HEADER HYDROLASE 12-MAR-15 4YOR TITLE CRYSTAL STRUCTURE OF A TRIMERIC EXONUCLEASE PHOEXO I FROM PYROCOCCUS TITLE 2 HORIKOSHII OT3 AT 1.52A RESOLUTION. COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-5 EXONUCLEASE PHOEXO I; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 53953; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET26B KEYWDS EXONUCLEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.MIYAZONO,K.TSUTSUMI,M.TANOKURA REVDAT 3 05-FEB-20 4YOR 1 JRNL REMARK REVDAT 2 16-SEP-15 4YOR 1 JRNL REVDAT 1 15-JUL-15 4YOR 0 JRNL AUTH K.MIYAZONO,S.ISHINO,K.TSUTSUMI,T.ITO,Y.ISHINO,M.TANOKURA JRNL TITL STRUCTURAL BASIS FOR SUBSTRATE RECOGNITION AND PROCESSIVE JRNL TITL 2 CLEAVAGE MECHANISMS OF THE TRIMERIC EXONUCLEASE PHOEXO I JRNL REF NUCLEIC ACIDS RES. V. 43 7122 2015 JRNL REFN ESSN 1362-4962 JRNL PMID 26138487 JRNL DOI 10.1093/NAR/GKV654 REMARK 2 REMARK 2 RESOLUTION. 1.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.020 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 73987 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 7019 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 19.6978 - 4.7022 0.98 4524 225 0.1563 0.1574 REMARK 3 2 4.7022 - 3.7406 1.00 4634 208 0.1338 0.1471 REMARK 3 3 3.7406 - 3.2702 1.00 4652 255 0.1465 0.1571 REMARK 3 4 3.2702 - 2.9723 1.00 4628 237 0.1556 0.2059 REMARK 3 5 2.9723 - 2.7599 1.00 4550 284 0.1577 0.1664 REMARK 3 6 2.7599 - 2.5976 1.00 4615 234 0.1613 0.1928 REMARK 3 7 2.5976 - 2.4677 1.00 4635 249 0.1551 0.1931 REMARK 3 8 2.4677 - 2.3605 1.00 4588 247 0.1593 0.1674 REMARK 3 9 2.3605 - 2.2698 1.00 4613 247 0.1559 0.1618 REMARK 3 10 2.2698 - 2.1916 1.00 4621 245 0.1447 0.1663 REMARK 3 11 2.1916 - 2.1231 1.00 4606 245 0.1545 0.1735 REMARK 3 12 2.1231 - 2.0625 1.00 4614 257 0.1493 0.1633 REMARK 3 13 2.0625 - 2.0082 1.00 4674 217 0.1581 0.1921 REMARK 3 14 2.0082 - 1.9593 1.00 4610 210 0.1621 0.2147 REMARK 3 15 1.9593 - 1.9148 1.00 4607 247 0.1577 0.1692 REMARK 3 16 1.9148 - 1.8741 1.00 4609 255 0.1595 0.2099 REMARK 3 17 1.8741 - 1.8366 1.00 4570 271 0.1718 0.1972 REMARK 3 18 1.8366 - 1.8020 1.00 4593 259 0.1696 0.2289 REMARK 3 19 1.8020 - 1.7698 0.99 4612 258 0.1816 0.2294 REMARK 3 20 1.7698 - 1.7398 0.99 4557 254 0.1793 0.2035 REMARK 3 21 1.7398 - 1.7118 0.98 4523 243 0.1924 0.2049 REMARK 3 22 1.7118 - 1.6855 0.97 4459 271 0.1884 0.1884 REMARK 3 23 1.6855 - 1.6607 0.97 4454 235 0.1933 0.2053 REMARK 3 24 1.6607 - 1.6373 0.96 4434 209 0.2015 0.2424 REMARK 3 25 1.6373 - 1.6152 0.94 4322 241 0.2245 0.2311 REMARK 3 26 1.6152 - 1.5942 0.90 4195 194 0.2306 0.2587 REMARK 3 27 1.5942 - 1.5743 0.82 3767 201 0.2499 0.2580 REMARK 3 28 1.5743 - 1.5553 0.75 3418 200 0.2583 0.2536 REMARK 3 29 1.5553 - 1.5373 0.68 3160 164 0.2695 0.2853 REMARK 3 30 1.5373 - 1.5200 0.61 2843 157 0.2875 0.3360 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.41 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.40 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 : 0.007 3635 REMARK 3 ANGLE : 1.080 4914 REMARK 3 CHIRALITY : 0.045 559 REMARK 3 PLANARITY : 0.005 621 REMARK 3 DIHEDRAL : 12.738 1393 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 44 ) REMARK 3 ORIGIN FOR THE GROUP (A): 35.8668 -37.3576 14.4396 REMARK 3 T TENSOR REMARK 3 T11: 0.1237 T22: 0.1547 REMARK 3 T33: 0.1130 T12: -0.0025 REMARK 3 T13: -0.0027 T23: 0.0136 REMARK 3 L TENSOR REMARK 3 L11: 3.3335 L22: 5.6869 REMARK 3 L33: 0.8281 L12: -1.4850 REMARK 3 L13: 0.0151 L23: 0.5823 REMARK 3 S TENSOR REMARK 3 S11: 0.1469 S12: 0.0357 S13: -0.2376 REMARK 3 S21: -0.1110 S22: -0.1026 S23: 0.2167 REMARK 3 S31: 0.0454 S32: -0.0584 S33: -0.0304 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 45 THROUGH 72 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.9985 -40.0472 5.7151 REMARK 3 T TENSOR REMARK 3 T11: 0.2240 T22: 0.2923 REMARK 3 T33: 0.2789 T12: -0.0068 REMARK 3 T13: -0.0888 T23: -0.0515 REMARK 3 L TENSOR REMARK 3 L11: 1.6575 L22: 7.4871 REMARK 3 L33: 3.0345 L12: -0.1455 REMARK 3 L13: 0.8221 L23: -0.2319 REMARK 3 S TENSOR REMARK 3 S11: 0.2114 S12: 0.4082 S13: -0.5270 REMARK 3 S21: -0.7967 S22: -0.0698 S23: 0.1844 REMARK 3 S31: 0.3198 S32: 0.0122 S33: -0.0971 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 73 THROUGH 138 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.3126 -28.3606 -2.5874 REMARK 3 T TENSOR REMARK 3 T11: 0.2949 T22: 0.3959 REMARK 3 T33: 0.1679 T12: 0.0094 REMARK 3 T13: -0.0193 T23: -0.0056 REMARK 3 L TENSOR REMARK 3 L11: 2.8228 L22: 3.3952 REMARK 3 L33: 3.6312 L12: 0.4716 REMARK 3 L13: 0.6489 L23: -0.5847 REMARK 3 S TENSOR REMARK 3 S11: 0.0202 S12: 0.9404 S13: -0.0864 REMARK 3 S21: -0.7391 S22: 0.0748 S23: -0.0120 REMARK 3 S31: 0.1823 S32: 0.2111 S33: -0.0649 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 139 THROUGH 227 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.4250 -44.0192 21.2651 REMARK 3 T TENSOR REMARK 3 T11: 0.1449 T22: 0.1716 REMARK 3 T33: 0.1695 T12: -0.0171 REMARK 3 T13: 0.0049 T23: 0.0418 REMARK 3 L TENSOR REMARK 3 L11: 2.2527 L22: 2.1452 REMARK 3 L33: 0.9778 L12: -0.5386 REMARK 3 L13: -0.2815 L23: 0.1696 REMARK 3 S TENSOR REMARK 3 S11: -0.0256 S12: -0.2706 S13: -0.3899 REMARK 3 S21: 0.1587 S22: -0.0045 S23: 0.1986 REMARK 3 S31: 0.1668 S32: -0.0719 S33: 0.0317 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 56 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.8207 -21.6261 20.8383 REMARK 3 T TENSOR REMARK 3 T11: 0.1705 T22: 0.1466 REMARK 3 T33: 0.1736 T12: 0.0132 REMARK 3 T13: 0.0127 T23: 0.0244 REMARK 3 L TENSOR REMARK 3 L11: 5.0445 L22: 2.3875 REMARK 3 L33: 0.6246 L12: 0.0319 REMARK 3 L13: 0.1884 L23: -0.0964 REMARK 3 S TENSOR REMARK 3 S11: -0.0365 S12: -0.3529 S13: -0.5650 REMARK 3 S21: 0.0531 S22: 0.0055 S23: 0.1259 REMARK 3 S31: 0.1033 S32: -0.0545 S33: 0.0452 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 57 THROUGH 138 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.7487 -19.3157 34.4443 REMARK 3 T TENSOR REMARK 3 T11: 0.2953 T22: 0.3092 REMARK 3 T33: 0.1656 T12: 0.0130 REMARK 3 T13: 0.0079 T23: 0.0701 REMARK 3 L TENSOR REMARK 3 L11: 2.7507 L22: 3.4494 REMARK 3 L33: 3.7490 L12: 0.2151 REMARK 3 L13: 0.4556 L23: 0.2324 REMARK 3 S TENSOR REMARK 3 S11: -0.0048 S12: -0.7181 S13: -0.1322 REMARK 3 S21: 0.7677 S22: 0.0199 S23: 0.0958 REMARK 3 S31: 0.0432 S32: -0.1654 S33: 0.0400 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 139 THROUGH 227 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.0183 -18.3537 12.9266 REMARK 3 T TENSOR REMARK 3 T11: 0.1788 T22: 0.1450 REMARK 3 T33: 0.1935 T12: 0.0001 REMARK 3 T13: -0.0082 T23: -0.0429 REMARK 3 L TENSOR REMARK 3 L11: 2.5980 L22: 2.0646 REMARK 3 L33: 1.0778 L12: -0.1432 REMARK 3 L13: -0.1562 L23: 0.2237 REMARK 3 S TENSOR REMARK 3 S11: 0.0037 S12: 0.2176 S13: -0.4358 REMARK 3 S21: -0.2372 S22: -0.0921 S23: 0.2027 REMARK 3 S31: 0.1529 S32: -0.1295 S33: 0.0688 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 4YOR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000207852. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAY-10 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 8.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NE3A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 74001 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.520 REMARK 200 RESOLUTION RANGE LOW (A) : 87.501 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03300 REMARK 200 FOR THE DATA SET : 30.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.53600 REMARK 200 R SYM FOR SHELL (I) : 0.53600 REMARK 200 FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, PH 8.9, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+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 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 56.03250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 32.35038 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 67.42733 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 56.03250 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 32.35038 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 67.42733 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 56.03250 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 32.35038 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 67.42733 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 56.03250 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 32.35038 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 67.42733 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 56.03250 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 32.35038 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 67.42733 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 56.03250 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 32.35038 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 67.42733 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 64.70076 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 134.85467 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 64.70076 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 134.85467 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 64.70076 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 134.85467 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 64.70076 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 134.85467 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 64.70076 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 134.85467 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 64.70076 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 134.85467 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 KCAL/MOL 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 BIOMT1 2 -0.500000 -0.866025 0.000000 56.03250 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -97.05114 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 112.06500 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 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: 28270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 KCAL/MOL 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 406 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 448 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LYS A 228 REMARK 465 SER A 229 REMARK 465 ASP B 51 REMARK 465 LEU B 52 REMARK 465 SER B 53 REMARK 465 GLY B 54 REMARK 465 ARG B 55 REMARK 465 LYS B 228 REMARK 465 SER B 229 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 49 68.94 -157.25 REMARK 500 GLN A 100 54.59 -92.77 REMARK 500 TYR A 173 65.42 27.26 REMARK 500 LYS A 180 105.74 -55.43 REMARK 500 TYR B 173 66.49 27.96 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 MG A 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 7 OD1 REMARK 620 2 ASP A 80 OD2 94.9 REMARK 620 3 HOH A 589 O 96.0 84.8 REMARK 620 4 HOH A 587 O 172.2 92.5 87.3 REMARK 620 5 HOH A 590 O 82.3 158.8 74.7 91.8 REMARK 620 6 HOH A 588 O 87.4 86.4 170.8 90.4 114.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 7 OD1 REMARK 620 2 ASP B 80 OD2 93.0 REMARK 620 3 HOH B 565 O 85.4 93.1 REMARK 620 4 HOH B 566 O 175.6 90.5 91.9 REMARK 620 5 HOH B 567 O 85.8 171.5 78.4 90.3 REMARK 620 6 HOH B 568 O 94.5 99.2 167.7 87.4 89.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YOT RELATED DB: PDB REMARK 900 RELATED ID: 4YOU RELATED DB: PDB REMARK 900 RELATED ID: 4YOV RELATED DB: PDB REMARK 900 RELATED ID: 4YOW RELATED DB: PDB REMARK 900 RELATED ID: 4YOX RELATED DB: PDB REMARK 900 RELATED ID: 4YOY RELATED DB: PDB DBREF1 4YOR A 1 229 UNP A0A060P168_PYRHR DBREF2 4YOR A A0A060P168 1 229 DBREF1 4YOR B 1 229 UNP A0A060P168_PYRHR DBREF2 4YOR B A0A060P168 1 229 SEQRES 1 A 229 MET ARG ILE VAL ALA ALA ASP THR GLY GLY ALA VAL LEU SEQRES 2 A 229 ASP GLU SER PHE GLN PRO VAL GLY LEU ILE ALA THR VAL SEQRES 3 A 229 ALA VAL LEU VAL GLU LYS PRO TYR LYS THR SER LYS ARG SEQRES 4 A 229 PHE LEU VAL LYS TYR ALA ASP PRO TYR ASN TYR ASP LEU SEQRES 5 A 229 SER GLY ARG GLN ALA ILE ARG ASP GLU ILE GLU LEU ALA SEQRES 6 A 229 ILE GLU LEU ALA ARG GLU VAL SER PRO ASP VAL ILE HIS SEQRES 7 A 229 LEU ASP SER THR LEU GLY GLY ILE GLU VAL ARG LYS LEU SEQRES 8 A 229 ASP GLU SER THR ILE ASP ALA LEU GLN ILE SER ASP ARG SEQRES 9 A 229 GLY LYS GLU ILE TRP LYS GLU LEU SER LYS ASP LEU GLN SEQRES 10 A 229 PRO LEU ALA LYS LYS PHE TRP GLU GLU THR GLY ILE GLU SEQRES 11 A 229 ILE ILE ALA ILE GLY LYS SER SER VAL PRO VAL ARG ILE SEQRES 12 A 229 ALA GLU ILE TYR ALA GLY ILE PHE SER VAL LYS TRP ALA SEQRES 13 A 229 LEU ASP ASN VAL LYS GLU LYS GLY GLY LEU LEU VAL GLY SEQRES 14 A 229 LEU PRO ARG TYR MET GLU VAL GLU ILE LYS LYS ASP LYS SEQRES 15 A 229 ILE ILE GLY LYS SER LEU ASP PRO ARG GLU GLY GLY LEU SEQRES 16 A 229 TYR GLY GLU VAL LYS THR GLU VAL PRO GLN GLY ILE LYS SEQRES 17 A 229 TRP GLU LEU TYR PRO ASN PRO LEU VAL ARG ARG PHE MET SEQRES 18 A 229 VAL PHE GLU ILE THR SER LYS SER SEQRES 1 B 229 MET ARG ILE VAL ALA ALA ASP THR GLY GLY ALA VAL LEU SEQRES 2 B 229 ASP GLU SER PHE GLN PRO VAL GLY LEU ILE ALA THR VAL SEQRES 3 B 229 ALA VAL LEU VAL GLU LYS PRO TYR LYS THR SER LYS ARG SEQRES 4 B 229 PHE LEU VAL LYS TYR ALA ASP PRO TYR ASN TYR ASP LEU SEQRES 5 B 229 SER GLY ARG GLN ALA ILE ARG ASP GLU ILE GLU LEU ALA SEQRES 6 B 229 ILE GLU LEU ALA ARG GLU VAL SER PRO ASP VAL ILE HIS SEQRES 7 B 229 LEU ASP SER THR LEU GLY GLY ILE GLU VAL ARG LYS LEU SEQRES 8 B 229 ASP GLU SER THR ILE ASP ALA LEU GLN ILE SER ASP ARG SEQRES 9 B 229 GLY LYS GLU ILE TRP LYS GLU LEU SER LYS ASP LEU GLN SEQRES 10 B 229 PRO LEU ALA LYS LYS PHE TRP GLU GLU THR GLY ILE GLU SEQRES 11 B 229 ILE ILE ALA ILE GLY LYS SER SER VAL PRO VAL ARG ILE SEQRES 12 B 229 ALA GLU ILE TYR ALA GLY ILE PHE SER VAL LYS TRP ALA SEQRES 13 B 229 LEU ASP ASN VAL LYS GLU LYS GLY GLY LEU LEU VAL GLY SEQRES 14 B 229 LEU PRO ARG TYR MET GLU VAL GLU ILE LYS LYS ASP LYS SEQRES 15 B 229 ILE ILE GLY LYS SER LEU ASP PRO ARG GLU GLY GLY LEU SEQRES 16 B 229 TYR GLY GLU VAL LYS THR GLU VAL PRO GLN GLY ILE LYS SEQRES 17 B 229 TRP GLU LEU TYR PRO ASN PRO LEU VAL ARG ARG PHE MET SEQRES 18 B 229 VAL PHE GLU ILE THR SER LYS SER HET MG A 301 1 HET MG B 301 1 HETNAM MG MAGNESIUM ION FORMUL 3 MG 2(MG 2+) FORMUL 5 HOH *386(H2 O) HELIX 1 AA1 ASP A 46 TYR A 50 5 5 HELIX 2 AA2 GLY A 54 SER A 73 1 20 HELIX 3 AA3 GLU A 87 LEU A 91 5 5 HELIX 4 AA4 ASP A 92 LEU A 99 1 8 HELIX 5 AA5 SER A 102 GLY A 128 1 27 HELIX 6 AA6 ILE A 134 SER A 137 5 4 HELIX 7 AA7 SER A 138 GLY A 164 1 27 HELIX 8 AA8 ASP A 189 GLY A 193 5 5 HELIX 9 AA9 ASP B 46 TYR B 50 5 5 HELIX 10 AB1 ALA B 57 SER B 73 1 17 HELIX 11 AB2 GLU B 87 LEU B 91 5 5 HELIX 12 AB3 ASP B 92 LEU B 99 1 8 HELIX 13 AB4 SER B 102 GLY B 128 1 27 HELIX 14 AB5 ILE B 134 SER B 137 5 4 HELIX 15 AB6 SER B 138 GLY B 164 1 27 HELIX 16 AB7 ASP B 189 GLY B 193 5 5 SHEET 1 AA1 5 ARG A 39 TYR A 44 0 SHEET 2 AA1 5 PRO A 19 VAL A 30 -1 N THR A 25 O LYS A 43 SHEET 3 AA1 5 ILE A 3 LEU A 13 -1 N VAL A 12 O VAL A 20 SHEET 4 AA1 5 VAL A 76 HIS A 78 1 O HIS A 78 N VAL A 4 SHEET 5 AA1 5 GLU A 130 ILE A 132 1 O ILE A 132 N ILE A 77 SHEET 1 AA2 6 ARG A 39 TYR A 44 0 SHEET 2 AA2 6 PRO A 19 VAL A 30 -1 N THR A 25 O LYS A 43 SHEET 3 AA2 6 ILE A 3 LEU A 13 -1 N VAL A 12 O VAL A 20 SHEET 4 AA2 6 GLY A 165 ARG A 172 -1 O GLY A 169 N ALA A 11 SHEET 5 AA2 6 PHE A 220 THR A 226 -1 O PHE A 223 N VAL A 168 SHEET 6 AA2 6 LYS A 208 PRO A 213 -1 N TYR A 212 O VAL A 222 SHEET 1 AA3 3 MET A 174 LYS A 179 0 SHEET 2 AA3 3 LYS A 182 SER A 187 -1 O ILE A 184 N GLU A 177 SHEET 3 AA3 3 TYR A 196 LYS A 200 -1 O VAL A 199 N ILE A 183 SHEET 1 AA4 5 ARG B 39 TYR B 44 0 SHEET 2 AA4 5 PRO B 19 VAL B 30 -1 N THR B 25 O LYS B 43 SHEET 3 AA4 5 ILE B 3 LEU B 13 -1 N VAL B 12 O VAL B 20 SHEET 4 AA4 5 VAL B 76 HIS B 78 1 O HIS B 78 N VAL B 4 SHEET 5 AA4 5 GLU B 130 ILE B 132 1 O ILE B 132 N ILE B 77 SHEET 1 AA5 6 ARG B 39 TYR B 44 0 SHEET 2 AA5 6 PRO B 19 VAL B 30 -1 N THR B 25 O LYS B 43 SHEET 3 AA5 6 ILE B 3 LEU B 13 -1 N VAL B 12 O VAL B 20 SHEET 4 AA5 6 GLY B 165 ARG B 172 -1 O GLY B 169 N ALA B 11 SHEET 5 AA5 6 PHE B 220 THR B 226 -1 O PHE B 223 N VAL B 168 SHEET 6 AA5 6 LYS B 208 PRO B 213 -1 N TYR B 212 O VAL B 222 SHEET 1 AA6 3 MET B 174 LYS B 179 0 SHEET 2 AA6 3 LYS B 182 SER B 187 -1 O ILE B 184 N GLU B 177 SHEET 3 AA6 3 TYR B 196 LYS B 200 -1 O VAL B 199 N ILE B 183 LINK OD1 ASP A 7 MG MG A 301 1555 1555 2.04 LINK OD2 ASP A 80 MG MG A 301 1555 1555 1.95 LINK OD1 ASP B 7 MG MG B 301 1555 1555 2.05 LINK OD2 ASP B 80 MG MG B 301 1555 1555 1.97 LINK MG MG A 301 O HOH A 589 1555 1555 2.43 LINK MG MG A 301 O HOH A 587 1555 1555 2.09 LINK MG MG A 301 O HOH A 590 1555 1555 2.04 LINK MG MG A 301 O HOH A 588 1555 1555 2.25 LINK MG MG B 301 O HOH B 565 1555 1555 2.17 LINK MG MG B 301 O HOH B 566 1555 1555 2.09 LINK MG MG B 301 O HOH B 567 1555 1555 2.24 LINK MG MG B 301 O HOH B 568 1555 1555 2.00 CISPEP 1 LYS A 32 PRO A 33 0 4.85 CISPEP 2 LYS B 32 PRO B 33 0 7.88 SITE 1 AC1 6 ASP A 7 ASP A 80 HOH A 587 HOH A 588 SITE 2 AC1 6 HOH A 589 HOH A 590 SITE 1 AC2 6 ASP B 7 ASP B 80 HOH B 565 HOH B 566 SITE 2 AC2 6 HOH B 567 HOH B 568 CRYST1 112.065 112.065 202.282 90.00 90.00 120.00 H 3 2 36 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 0.008923 0.005152 0.000000 0.00000 SCALE2 0.000000 0.010304 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004944 0.00000 MASTER 496 0 2 16 28 0 4 6 0 0 0 36 END