HEADER HYDROLASE/DNA 10-SEP-20 7K31 TITLE CRYSTAL STRUCTURE OF ENDONUCLEASE Q COMPLEX WITH 27-MER DUPLEX TITLE 2 SUBSTRATE WITH DI 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 7K31 1 REMARK REVDAT 1 17-MAR-21 7K31 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. 2.88 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 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) : 2.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 87.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.980 REMARK 3 COMPLETENESS FOR RANGE (%) : 67.5 REMARK 3 NUMBER OF REFLECTIONS : 15265 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.180 REMARK 3 FREE R VALUE TEST SET COUNT : 790 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 87.4700 - 5.2400 0.93 3303 204 0.1528 0.2011 REMARK 3 2 5.2400 - 4.1600 0.93 3322 151 0.1514 0.1971 REMARK 3 3 4.1600 - 3.6300 0.96 3434 198 0.1951 0.2403 REMARK 3 4 3.6300 - 3.3000 0.83 2954 151 0.2331 0.3325 REMARK 3 5 3.3000 - 3.0600 0.32 1146 73 0.2512 0.3104 REMARK 3 6 3.0600 - 2.8800 0.09 316 13 0.3485 0.3858 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) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.670 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.82 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.47 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 : 11 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 91 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.2003 27.6937 -20.7602 REMARK 3 T TENSOR REMARK 3 T11: 0.0000 T22: 0.0000 REMARK 3 T33: 0.0000 T12: 0.0000 REMARK 3 T13: 0.0000 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.0000 L22: 0.0000 REMARK 3 L33: 0.0000 L12: 0.0000 REMARK 3 L13: 0.0000 L23: 0.0000 REMARK 3 S TENSOR REMARK 3 S11: 0.0000 S12: 0.0000 S13: 0.0000 REMARK 3 S21: 0.0000 S22: 0.0000 S23: 0.0000 REMARK 3 S31: 0.0000 S32: 0.0000 S33: 0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 92 THROUGH 224 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.3067 35.8485 -27.7059 REMARK 3 T TENSOR REMARK 3 T11: 0.0000 T22: 0.0000 REMARK 3 T33: 0.0000 T12: 0.0000 REMARK 3 T13: 0.0000 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.0000 L22: 0.0000 REMARK 3 L33: 0.0000 L12: 0.0000 REMARK 3 L13: 0.0000 L23: 0.0000 REMARK 3 S TENSOR REMARK 3 S11: 0.0000 S12: 0.0000 S13: 0.0000 REMARK 3 S21: 0.0000 S22: 0.0000 S23: 0.0000 REMARK 3 S31: 0.0000 S32: 0.0000 S33: 0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 225 THROUGH 278 ) REMARK 3 ORIGIN FOR THE GROUP (A): 47.4572 27.3858 -26.7755 REMARK 3 T TENSOR REMARK 3 T11: 0.0000 T22: 0.0000 REMARK 3 T33: 0.0000 T12: 0.0000 REMARK 3 T13: 0.0000 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.0000 L22: 0.0000 REMARK 3 L33: 0.0000 L12: 0.0000 REMARK 3 L13: 0.0000 L23: 0.0000 REMARK 3 S TENSOR REMARK 3 S11: 0.0000 S12: 0.0000 S13: 0.0000 REMARK 3 S21: 0.0000 S22: 0.0000 S23: 0.0000 REMARK 3 S31: 0.0000 S32: 0.0000 S33: 0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 279 THROUGH 312 ) REMARK 3 ORIGIN FOR THE GROUP (A): 44.7122 35.5335 -18.0304 REMARK 3 T TENSOR REMARK 3 T11: 0.0000 T22: 0.0000 REMARK 3 T33: 0.0000 T12: 0.0000 REMARK 3 T13: 0.0000 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.0000 L22: 0.0000 REMARK 3 L33: 0.0000 L12: 0.0000 REMARK 3 L13: 0.0000 L23: 0.0000 REMARK 3 S TENSOR REMARK 3 S11: 0.0000 S12: 0.0000 S13: 0.0000 REMARK 3 S21: 0.0000 S22: 0.0000 S23: 0.0000 REMARK 3 S31: 0.0000 S32: 0.0000 S33: 0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 313 THROUGH 352 ) REMARK 3 ORIGIN FOR THE GROUP (A): 36.7840 21.4701 -0.3034 REMARK 3 T TENSOR REMARK 3 T11: 0.0000 T22: 0.0000 REMARK 3 T33: 0.0000 T12: 0.0000 REMARK 3 T13: 0.0000 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.0000 L22: 0.0000 REMARK 3 L33: 0.0000 L12: 0.0000 REMARK 3 L13: 0.0000 L23: 0.0000 REMARK 3 S TENSOR REMARK 3 S11: 0.0000 S12: 0.0000 S13: 0.0000 REMARK 3 S21: 0.0000 S22: 0.0000 S23: 0.0000 REMARK 3 S31: 0.0000 S32: 0.0000 S33: 0.0000 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 353 THROUGH 395 ) REMARK 3 ORIGIN FOR THE GROUP (A): 50.8882 23.8122 -4.3763 REMARK 3 T TENSOR REMARK 3 T11: 0.0000 T22: 0.0000 REMARK 3 T33: 0.0000 T12: 0.0000 REMARK 3 T13: 0.0000 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.0000 L22: 0.0000 REMARK 3 L33: 0.0000 L12: 0.0000 REMARK 3 L13: 0.0000 L23: 0.0000 REMARK 3 S TENSOR REMARK 3 S11: 0.0000 S12: 0.0000 S13: 0.0000 REMARK 3 S21: 0.0000 S22: 0.0000 S23: 0.0000 REMARK 3 S31: 0.0000 S32: 0.0000 S33: 0.0000 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.1174 -2.7842 -7.2931 REMARK 3 T TENSOR REMARK 3 T11: 0.0000 T22: 0.0000 REMARK 3 T33: 0.0000 T12: 0.0000 REMARK 3 T13: 0.0000 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.0000 L22: 0.0000 REMARK 3 L33: 0.0000 L12: 0.0000 REMARK 3 L13: 0.0000 L23: 0.0000 REMARK 3 S TENSOR REMARK 3 S11: 0.0000 S12: 0.0000 S13: 0.0000 REMARK 3 S21: 0.0000 S22: 0.0000 S23: 0.0000 REMARK 3 S31: 0.0000 S32: 0.0000 S33: 0.0000 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 11 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.5114 7.8306 -30.8639 REMARK 3 T TENSOR REMARK 3 T11: 0.0000 T22: 0.0000 REMARK 3 T33: 0.0000 T12: 0.0000 REMARK 3 T13: 0.0000 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.0000 L22: 0.0000 REMARK 3 L33: 0.0000 L12: 0.0000 REMARK 3 L13: 0.0000 L23: 0.0000 REMARK 3 S TENSOR REMARK 3 S11: 0.0000 S12: 0.0000 S13: 0.0000 REMARK 3 S21: 0.0000 S22: 0.0000 S23: 0.0000 REMARK 3 S31: 0.0000 S32: 0.0000 S33: 0.0000 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 16 THROUGH 27 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.5050 15.6935 -52.5493 REMARK 3 T TENSOR REMARK 3 T11: 0.0000 T22: 0.0000 REMARK 3 T33: 0.0000 T12: 0.0000 REMARK 3 T13: 0.0000 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.0000 L22: 0.0000 REMARK 3 L33: 0.0000 L12: 0.0000 REMARK 3 L13: 0.0000 L23: 0.0000 REMARK 3 S TENSOR REMARK 3 S11: 0.0000 S12: 0.0000 S13: 0.0000 REMARK 3 S21: 0.0000 S22: 0.0000 S23: 0.0000 REMARK 3 S31: 0.0000 S32: 0.0000 S33: 0.0000 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 42.2765 15.1293 -55.5164 REMARK 3 T TENSOR REMARK 3 T11: 0.0000 T22: 0.0000 REMARK 3 T33: 0.0000 T12: 0.0000 REMARK 3 T13: 0.0000 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.0000 L22: 0.0000 REMARK 3 L33: 0.0000 L12: 0.0000 REMARK 3 L13: 0.0000 L23: 0.0000 REMARK 3 S TENSOR REMARK 3 S11: 0.0000 S12: 0.0000 S13: 0.0000 REMARK 3 S21: 0.0000 S22: 0.0000 S23: 0.0000 REMARK 3 S31: 0.0000 S32: 0.0000 S33: 0.0000 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 11 THROUGH 27 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.0497 5.5660 -16.3908 REMARK 3 T TENSOR REMARK 3 T11: 0.0000 T22: 0.0000 REMARK 3 T33: 0.0000 T12: 0.0000 REMARK 3 T13: 0.0000 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.0000 L22: 0.0000 REMARK 3 L33: 0.0000 L12: 0.0000 REMARK 3 L13: 0.0000 L23: 0.0000 REMARK 3 S TENSOR REMARK 3 S11: 0.0000 S12: 0.0000 S13: 0.0000 REMARK 3 S21: 0.0000 S22: 0.0000 S23: 0.0000 REMARK 3 S31: 0.0000 S32: 0.0000 S33: 0.0000 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 7K31 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_1000251754. 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 : 7.4 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22027 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.850 REMARK 200 RESOLUTION RANGE LOW (A) : 87.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 1.01000 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 (%): 70.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.20 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 75.56000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 43.62459 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.19333 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 75.56000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 43.62459 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 39.19333 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 75.56000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 43.62459 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 39.19333 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 87.24917 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 78.38667 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 87.24917 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 78.38667 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 87.24917 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 78.38667 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: 5850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -126.0 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 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 OH TYR A 377 OP2 DT C 15 2.06 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 DT B 19 O3' DT B 19 C3' -0.041 REMARK 500 DA C 12 O3' DA C 12 C3' -0.039 REMARK 500 DI C 14 P DI C 14 O5' -0.129 REMARK 500 DI C 14 N9 DI C 14 C4 -0.138 REMARK 500 DA C 18 O3' DA C 18 C3' -0.036 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 3 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT B 14 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC B 17 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG B 22 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG C 4 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC C 13 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DI C 14 OP1 - P - OP2 ANGL. DEV. = -20.5 DEGREES REMARK 500 DI C 14 O5' - P - OP1 ANGL. DEV. = 14.3 DEGREES REMARK 500 DG C 19 C3' - C2' - C1' ANGL. DEV. = -5.7 DEGREES REMARK 500 DG C 19 O4' - C1' - N9 ANGL. DEV. = 2.4 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 HIS A 139 58.61 39.57 REMARK 500 ALA A 140 2.11 -67.67 REMARK 500 PHE A 333 -166.49 -126.27 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 404 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 8 NE2 REMARK 620 2 HIS A 10 NE2 111.1 REMARK 620 3 GLU A 76 OE1 87.2 82.0 REMARK 620 4 ASN A 193 OD1 86.8 154.1 118.6 REMARK 620 5 DI C 14 OP1 162.0 86.4 91.3 78.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 76 OE1 REMARK 620 2 GLU A 76 OE2 64.6 REMARK 620 3 HIS A 84 ND1 114.7 87.5 REMARK 620 4 HIS A 139 NE2 131.4 81.5 96.5 REMARK 620 5 DI C 14 OP2 115.4 178.4 91.2 99.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 405 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 169 O REMARK 620 2 LEU A 170 O 74.3 REMARK 620 3 ALA A 172 O 74.8 86.6 REMARK 620 4 GLU A 205 OE2 85.1 101.2 155.7 REMARK 620 5 LEU A 237 O 150.5 77.3 111.3 92.9 REMARK 620 6 TYR A 299 OH 123.6 157.6 85.9 94.3 85.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 249 SG REMARK 620 2 CYS A 252 SG 116.3 REMARK 620 3 CYS A 268 SG 106.4 100.4 REMARK 620 4 CYS A 271 SG 99.1 109.6 126.1 REMARK 620 N 1 2 3 DBREF 7K31 A 1 395 UNP I6V2I0 I6V2I0_9EURY 1 395 DBREF 7K31 B 1 27 PDB 7K31 7K31 1 27 DBREF 7K31 C 1 27 PDB 7K31 7K31 1 27 SEQADV 7K31 ASN A 193 UNP I6V2I0 ASP 193 ENGINEERED MUTATION SEQRES 1 A 395 MET ILE VAL ASP GLY ASP LEU HIS ILE HIS SER HIS TYR SEQRES 2 A 395 SER LYS ALA VAL SER LYS LEU MET THR PHE PRO ILE ILE SEQRES 3 A 395 ALA GLU ASN ALA LYS LEU LYS GLY LEU ASN LEU VAL GLY SEQRES 4 A 395 THR GLY ASP SER LEU ASN PRO HIS TRP GLU LYS GLU LEU SEQRES 5 A 395 LEU LYS HIS SER LYS PRO ILE ASP ASP GLY THR PHE GLU SEQRES 6 A 395 VAL ASN GLY VAL LYS PHE ILE LEU THR CYS GLU VAL GLU SEQRES 7 A 395 ASP LYS ARG ARG VAL HIS HIS LEU LEU ILE PHE PRO THR SEQRES 8 A 395 LEU SER GLN VAL ARG GLU PHE ARG GLU LYS VAL LYS ILE SEQRES 9 A 395 TYR SER THR ASN ILE GLU SER GLU GLY ARG PRO ASN LEU SEQRES 10 A 395 ASN LEU THR ALA GLU GLU ILE ALA GLU MET ALA ASN GLU SEQRES 11 A 395 LEU ASP ILE LEU ILE GLY PRO ALA HIS ALA PHE THR PRO SEQRES 12 A 395 TRP THR SER LEU TYR LYS GLU TYR ASP SER LEU LYS ASP SEQRES 13 A 395 ALA TYR GLY ASP ALA LYS ILE ASP PHE LEU GLU LEU GLY SEQRES 14 A 395 LEU SER ALA ASP SER ASP MET ALA ASP MET ILE LYS ALA SEQRES 15 A 395 HIS HIS SER ILE PRO TYR LEU SER ASN SER ASN ALA HIS SEQRES 16 A 395 SER PRO ASN PRO HIS ARG LEU GLY ARG GLU PHE ASN ARG SEQRES 17 A 395 PHE GLU VAL LYS ASP VAL THR PHE GLU GLU ILE ARG LYS SEQRES 18 A 395 ALA ILE LYS GLY VAL GLY GLY ARG LYS ILE MET LEU ASN SEQRES 19 A 395 ALA GLY LEU ASP PRO ARG LEU GLY LYS TYR HIS LEU THR SEQRES 20 A 395 ALA CYS SER ARG CYS TYR THR LYS TYR THR LEU GLN ASP SEQRES 21 A 395 ALA VAL SER LEU SER TRP LYS CYS PRO LYS CYS GLY GLY SEQRES 22 A 395 ILE ILE LYS LYS GLY VAL ARG ASP ARG ILE LEU GLU LEU SEQRES 23 A 395 ALA ASP THR SER GLU LYS PRO LYS ASP ARG PRO PRO TYR SEQRES 24 A 395 VAL ARG LEU ALA PRO LEU ALA GLU ILE ILE ALA MET VAL SEQRES 25 A 395 LEU GLY LYS GLY ILE GLU SER LYS ALA VAL LYS LEU LEU SEQRES 26 A 395 TRP ASN ARG PHE LEU ARG GLU PHE GLY SER GLU ILE ARG SEQRES 27 A 395 VAL LEU ILE ASP LEU PRO ILE GLU SER ILE ALA SER VAL SEQRES 28 A 395 HIS GLU GLY VAL ALA LYS ALA ILE TRP ALA TYR ARG ASN SEQRES 29 A 395 ASN LYS LEU ILE ILE VAL PRO GLY GLY GLY GLY LYS TYR SEQRES 30 A 395 GLY GLU ILE ARG ILE PRO GLU GLU ILE LEU LYS ALA LYS SEQRES 31 A 395 ILE GLU ASP LEU ASN 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 DI DT DG DT DA DG DC DG DA DA DC DG DA SEQRES 3 C 27 DC HET EDO A 401 4 HET ZN A 402 1 HET ZN A 403 1 HET ZN A 404 1 HET MG A 405 1 HET CL A 406 1 HET CL A 407 1 HETNAM EDO 1,2-ETHANEDIOL HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 4 EDO C2 H6 O2 FORMUL 5 ZN 3(ZN 2+) FORMUL 8 MG MG 2+ FORMUL 9 CL 2(CL 1-) FORMUL 11 HOH *8(H2 O) HELIX 1 AA1 THR A 22 GLY A 34 1 13 HELIX 2 AA2 ASN A 45 SER A 56 1 12 HELIX 3 AA3 THR A 91 VAL A 102 1 12 HELIX 4 AA4 LYS A 103 SER A 106 5 4 HELIX 5 AA5 THR A 120 LEU A 131 1 12 HELIX 6 AA6 SER A 146 TYR A 151 1 6 HELIX 7 AA7 SER A 153 GLY A 159 1 7 HELIX 8 AA8 ASP A 173 MET A 179 1 7 HELIX 9 AA9 ILE A 180 ILE A 186 5 7 HELIX 10 AB1 THR A 215 GLY A 225 1 11 HELIX 11 AB2 PRO A 239 GLY A 242 5 4 HELIX 12 AB3 THR A 257 SER A 265 1 9 HELIX 13 AB4 GLY A 278 LEU A 286 1 9 HELIX 14 AB5 PRO A 304 LEU A 313 1 10 HELIX 15 AB6 SER A 319 PHE A 333 1 15 HELIX 16 AB7 SER A 335 ILE A 341 1 7 HELIX 17 AB8 PRO A 344 SER A 350 1 7 HELIX 18 AB9 HIS A 352 ASN A 364 1 13 HELIX 19 AC1 PRO A 383 ALA A 389 1 7 SHEET 1 AA1 5 LYS A 57 PRO A 58 0 SHEET 2 AA1 5 THR A 63 VAL A 66 -1 O GLU A 65 N LYS A 57 SHEET 3 AA1 5 VAL A 69 GLU A 78 -1 O PHE A 71 N PHE A 64 SHEET 4 AA1 5 HIS A 84 PHE A 89 -1 O LEU A 87 N CYS A 75 SHEET 5 AA1 5 LEU A 134 PRO A 137 -1 O GLY A 136 N LEU A 86 SHEET 1 AA2 8 LYS A 57 PRO A 58 0 SHEET 2 AA2 8 THR A 63 VAL A 66 -1 O GLU A 65 N LYS A 57 SHEET 3 AA2 8 VAL A 69 GLU A 78 -1 O PHE A 71 N PHE A 64 SHEET 4 AA2 8 LEU A 37 GLY A 39 1 N VAL A 38 O LYS A 70 SHEET 5 AA2 8 ILE A 2 ASP A 6 1 N ASP A 6 O GLY A 39 SHEET 6 AA2 8 PHE A 206 GLU A 210 -1 O ASN A 207 N GLY A 5 SHEET 7 AA2 8 LYS A 230 LEU A 237 -1 O LYS A 230 N GLU A 210 SHEET 8 AA2 8 TYR A 299 LEU A 302 1 O LEU A 302 N GLY A 236 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 ALA A 248 CYS A 249 0 SHEET 2 AA4 2 ILE A 275 LYS A 276 -1 O LYS A 276 N ALA A 248 SHEET 1 AA5 2 ILE A 368 VAL A 370 0 SHEET 2 AA5 2 GLU A 379 ARG A 381 -1 O ARG A 381 N ILE A 368 LINK NE2 HIS A 8 ZN ZN A 404 1555 1555 2.08 LINK NE2 HIS A 10 ZN ZN A 404 1555 1555 2.01 LINK OE1 GLU A 76 ZN ZN A 403 1555 1555 2.08 LINK OE2 GLU A 76 ZN ZN A 403 1555 1555 1.98 LINK OE1 GLU A 76 ZN ZN A 404 1555 1555 2.04 LINK ND1 HIS A 84 ZN ZN A 403 1555 1555 2.33 LINK NE2 HIS A 139 ZN ZN A 403 1555 1555 2.09 LINK O GLY A 169 MG MG A 405 1555 1555 2.66 LINK O LEU A 170 MG MG A 405 1555 1555 2.51 LINK O ALA A 172 MG MG A 405 1555 1555 2.60 LINK OD1 ASN A 193 ZN ZN A 404 1555 1555 2.00 LINK OE2 GLU A 205 MG MG A 405 1555 1555 2.20 LINK O LEU A 237 MG MG A 405 1555 1555 2.83 LINK SG CYS A 249 ZN ZN A 402 1555 1555 2.34 LINK SG CYS A 252 ZN ZN A 402 1555 1555 2.25 LINK SG CYS A 268 ZN ZN A 402 1555 1555 2.33 LINK SG CYS A 271 ZN ZN A 402 1555 1555 2.30 LINK OH TYR A 299 MG MG A 405 1555 1555 2.10 LINK ZN ZN A 403 OP2 DI C 14 1555 1555 2.22 LINK ZN ZN A 404 OP1 DI C 14 1555 1555 2.25 CRYST1 151.120 151.120 117.580 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 0.006617 0.003820 0.000000 0.00000 SCALE2 0.000000 0.007641 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008505 0.00000