE OF ENDONUCLEASE Q COMPLEX WITH 27-MER DUPLEX TITLE 2 SUBSTRATE WITH AN ABASIC LESION AT THE ACTIVE SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDONUCLEASE Q; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (27-MER); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (27-MER); COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 2261; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 9 ORGANISM_TAXID: 32630; SOURCE 10 MOL_ID: 3; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS HYDROLASE, DEAMINATION, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.SHI,N.M.MOELLER,S.BANERJEE,L.YIN,K.ORELLANA,H.AIHARA REVDAT 2 18-OCT-23 7K33 1 REMARK REVDAT 1 17-MAR-21 7K33 0 JRNL AUTH K.SHI,N.H.MOELLER,S.BANERJEE,J.L.MCCANN,M.A.CARPENTER,L.YIN, JRNL AUTH 2 R.MOORTHY,K.ORELLANA,D.A.HARKI,R.S.HARRIS,H.AIHARA JRNL TITL STRUCTURAL BASIS FOR RECOGNITION OF DISTINCT DEAMINATED DNA JRNL TITL 2 LESIONS BY ENDONUCLEASE Q. JRNL REF PROC.NATL.ACAD.SCI.USA V. 118 2021 JRNL REFN ESSN 1091-6490 JRNL PMID 33658373 JRNL DOI 10.1073/PNAS.2021120118 REMARK 2 REMARK 2 RESOLUTION. 3.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4092 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) : 3.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 88.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 67.4 REMARK 3 NUMBER OF REFLECTIONS : 12336 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 618 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 88.3000 - 4.9400 0.95 4144 209 0.1491 0.1985 REMARK 3 2 4.9400 - 3.9200 0.95 4133 229 0.2450 0.2464 REMARK 3 3 3.9200 - 3.4300 0.67 2888 146 0.2764 0.3415 REMARK 3 4 3.4300 - 3.1100 0.13 553 34 0.4210 0.4810 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) : 0.470 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 134.8 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 145.4 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 'A' AND (RESID 1 THROUGH 105 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.2397 28.8827 -23.0123 REMARK 3 T TENSOR REMARK 3 T11: 0.7071 T22: 0.8552 REMARK 3 T33: 0.5614 T12: -0.0663 REMARK 3 T13: 0.1472 T23: -0.0209 REMARK 3 L TENSOR REMARK 3 L11: 2.3947 L22: 5.9279 REMARK 3 L33: 7.9836 L12: 0.5830 REMARK 3 L13: 1.8985 L23: -0.3963 REMARK 3 S TENSOR REMARK 3 S11: -0.0513 S12: -0.1096 S13: -0.2699 REMARK 3 S21: 0.4457 S22: 0.0140 S23: 0.3778 REMARK 3 S31: 1.1769 S32: -1.0518 S33: 0.0048 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 106 THROUGH 297 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.3460 34.9038 -26.5272 REMARK 3 T TENSOR REMARK 3 T11: 0.5845 T22: 0.7383 REMARK 3 T33: 0.5469 T12: 0.0700 REMARK 3 T13: 0.0503 T23: 0.1648 REMARK 3 L TENSOR REMARK 3 L11: 3.8182 L22: 2.8547 REMARK 3 L33: 7.0875 L12: 0.3185 REMARK 3 L13: 0.6074 L23: -1.0953 REMARK 3 S TENSOR REMARK 3 S11: -0.3013 S12: 0.4434 S13: -0.0704 REMARK 3 S21: -0.2610 S22: -0.1516 S23: -0.5354 REMARK 3 S31: 0.2128 S32: 0.7489 S33: 0.2928 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 298 THROUGH 395 ) REMARK 3 ORIGIN FOR THE GROUP (A): 43.7015 23.3398 -3.2152 REMARK 3 T TENSOR REMARK 3 T11: 1.1570 T22: 0.8112 REMARK 3 T33: 0.6971 T12: 0.3674 REMARK 3 T13: -0.0506 T23: 0.0947 REMARK 3 L TENSOR REMARK 3 L11: 5.2226 L22: 4.4819 REMARK 3 L33: 7.9640 L12: -0.7361 REMARK 3 L13: -0.4137 L23: 1.1263 REMARK 3 S TENSOR REMARK 3 S11: 0.0883 S12: -0.3626 S13: -0.3854 REMARK 3 S21: 0.7313 S22: -0.1799 S23: -0.3313 REMARK 3 S31: 1.0518 S32: 1.1741 S33: 0.0751 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.1335 -2.6984 -7.2264 REMARK 3 T TENSOR REMARK 3 T11: 2.9121 T22: 1.6385 REMARK 3 T33: 1.8438 T12: 0.2687 REMARK 3 T13: 0.0977 T23: 0.0409 REMARK 3 L TENSOR REMARK 3 L11: 7.1436 L22: 5.7771 REMARK 3 L33: 7.3827 L12: 0.8089 REMARK 3 L13: 1.3121 L23: -3.8065 REMARK 3 S TENSOR REMARK 3 S11: -0.4039 S12: 0.1963 S13: -1.3925 REMARK 3 S21: -2.0647 S22: 0.2065 S23: -1.0916 REMARK 3 S31: 2.5287 S32: -0.4263 S33: 0.3654 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 11 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.2859 8.2428 -30.9288 REMARK 3 T TENSOR REMARK 3 T11: 2.9906 T22: 2.4278 REMARK 3 T33: 1.8105 T12: -0.0193 REMARK 3 T13: 0.2601 T23: -0.2211 REMARK 3 L TENSOR REMARK 3 L11: 6.7079 L22: 6.0953 REMARK 3 L33: 7.8660 L12: -0.3890 REMARK 3 L13: 4.1547 L23: -2.9525 REMARK 3 S TENSOR REMARK 3 S11: 0.1801 S12: 1.3542 S13: -1.1958 REMARK 3 S21: -2.1619 S22: 0.4222 S23: 0.2260 REMARK 3 S31: 2.1271 S32: 1.2907 S33: -0.3780 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 16 THROUGH 27 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.5541 16.1531 -53.1690 REMARK 3 T TENSOR REMARK 3 T11: 2.7820 T22: 2.8629 REMARK 3 T33: 2.0587 T12: 0.2855 REMARK 3 T13: 0.5077 T23: -0.3161 REMARK 3 L TENSOR REMARK 3 L11: 1.5987 L22: 1.1149 REMARK 3 L33: 7.6908 L12: -1.1255 REMARK 3 L13: -3.0428 L23: 2.6898 REMARK 3 S TENSOR REMARK 3 S11: 0.2396 S12: 0.2595 S13: 0.2829 REMARK 3 S21: -0.3832 S22: -0.3360 S23: -0.4043 REMARK 3 S31: 0.4308 S32: 1.1720 S33: 0.3430 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 42.2871 15.6104 -56.3246 REMARK 3 T TENSOR REMARK 3 T11: 2.7246 T22: 2.8184 REMARK 3 T33: 1.9676 T12: 0.5285 REMARK 3 T13: 0.4603 T23: -0.5334 REMARK 3 L TENSOR REMARK 3 L11: 9.0085 L22: 4.3921 REMARK 3 L33: 4.8083 L12: -4.1471 REMARK 3 L13: -1.4746 L23: 4.0975 REMARK 3 S TENSOR REMARK 3 S11: 1.1385 S12: 0.1043 S13: 1.7801 REMARK 3 S21: 0.3913 S22: -0.2597 S23: 1.5350 REMARK 3 S31: 0.9138 S32: 0.6992 S33: -0.7374 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 11 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 36.7515 18.6724 -30.7759 REMARK 3 T TENSOR REMARK 3 T11: 2.2391 T22: 1.6490 REMARK 3 T33: 1.1905 T12: 0.2835 REMARK 3 T13: 0.2543 T23: -0.3139 REMARK 3 L TENSOR REMARK 3 L11: 2.6827 L22: 2.4893 REMARK 3 L33: 6.3707 L12: 2.3276 REMARK 3 L13: -3.1540 L23: -3.8533 REMARK 3 S TENSOR REMARK 3 S11: 0.7221 S12: 0.2624 S13: 0.0113 REMARK 3 S21: -2.8273 S22: -2.7000 S23: -1.2006 REMARK 3 S31: 0.1273 S32: -1.1051 S33: 0.5838 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 16 THROUGH 27 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.1723 -0.0357 -10.5904 REMARK 3 T TENSOR REMARK 3 T11: 2.7856 T22: 1.5200 REMARK 3 T33: 1.9571 T12: 0.2631 REMARK 3 T13: 0.1369 T23: 0.0276 REMARK 3 L TENSOR REMARK 3 L11: 4.1946 L22: 8.4705 REMARK 3 L33: 6.6967 L12: -3.1310 REMARK 3 L13: 4.4125 L23: -5.2258 REMARK 3 S TENSOR REMARK 3 S11: 0.9544 S12: -0.1007 S13: -1.0667 REMARK 3 S21: -1.3412 S22: -0.2187 S23: 0.2547 REMARK 3 S31: 3.4964 S32: 0.7418 S33: -0.7287 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 7K33 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1000251756. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-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 : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17780 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 88.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 1.30100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 5ZB8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15 MM TRIS-HCL PH 7.4, 0.15 M NACL, 1 REMARK 280 MM MGCL2, AND 4 MM BETA-MERCAPTOETHANOL, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 75.75000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 43.73428 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.79333 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 75.75000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 43.73428 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 39.79333 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 75.75000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 43.73428 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 39.79333 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 87.46857 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 79.58667 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 87.46857 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 79.58667 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 87.46857 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 79.58667 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 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -70.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 SER A 396 REMARK 465 ILE A 397 REMARK 465 GLU A 398 REMARK 465 ILE A 399 REMARK 465 SER A 400 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 OG1 THR A 91 OE1 GLN A 94 2.19 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 DC B 17 O4' - C1' - N1 ANGL. DEV. = 1.8 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 LEU A 7 40.33 -109.29 REMARK 500 HIS A 8 92.56 -161.53 REMARK 500 ASP A 60 -127.68 -132.57 REMARK 500 ARG A 82 62.27 64.31 REMARK 500 GLU A 110 38.11 -97.63 REMARK 500 SER A 111 -30.92 -149.34 REMARK 500 HIS A 139 60.16 39.75 REMARK 500 SER A 171 6.18 -67.73 REMARK 500 ARG A 201 -62.87 -103.58 REMARK 500 HIS A 245 -70.71 -61.94 REMARK 500 LYS A 270 36.44 -92.23 REMARK 500 CYS A 271 -43.49 -163.55 REMARK 500 LEU A 286 42.40 -89.71 REMARK 500 ASP A 288 -75.80 -108.07 REMARK 500 PHE A 333 -158.20 -124.29 REMARK 500 ILE A 341 -53.35 -121.21 REMARK 500 LYS A 390 -138.81 -83.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 114 0.22 SIDE CHAIN 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 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 76 OE1 REMARK 620 2 GLU A 76 OE2 63.3 REMARK 620 3 HIS A 84 ND1 91.0 101.4 REMARK 620 4 HIS A 139 NE2 74.6 137.5 84.6 REMARK 620 5 ASN A 193 OD1 79.6 93.3 156.8 72.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 169 O REMARK 620 2 LEU A 170 O 78.8 REMARK 620 3 ALA A 172 O 76.4 84.7 REMARK 620 4 GLU A 205 OE2 76.0 103.9 148.7 REMARK 620 5 LEU A 237 O 158.6 83.4 113.9 97.1 REMARK 620 6 TYR A 299 OH 114.7 159.9 84.3 94.2 85.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 249 SG REMARK 620 2 CYS A 252 SG 101.8 REMARK 620 3 CYS A 268 SG 116.8 91.4 REMARK 620 4 CYS A 271 SG 121.0 101.0 116.2 REMARK 620 N 1 2 3 DBREF 7K33 A 1 400 UNP I6V2I0 I6V2I0_9EURY 1 400 DBREF 7K33 B 1 27 PDB 7K33 7K33 1 27 DBREF 7K33 C 1 27 PDB 7K33 7K33 1 27 SEQADV 7K33 ASN A 193 UNP I6V2I0 ASP 193 ENGINEERED MUTATION SEQRES 1 A 400 MET ILE VAL ASP GLY ASP LEU HIS ILE HIS SER HIS TYR SEQRES 2 A 400 SER LYS ALA VAL SER LYS LEU MET THR PHE PRO ILE ILE SEQRES 3 A 400 ALA GLU ASN ALA LYS LEU LYS GLY LEU ASN LEU VAL GLY SEQRES 4 A 400 THR GLY ASP SER LEU ASN PRO HIS TRP GLU LYS GLU LEU SEQRES 5 A 400 LEU LYS HIS SER LYS PRO ILE ASP ASP GLY THR PHE GLU SEQRES 6 A 400 VAL ASN GLY VAL LYS PHE ILE LEU THR CYS GLU VAL GLU SEQRES 7 A 400 ASP LYS ARG ARG VAL HIS HIS LEU LEU ILE PHE PRO THR SEQRES 8 A 400 LEU SER GLN VAL ARG GLU PHE ARG GLU LYS VAL LYS ILE SEQRES 9 A 400 TYR SER THR ASN ILE GLU SER GLU GLY ARG PRO ASN LEU SEQRES 10 A 400 ASN LEU THR ALA GLU GLU ILE ALA GLU MET ALA ASN GLU SEQRES 11 A 400 LEU ASP ILE LEU ILE GLY PRO ALA HIS ALA PHE THR PRO SEQRES 12 A 400 TRP THR SER LEU TYR LYS GLU TYR ASP SER LEU LYS ASP SEQRES 13 A 400 ALA TYR GLY ASP ALA LYS ILE ASP PHE LEU GLU LEU GLY SEQRES 14 A 400 LEU SER ALA ASP SER ASP MET ALA ASP MET ILE LYS ALA SEQRES 15 A 400 HIS HIS SER ILE PRO TYR LEU SER ASN SER ASN ALA HIS SEQRES 16 A 400 SER PRO ASN PRO HIS ARG LEU GLY ARG GLU PHE ASN ARG SEQRES 17 A 400 PHE GLU VAL LYS ASP VAL THR PHE GLU GLU ILE ARG LYS SEQRES 18 A 400 ALA ILE LYS GLY VAL GLY GLY ARG LYS ILE MET LEU ASN SEQRES 19 A 400 ALA GLY LEU ASP PRO ARG LEU GLY LYS TYR HIS LEU THR SEQRES 20 A 400 ALA CYS SER ARG CYS TYR THR LYS TYR THR LEU GLN ASP SEQRES 21 A 400 ALA VAL SER LEU SER TRP LYS CYS PRO LYS CYS GLY GLY SEQRES 22 A 400 ILE ILE LYS LYS GLY VAL ARG ASP ARG ILE LEU GLU LEU SEQRES 23 A 400 ALA ASP THR SER GLU LYS PRO LYS ASP ARG PRO PRO TYR SEQRES 24 A 400 VAL ARG LEU ALA PRO LEU ALA GLU ILE ILE ALA MET VAL SEQRES 25 A 400 LEU GLY LYS GLY ILE GLU SER LYS ALA VAL LYS LEU LEU SEQRES 26 A 400 TRP ASN ARG PHE LEU ARG GLU PHE GLY SER GLU ILE ARG SEQRES 27 A 400 VAL LEU ILE ASP LEU PRO ILE GLU SER ILE ALA SER VAL SEQRES 28 A 400 HIS GLU GLY VAL ALA LYS ALA ILE TRP ALA TYR ARG ASN SEQRES 29 A 400 ASN LYS LEU ILE ILE VAL PRO GLY GLY GLY GLY LYS TYR SEQRES 30 A 400 GLY GLU ILE ARG ILE PRO GLU GLU ILE LEU LYS ALA LYS SEQRES 31 A 400 ILE GLU ASP LEU ASN SER ILE GLU ILE SER SEQRES 1 B 27 DG DT DC DG DT DT DC DG DC DT DA DC DA SEQRES 2 B 27 DT DG DT DC DG DT DC DG DG DT DC DT DG SEQRES 3 B 27 DC SEQRES 1 C 27 DG DC DA DG DA DC DC DG DA DC DG DA DC SEQRES 2 C 27 3DR DT DG DT DA DG DC DG DA DA DC DG DA SEQRES 3 C 27 DC HET 3DR C 14 11 HET ZN A 501 1 HET ZN A 502 1 HET MG A 503 1 HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETSYN 3DR ABASIC DIDEOXYRIBOSE FORMUL 3 3DR C5 H11 O6 P FORMUL 4 ZN 2(ZN 2+) FORMUL 6 MG MG 2+ HELIX 1 AA1 THR A 22 LYS A 33 1 12 HELIX 2 AA2 ASN A 45 SER A 56 1 12 HELIX 3 AA3 THR A 91 LYS A 103 1 13 HELIX 4 AA4 ILE A 104 SER A 106 5 3 HELIX 5 AA5 THR A 120 LEU A 131 1 12 HELIX 6 AA6 SER A 153 GLY A 159 1 7 HELIX 7 AA7 ASP A 173 MET A 179 1 7 HELIX 8 AA8 LYS A 181 ILE A 186 5 6 HELIX 9 AA9 THR A 215 GLY A 225 1 11 HELIX 10 AB1 PRO A 239 GLY A 242 5 4 HELIX 11 AB2 THR A 257 SER A 265 1 9 HELIX 12 AB3 GLY A 278 LEU A 286 1 9 HELIX 13 AB4 PRO A 304 GLY A 314 1 11 HELIX 14 AB5 SER A 319 PHE A 333 1 15 HELIX 15 AB6 SER A 335 ILE A 341 1 7 HELIX 16 AB7 PRO A 344 ALA A 349 1 6 HELIX 17 AB8 HIS A 352 ASN A 364 1 13 HELIX 18 AB9 PRO A 383 ALA A 389 1 7 SHEET 1 AA1 8 LYS A 57 PRO A 58 0 SHEET 2 AA1 8 THR A 63 VAL A 66 -1 O GLU A 65 N LYS A 57 SHEET 3 AA1 8 VAL A 69 ILE A 72 -1 O PHE A 71 N PHE A 64 SHEET 4 AA1 8 LEU A 37 GLY A 39 1 N VAL A 38 O LYS A 70 SHEET 5 AA1 8 ILE A 2 ASP A 6 1 N ASP A 4 O LEU A 37 SHEET 6 AA1 8 PHE A 206 GLU A 210 -1 O PHE A 209 N VAL A 3 SHEET 7 AA1 8 LYS A 230 LEU A 237 -1 O LYS A 230 N GLU A 210 SHEET 8 AA1 8 TYR A 299 LEU A 302 1 O LEU A 302 N GLY A 236 SHEET 1 AA2 3 THR A 74 GLU A 78 0 SHEET 2 AA2 3 HIS A 84 ILE A 88 -1 O HIS A 85 N VAL A 77 SHEET 3 AA2 3 LEU A 134 PRO A 137 -1 O GLY A 136 N LEU A 86 SHEET 1 AA3 2 LEU A 166 GLU A 167 0 SHEET 2 AA3 2 TYR A 188 LEU A 189 1 O LEU A 189 N LEU A 166 SHEET 1 AA4 2 ILE A 368 VAL A 370 0 SHEET 2 AA4 2 GLU A 379 ARG A 381 -1 O ARG A 381 N ILE A 368 LINK O3' DC C 13 P 3DR C 14 1555 1555 1.61 LINK O3' 3DR C 14 P DT C 15 1555 1555 1.61 LINK OE1 GLU A 76 ZN ZN A 502 1555 1555 2.05 LINK OE2 GLU A 76 ZN ZN A 502 1555 1555 2.07 LINK ND1 HIS A 84 ZN ZN A 502 1555 1555 2.07 LINK NE2 HIS A 139 ZN ZN A 502 1555 1555 2.11 LINK O GLY A 169 MG MG A 503 1555 1555 2.58 LINK O LEU A 170 MG MG A 503 1555 1555 2.51 LINK O ALA A 172 MG MG A 503 1555 1555 2.63 LINK OD1 ASN A 193 ZN ZN A 502 1555 1555 2.12 LINK OE2 GLU A 205 MG MG A 503 1555 1555 2.16 LINK O LEU A 237 MG MG A 503 1555 1555 2.64 LINK SG CYS A 249 ZN ZN A 501 1555 1555 2.32 LINK SG CYS A 252 ZN ZN A 501 1555 1555 2.30 LINK SG CYS A 268 ZN ZN A 501 1555 1555 2.30 LINK SG CYS A 271 ZN ZN A 501 1555 1555 2.30 LINK OH TYR A 299 MG MG A 503 1555 1555 2.05 CRYST1 151.500 151.500 119.380 90.00 90.00 120.00 H 3 9 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 0.006601 0.003811 0.000000 0.00000 SCALE2 0.000000 0.007622 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008377 0.00000