HEADER HYDROLASE 06-DEC-12 3W2X TITLE CRYSTAL STRUCTURE OF DNA URIDINE ENDONUCLEASE MTH212 COMPND MOL_ID: 1; COMPND 2 MOLECULE: EXODEOXYRIBONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.11.2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOTHERMOBACTER THERMAUTOTROPHICUS; SOURCE 3 ORGANISM_TAXID: 187420; SOURCE 4 STRAIN: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / DELTA H; SOURCE 5 GENE: MTH212, MTH_212; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS ALPHA/BETA-SANDWICH, HYDROLASE, DNA BINDING EXPDTA X-RAY DIFFRACTION AUTHOR N.TABATA,T.SHIDA,R.ARAI REVDAT 3 08-NOV-23 3W2X 1 REMARK SEQADV LINK REVDAT 2 22-NOV-17 3W2X 1 REMARK REVDAT 1 11-DEC-13 3W2X 0 JRNL AUTH N.TABATA,T.SHIDA,R.ARAI JRNL TITL CRYSTAL STRUCTURE OF DNA URIDINE ENDONUCLEASE MTH212 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 35667 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1778 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2629 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.75 REMARK 3 BIN R VALUE (WORKING SET) : 0.2300 REMARK 3 BIN FREE R VALUE SET COUNT : 145 REMARK 3 BIN FREE R VALUE : 0.2140 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2137 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 187 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.83000 REMARK 3 B22 (A**2) : 0.83000 REMARK 3 B33 (A**2) : -1.24000 REMARK 3 B12 (A**2) : 0.41000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.109 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.104 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.075 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.707 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2211 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2978 ; 1.228 ; 1.941 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 257 ; 6.450 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 121 ;35.820 ;22.810 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 383 ;14.821 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;14.275 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 297 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1730 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1278 ; 0.505 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2063 ; 0.878 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 933 ; 1.441 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 915 ; 2.177 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 13 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 25 REMARK 3 ORIGIN FOR THE GROUP (A): -40.2300 4.5670 18.3468 REMARK 3 T TENSOR REMARK 3 T11: 0.1257 T22: 0.0982 REMARK 3 T33: 0.1561 T12: -0.0236 REMARK 3 T13: -0.0429 T23: -0.0029 REMARK 3 L TENSOR REMARK 3 L11: 1.7535 L22: 1.7783 REMARK 3 L33: 2.5123 L12: -0.4287 REMARK 3 L13: 0.1043 L23: 0.0673 REMARK 3 S TENSOR REMARK 3 S11: 0.0787 S12: -0.0582 S13: -0.1547 REMARK 3 S21: -0.1494 S22: -0.0432 S23: 0.2494 REMARK 3 S31: 0.0884 S32: -0.1070 S33: -0.0355 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 26 A 43 REMARK 3 ORIGIN FOR THE GROUP (A): -39.8566 8.3152 17.1073 REMARK 3 T TENSOR REMARK 3 T11: 0.1392 T22: 0.1277 REMARK 3 T33: 0.1714 T12: -0.0108 REMARK 3 T13: -0.0452 T23: -0.0090 REMARK 3 L TENSOR REMARK 3 L11: 1.2887 L22: 2.4236 REMARK 3 L33: 3.2122 L12: -1.0021 REMARK 3 L13: -0.8110 L23: 0.3246 REMARK 3 S TENSOR REMARK 3 S11: 0.0521 S12: -0.0203 S13: -0.1985 REMARK 3 S21: -0.1901 S22: -0.0263 S23: 0.2822 REMARK 3 S31: 0.0928 S32: -0.1611 S33: -0.0258 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 44 A 53 REMARK 3 ORIGIN FOR THE GROUP (A): -44.1715 8.4299 5.2263 REMARK 3 T TENSOR REMARK 3 T11: 0.3605 T22: 0.2109 REMARK 3 T33: 0.1688 T12: 0.0537 REMARK 3 T13: -0.2117 T23: -0.0893 REMARK 3 L TENSOR REMARK 3 L11: 9.1012 L22: 3.4251 REMARK 3 L33: 8.4015 L12: -1.3765 REMARK 3 L13: -1.5443 L23: -0.6303 REMARK 3 S TENSOR REMARK 3 S11: 0.3614 S12: 1.1374 S13: -0.6027 REMARK 3 S21: -0.9931 S22: -0.1892 S23: 0.5270 REMARK 3 S31: 0.2449 S32: -0.8216 S33: -0.1722 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 54 A 67 REMARK 3 ORIGIN FOR THE GROUP (A): -36.0625 12.4048 8.6273 REMARK 3 T TENSOR REMARK 3 T11: 0.2193 T22: 0.1296 REMARK 3 T33: 0.1147 T12: 0.0081 REMARK 3 T13: -0.0280 T23: -0.0068 REMARK 3 L TENSOR REMARK 3 L11: 3.2957 L22: 2.4925 REMARK 3 L33: 3.1117 L12: -0.8375 REMARK 3 L13: -0.6990 L23: 0.2007 REMARK 3 S TENSOR REMARK 3 S11: 0.0873 S12: 0.1940 S13: -0.0908 REMARK 3 S21: -0.3974 S22: -0.1024 S23: 0.0553 REMARK 3 S31: 0.1342 S32: 0.0367 S33: 0.0151 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 68 A 101 REMARK 3 ORIGIN FOR THE GROUP (A): -29.2410 17.0084 12.6681 REMARK 3 T TENSOR REMARK 3 T11: 0.1382 T22: 0.1540 REMARK 3 T33: 0.1314 T12: -0.0060 REMARK 3 T13: 0.0144 T23: 0.0082 REMARK 3 L TENSOR REMARK 3 L11: 0.8975 L22: 1.9494 REMARK 3 L33: 1.1871 L12: -0.6011 REMARK 3 L13: 0.5143 L23: -0.6363 REMARK 3 S TENSOR REMARK 3 S11: 0.0325 S12: 0.1103 S13: 0.1031 REMARK 3 S21: -0.2125 S22: -0.1355 S23: -0.1788 REMARK 3 S31: -0.0293 S32: 0.2051 S33: 0.1031 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 102 A 107 REMARK 3 ORIGIN FOR THE GROUP (A): -35.5050 24.2783 22.6618 REMARK 3 T TENSOR REMARK 3 T11: 0.1790 T22: 0.1195 REMARK 3 T33: 0.1329 T12: -0.0091 REMARK 3 T13: -0.0251 T23: -0.0374 REMARK 3 L TENSOR REMARK 3 L11: 5.3567 L22: 8.4967 REMARK 3 L33: 6.3610 L12: 4.9777 REMARK 3 L13: 4.3797 L23: 0.7957 REMARK 3 S TENSOR REMARK 3 S11: -0.1616 S12: -0.2820 S13: 0.3958 REMARK 3 S21: 0.3706 S22: -0.0771 S23: 0.4227 REMARK 3 S31: -0.5640 S32: -0.3814 S33: 0.2387 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 108 A 135 REMARK 3 ORIGIN FOR THE GROUP (A): -17.4709 10.6771 17.0965 REMARK 3 T TENSOR REMARK 3 T11: 0.0618 T22: 0.2117 REMARK 3 T33: 0.1648 T12: -0.0205 REMARK 3 T13: 0.0423 T23: 0.0577 REMARK 3 L TENSOR REMARK 3 L11: 2.0713 L22: 2.5688 REMARK 3 L33: 2.2846 L12: -0.9514 REMARK 3 L13: 0.3253 L23: -0.1823 REMARK 3 S TENSOR REMARK 3 S11: 0.0220 S12: 0.2181 S13: -0.0020 REMARK 3 S21: -0.2254 S22: -0.1936 S23: -0.4562 REMARK 3 S31: 0.1037 S32: 0.4940 S33: 0.1717 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 136 A 154 REMARK 3 ORIGIN FOR THE GROUP (A): -24.9383 20.4821 23.9294 REMARK 3 T TENSOR REMARK 3 T11: 0.1564 T22: 0.1418 REMARK 3 T33: 0.1486 T12: -0.0633 REMARK 3 T13: -0.0504 T23: -0.0010 REMARK 3 L TENSOR REMARK 3 L11: 1.4819 L22: 3.7189 REMARK 3 L33: 0.7907 L12: -0.6536 REMARK 3 L13: 0.2276 L23: 0.1973 REMARK 3 S TENSOR REMARK 3 S11: -0.0868 S12: -0.0128 S13: 0.2671 REMARK 3 S21: -0.0055 S22: -0.0784 S23: -0.2635 REMARK 3 S31: -0.2317 S32: 0.1481 S33: 0.1653 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 155 A 170 REMARK 3 ORIGIN FOR THE GROUP (A): -17.2567 -1.6804 31.4457 REMARK 3 T TENSOR REMARK 3 T11: 0.0671 T22: 0.2004 REMARK 3 T33: 0.1678 T12: 0.0044 REMARK 3 T13: -0.0481 T23: 0.0392 REMARK 3 L TENSOR REMARK 3 L11: 2.6932 L22: 3.0036 REMARK 3 L33: 2.8836 L12: 0.1493 REMARK 3 L13: 0.0445 L23: -0.6772 REMARK 3 S TENSOR REMARK 3 S11: -0.0265 S12: -0.0217 S13: -0.1944 REMARK 3 S21: 0.1373 S22: -0.1838 S23: -0.4414 REMARK 3 S31: 0.2130 S32: 0.4479 S33: 0.2104 REMARK 3 REMARK 3 TLS GROUP : 10 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 171 A 189 REMARK 3 ORIGIN FOR THE GROUP (A): -15.8856 11.1979 28.5515 REMARK 3 T TENSOR REMARK 3 T11: 0.0416 T22: 0.2099 REMARK 3 T33: 0.2087 T12: -0.0749 REMARK 3 T13: -0.0726 T23: 0.0614 REMARK 3 L TENSOR REMARK 3 L11: 0.9071 L22: 6.8529 REMARK 3 L33: 2.5171 L12: -1.1650 REMARK 3 L13: -0.3587 L23: 0.3778 REMARK 3 S TENSOR REMARK 3 S11: 0.0231 S12: -0.1178 S13: 0.0649 REMARK 3 S21: 0.1933 S22: -0.3055 S23: -0.5872 REMARK 3 S31: -0.2404 S32: 0.4267 S33: 0.2825 REMARK 3 REMARK 3 TLS GROUP : 11 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 190 A 229 REMARK 3 ORIGIN FOR THE GROUP (A): -28.1080 2.2736 29.9968 REMARK 3 T TENSOR REMARK 3 T11: 0.1425 T22: 0.1656 REMARK 3 T33: 0.1335 T12: -0.0190 REMARK 3 T13: -0.0184 T23: -0.0048 REMARK 3 L TENSOR REMARK 3 L11: 0.5870 L22: 2.7289 REMARK 3 L33: 0.9506 L12: -0.2606 REMARK 3 L13: 0.2263 L23: -0.3839 REMARK 3 S TENSOR REMARK 3 S11: -0.0577 S12: -0.0246 S13: -0.0103 REMARK 3 S21: 0.0918 S22: 0.0324 S23: -0.0660 REMARK 3 S31: 0.0229 S32: 0.0595 S33: 0.0253 REMARK 3 REMARK 3 TLS GROUP : 12 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 230 A 253 REMARK 3 ORIGIN FOR THE GROUP (A): -35.6733 7.9647 29.3238 REMARK 3 T TENSOR REMARK 3 T11: 0.1034 T22: 0.1519 REMARK 3 T33: 0.1324 T12: -0.0239 REMARK 3 T13: -0.0099 T23: 0.0030 REMARK 3 L TENSOR REMARK 3 L11: 1.0437 L22: 3.9066 REMARK 3 L33: 2.4256 L12: -0.3987 REMARK 3 L13: 0.7849 L23: 0.4912 REMARK 3 S TENSOR REMARK 3 S11: -0.0567 S12: -0.2138 S13: -0.0271 REMARK 3 S21: 0.2118 S22: 0.1044 S23: 0.2477 REMARK 3 S31: -0.0007 S32: -0.1068 S33: -0.0478 REMARK 3 REMARK 3 TLS GROUP : 13 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 254 A 257 REMARK 3 ORIGIN FOR THE GROUP (A): -40.6989 20.2076 32.9463 REMARK 3 T TENSOR REMARK 3 T11: 0.1624 T22: 0.4804 REMARK 3 T33: 0.1070 T12: 0.1632 REMARK 3 T13: -0.0103 T23: -0.1248 REMARK 3 L TENSOR REMARK 3 L11: 15.9492 L22: 23.8608 REMARK 3 L33: 6.5256 L12: -3.1540 REMARK 3 L13: -1.4757 L23: 2.8890 REMARK 3 S TENSOR REMARK 3 S11: -0.1836 S12: -0.4750 S13: 0.9826 REMARK 3 S21: -0.1327 S22: -0.0839 S23: -0.0972 REMARK 3 S31: -0.6030 S32: -1.6572 S33: 0.2676 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3W2X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-DEC-12. REMARK 100 THE DEPOSITION ID IS D_1000095818. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : NULL 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-NW12A 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 : NUMERICAL LINK TYPE SI(111) REMARK 200 DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36324 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 10.70 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.00 REMARK 200 R MERGE FOR SHELL (I) : 0.59800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3FZI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG3350, 50MM MAGNESIUM FORMATE REMARK 280 DIHYDRATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 88.47733 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 44.23867 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 66.35800 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 22.11933 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 110.59667 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 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 38 62.11 63.54 REMARK 500 SER A 69 -139.47 53.75 REMARK 500 PHE A 173 24.07 -145.45 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 ASN A 12 OD1 REMARK 620 2 GLU A 38 OE2 93.9 REMARK 620 3 HOH A 403 O 95.9 91.3 REMARK 620 4 HOH A 409 O 84.0 90.3 178.4 REMARK 620 5 HOH A 421 O 93.7 172.2 89.5 88.9 REMARK 620 6 HOH A 568 O 164.0 99.3 92.8 86.9 72.9 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 FMT A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3W2Y RELATED DB: PDB REMARK 900 THE MUTANT ENZYME (W205S) DBREF 3W2X A 1 257 UNP O26314 O26314_METTH 1 257 SEQADV 3W2X GLY A -2 UNP O26314 EXPRESSION TAG SEQADV 3W2X SER A -1 UNP O26314 EXPRESSION TAG SEQADV 3W2X HIS A 0 UNP O26314 EXPRESSION TAG SEQRES 1 A 260 GLY SER HIS MET THR VAL LEU LYS ILE ILE SER TRP ASN SEQRES 2 A 260 VAL ASN GLY LEU ARG ALA VAL HIS ARG LYS GLY PHE LEU SEQRES 3 A 260 LYS TRP PHE MET GLU GLU LYS PRO ASP ILE LEU CYS LEU SEQRES 4 A 260 GLN GLU ILE LYS ALA ALA PRO GLU GLN LEU PRO ARG LYS SEQRES 5 A 260 LEU ARG HIS VAL GLU GLY TYR ARG SER PHE PHE THR PRO SEQRES 6 A 260 ALA GLU ARG LYS GLY TYR SER GLY VAL ALA MET TYR THR SEQRES 7 A 260 LYS VAL PRO PRO SER SER LEU ARG GLU GLY PHE GLY VAL SEQRES 8 A 260 GLU ARG PHE ASP THR GLU GLY ARG ILE GLN ILE ALA ASP SEQRES 9 A 260 PHE ASP ASP PHE LEU LEU TYR ASN ILE TYR PHE PRO ASN SEQRES 10 A 260 GLY LYS MET SER GLU GLU ARG LEU LYS TYR LYS LEU GLU SEQRES 11 A 260 PHE TYR ASP ALA PHE LEU GLU ASP VAL ASN ARG GLU ARG SEQRES 12 A 260 ASP SER GLY ARG ASN VAL ILE ILE CYS GLY ASP PHE ASN SEQRES 13 A 260 THR ALA HIS ARG GLU ILE ASP LEU ALA ARG PRO LYS GLU SEQRES 14 A 260 ASN SER ASN VAL SER GLY PHE LEU PRO VAL GLU ARG ALA SEQRES 15 A 260 TRP ILE ASP LYS PHE ILE GLU ASN GLY TYR VAL ASP THR SEQRES 16 A 260 PHE ARG MET PHE ASN SER ASP PRO GLY GLN TYR THR TRP SEQRES 17 A 260 TRP SER TYR ARG THR ARG ALA ARG GLU ARG ASN VAL GLY SEQRES 18 A 260 TRP ARG LEU ASP TYR PHE PHE VAL ASN GLU GLU PHE LYS SEQRES 19 A 260 GLY LYS VAL LYS ARG SER TRP ILE LEU SER ASP VAL MET SEQRES 20 A 260 GLY SER ASP HIS CYS PRO ILE GLY LEU GLU ILE GLU LEU HET MG A 301 1 HET FMT A 302 3 HET FMT A 303 3 HET FMT A 304 3 HETNAM MG MAGNESIUM ION HETNAM FMT FORMIC ACID FORMUL 2 MG MG 2+ FORMUL 3 FMT 3(C H2 O2) FORMUL 6 HOH *187(H2 O) HELIX 1 1 GLY A 13 LYS A 20 1 8 HELIX 2 2 GLY A 21 LYS A 30 1 10 HELIX 3 3 ALA A 42 LEU A 46 5 5 HELIX 4 4 PRO A 47 HIS A 52 1 6 HELIX 5 5 VAL A 88 THR A 93 1 6 HELIX 6 6 SER A 118 SER A 142 1 25 HELIX 7 7 ARG A 157 LEU A 161 5 5 HELIX 8 8 LEU A 174 ASN A 187 1 14 HELIX 9 9 THR A 192 ASN A 197 1 6 HELIX 10 10 GLU A 229 GLY A 232 5 4 SHEET 1 A 6 ARG A 57 THR A 61 0 SHEET 2 A 6 VAL A 71 THR A 75 -1 O THR A 75 N ARG A 57 SHEET 3 A 6 ILE A 33 GLN A 37 -1 N LEU A 36 O ALA A 72 SHEET 4 A 6 VAL A 3 ASN A 10 1 N ILE A 7 O CYS A 35 SHEET 5 A 6 ILE A 251 GLU A 256 -1 O LEU A 253 N ILE A 6 SHEET 6 A 6 VAL A 234 ILE A 239 -1 N TRP A 238 O GLY A 252 SHEET 1 B 6 LEU A 82 ARG A 83 0 SHEET 2 B 6 ILE A 97 ASP A 101 -1 O ILE A 99 N ARG A 83 SHEET 3 B 6 LEU A 106 TYR A 111 -1 O ASN A 109 N GLN A 98 SHEET 4 B 6 VAL A 146 ASP A 151 1 O ILE A 147 N TYR A 108 SHEET 5 B 6 ASP A 222 ASN A 227 -1 O PHE A 225 N ILE A 148 SHEET 6 B 6 TYR A 189 ASP A 191 -1 N VAL A 190 O VAL A 226 SHEET 1 C 2 TRP A 205 TRP A 206 0 SHEET 2 C 2 GLY A 218 TRP A 219 -1 O TRP A 219 N TRP A 205 LINK OD1 ASN A 12 MG MG A 301 1555 1555 1.99 LINK OE2 GLU A 38 MG MG A 301 1555 1555 2.14 LINK MG MG A 301 O HOH A 403 1555 1555 1.95 LINK MG MG A 301 O HOH A 409 1555 1555 2.11 LINK MG MG A 301 O HOH A 421 1555 1555 2.07 LINK MG MG A 301 O HOH A 568 1555 1555 2.20 SITE 1 AC1 6 ASN A 12 GLU A 38 HOH A 403 HOH A 409 SITE 2 AC1 6 HOH A 421 HOH A 568 SITE 1 AC2 7 ALA A 41 ALA A 42 ALA A 63 ARG A 65 SITE 2 AC2 7 GLY A 67 HOH A 469 HOH A 493 SITE 1 AC3 4 ARG A 65 LYS A 183 ASN A 187 HOH A 505 CRYST1 61.481 61.481 132.716 90.00 90.00 120.00 P 65 6 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 0.016265 0.009391 0.000000 0.00000 SCALE2 0.000000 0.018781 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007535 0.00000