HEADER SUGAR BINDING PROTEIN 17-MAY-22 7XTM TITLE CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF BOMBYX MORI N- TITLE 2 ACETYLGLUCOSAMINYLTRANSFERASE IV COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-ACETYLGLUCOSAMINYLTRANSFERASE IV; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: GB:BDI24347.2 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOMBYX MORI; SOURCE 3 ORGANISM_COMMON: DOMESTIC SILKWORM; SOURCE 4 ORGANISM_TAXID: 7091; SOURCE 5 GENE: MGAT4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS GLYCOSYLTRANSFERASE, N-GLYCAN, N-GLYCOSYLATION, GOLGI, N- KEYWDS 2 ACETYLGLUCOSAMINE, CARBOHYDRATE-BINDING MODULE, LECTIN, SUGAR KEYWDS 3 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.MIYAZAKI,N.OKA,S.MORI REVDAT 4 03-APR-24 7XTM 1 REMARK REVDAT 3 07-DEC-22 7XTM 1 JRNL REVDAT 2 30-NOV-22 7XTM 1 COMPND SOURCE DBREF SEQADV REVDAT 1 28-SEP-22 7XTM 0 JRNL AUTH N.OKA,S.MORI,M.IKEGAYA,E.Y.PARK,T.MIYAZAKI JRNL TITL CRYSTAL STRUCTURE AND SUGAR-BINDING ABILITY OF THE JRNL TITL 2 C-TERMINAL DOMAIN OF N-ACETYLGLUCOSAMINYLTRANSFERASE IV JRNL TITL 3 ESTABLISH A NEW CARBOHYDRATE-BINDING MODULE FAMILY. JRNL REF GLYCOBIOLOGY V. 32 1153 2022 JRNL REFN ESSN 1460-2423 JRNL PMID 36106687 JRNL DOI 10.1093/GLYCOB/CWAC058 REMARK 2 REMARK 2 RESOLUTION. 1.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 53581 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.013 REMARK 3 FREE R VALUE TEST SET COUNT : 2686 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.47 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.51 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2963 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.3000 REMARK 3 BIN FREE R VALUE SET COUNT : 145 REMARK 3 BIN FREE R VALUE : 0.3590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2317 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 152 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.60000 REMARK 3 B22 (A**2) : -1.84800 REMARK 3 B33 (A**2) : 2.38600 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.13400 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.085 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.084 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.062 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.375 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.933 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2457 ; 0.012 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2203 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3344 ; 1.729 ; 1.651 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5085 ; 1.457 ; 1.580 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 289 ; 8.001 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 149 ;34.856 ;23.624 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 387 ;12.794 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;12.439 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 311 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2812 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 616 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 396 ; 0.203 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 61 ; 0.141 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1137 ; 0.185 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 135 ; 0.141 ; 0.200 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): 1126 ; 0.820 ; 1.042 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1125 ; 0.814 ; 1.040 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1407 ; 1.337 ; 1.558 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1408 ; 1.337 ; 1.560 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1331 ; 1.151 ; 1.242 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1332 ; 1.151 ; 1.244 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1931 ; 1.803 ; 1.796 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1932 ; 1.802 ; 1.798 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 409 A 421 REMARK 3 ORIGIN FOR THE GROUP (A): 5.1003 1.3202 4.7377 REMARK 3 T TENSOR REMARK 3 T11: 0.0540 T22: 0.1472 REMARK 3 T33: 0.0900 T12: 0.0046 REMARK 3 T13: 0.0060 T23: -0.0014 REMARK 3 L TENSOR REMARK 3 L11: 1.6414 L22: 5.9290 REMARK 3 L33: 2.1340 L12: 1.0281 REMARK 3 L13: 0.3366 L23: 1.0295 REMARK 3 S TENSOR REMARK 3 S11: -0.0295 S12: -0.0175 S13: 0.0876 REMARK 3 S21: -0.0728 S22: -0.0586 S23: 0.3582 REMARK 3 S31: -0.0642 S32: -0.1483 S33: 0.0881 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 422 A 454 REMARK 3 ORIGIN FOR THE GROUP (A): 11.1505 -0.4969 15.5930 REMARK 3 T TENSOR REMARK 3 T11: 0.1393 T22: 0.1714 REMARK 3 T33: 0.0264 T12: -0.0086 REMARK 3 T13: 0.0275 T23: -0.0003 REMARK 3 L TENSOR REMARK 3 L11: 0.8737 L22: 2.1063 REMARK 3 L33: 0.3911 L12: 0.1999 REMARK 3 L13: 0.3612 L23: 0.1288 REMARK 3 S TENSOR REMARK 3 S11: 0.0327 S12: -0.1188 S13: -0.0574 REMARK 3 S21: 0.3235 S22: -0.0484 S23: 0.1721 REMARK 3 S31: 0.0865 S32: -0.0910 S33: 0.0157 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 455 A 476 REMARK 3 ORIGIN FOR THE GROUP (A): 12.0297 -1.6127 1.9207 REMARK 3 T TENSOR REMARK 3 T11: 0.0977 T22: 0.1449 REMARK 3 T33: 0.0389 T12: 0.0011 REMARK 3 T13: -0.0049 T23: -0.0052 REMARK 3 L TENSOR REMARK 3 L11: 0.5104 L22: 2.3253 REMARK 3 L33: 1.1604 L12: 0.2535 REMARK 3 L13: 0.2590 L23: 0.9075 REMARK 3 S TENSOR REMARK 3 S11: 0.0156 S12: 0.0071 S13: 0.0099 REMARK 3 S21: -0.0506 S22: -0.0805 S23: 0.1606 REMARK 3 S31: 0.0143 S32: -0.0915 S33: 0.0649 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 477 A 502 REMARK 3 ORIGIN FOR THE GROUP (A): 20.7617 -2.8272 4.3263 REMARK 3 T TENSOR REMARK 3 T11: 0.1008 T22: 0.1418 REMARK 3 T33: 0.0269 T12: 0.0005 REMARK 3 T13: -0.0114 T23: -0.0065 REMARK 3 L TENSOR REMARK 3 L11: 0.0664 L22: 2.1177 REMARK 3 L33: 1.3404 L12: 0.2873 REMARK 3 L13: 0.1266 L23: 0.8024 REMARK 3 S TENSOR REMARK 3 S11: 0.0381 S12: -0.0065 S13: -0.0353 REMARK 3 S21: -0.0558 S22: 0.0294 S23: -0.1825 REMARK 3 S31: 0.0084 S32: 0.0533 S33: -0.0675 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 503 A 526 REMARK 3 ORIGIN FOR THE GROUP (A): 19.3219 -0.0071 -1.4145 REMARK 3 T TENSOR REMARK 3 T11: 0.1352 T22: 0.1538 REMARK 3 T33: 0.0108 T12: -0.0072 REMARK 3 T13: 0.0054 T23: 0.0004 REMARK 3 L TENSOR REMARK 3 L11: 0.5216 L22: 1.3848 REMARK 3 L33: 0.3772 L12: -0.0346 REMARK 3 L13: 0.2756 L23: 0.5450 REMARK 3 S TENSOR REMARK 3 S11: 0.0279 S12: 0.0792 S13: 0.0212 REMARK 3 S21: -0.0685 S22: -0.0039 S23: -0.0891 REMARK 3 S31: -0.0096 S32: 0.0589 S33: -0.0240 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 527 A 541 REMARK 3 ORIGIN FOR THE GROUP (A): 19.3795 3.6006 13.7109 REMARK 3 T TENSOR REMARK 3 T11: 0.1173 T22: 0.1551 REMARK 3 T33: 0.0059 T12: -0.0022 REMARK 3 T13: -0.0104 T23: 0.0054 REMARK 3 L TENSOR REMARK 3 L11: 1.1490 L22: 1.6189 REMARK 3 L33: 0.7864 L12: 0.0544 REMARK 3 L13: 0.3831 L23: -0.0281 REMARK 3 S TENSOR REMARK 3 S11: 0.0313 S12: -0.0184 S13: -0.0727 REMARK 3 S21: 0.2237 S22: -0.0091 S23: 0.0065 REMARK 3 S31: -0.0278 S32: 0.0228 S33: -0.0222 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 542 A 547 REMARK 3 ORIGIN FOR THE GROUP (A): 7.4267 0.4226 -5.8308 REMARK 3 T TENSOR REMARK 3 T11: 0.1676 T22: 0.1682 REMARK 3 T33: 0.2240 T12: -0.0601 REMARK 3 T13: -0.1078 T23: 0.0670 REMARK 3 L TENSOR REMARK 3 L11: 1.2468 L22: 5.9858 REMARK 3 L33: 18.4779 L12: -1.9593 REMARK 3 L13: 2.6394 L23: 1.0271 REMARK 3 S TENSOR REMARK 3 S11: 0.0842 S12: 0.1095 S13: -0.0486 REMARK 3 S21: -0.4002 S22: -0.1734 S23: 0.5661 REMARK 3 S31: 0.1802 S32: -0.2740 S33: 0.0892 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 : B 409 B 421 REMARK 3 ORIGIN FOR THE GROUP (A): 17.7804 -32.4003 34.9558 REMARK 3 T TENSOR REMARK 3 T11: 0.0611 T22: 0.1756 REMARK 3 T33: 0.0757 T12: -0.0122 REMARK 3 T13: -0.0189 T23: 0.0023 REMARK 3 L TENSOR REMARK 3 L11: 1.6138 L22: 7.5928 REMARK 3 L33: 1.7608 L12: 0.4764 REMARK 3 L13: 0.3975 L23: 0.9378 REMARK 3 S TENSOR REMARK 3 S11: 0.0023 S12: 0.0459 S13: -0.0359 REMARK 3 S21: 0.0064 S22: 0.0271 S23: 0.2315 REMARK 3 S31: 0.0527 S32: -0.0896 S33: -0.0295 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 : B 422 B 456 REMARK 3 ORIGIN FOR THE GROUP (A): 23.9897 -29.9850 24.2607 REMARK 3 T TENSOR REMARK 3 T11: 0.1495 T22: 0.1896 REMARK 3 T33: 0.0439 T12: 0.0031 REMARK 3 T13: -0.0287 T23: 0.0091 REMARK 3 L TENSOR REMARK 3 L11: 0.4837 L22: 1.3712 REMARK 3 L33: 0.5464 L12: -0.5962 REMARK 3 L13: 0.3578 L23: -0.2236 REMARK 3 S TENSOR REMARK 3 S11: 0.0736 S12: 0.0598 S13: 0.0603 REMARK 3 S21: -0.2300 S22: -0.1289 S23: 0.0625 REMARK 3 S31: -0.0027 S32: -0.0249 S33: 0.0553 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 : B 457 B 476 REMARK 3 ORIGIN FOR THE GROUP (A): 24.4970 -29.6037 38.1023 REMARK 3 T TENSOR REMARK 3 T11: 0.1116 T22: 0.1634 REMARK 3 T33: 0.0071 T12: -0.0126 REMARK 3 T13: -0.0194 T23: 0.0074 REMARK 3 L TENSOR REMARK 3 L11: 0.5859 L22: 3.3790 REMARK 3 L33: 1.5196 L12: -0.5487 REMARK 3 L13: 0.0958 L23: 0.8547 REMARK 3 S TENSOR REMARK 3 S11: 0.0128 S12: -0.0020 S13: 0.0065 REMARK 3 S21: 0.1247 S22: -0.0630 S23: 0.0486 REMARK 3 S31: 0.0068 S32: -0.1045 S33: 0.0502 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 : B 477 B 503 REMARK 3 ORIGIN FOR THE GROUP (A): 33.9668 -28.4791 35.0722 REMARK 3 T TENSOR REMARK 3 T11: 0.1083 T22: 0.1590 REMARK 3 T33: 0.0309 T12: -0.0046 REMARK 3 T13: -0.0212 T23: 0.0101 REMARK 3 L TENSOR REMARK 3 L11: 0.0695 L22: 2.0438 REMARK 3 L33: 1.2458 L12: -0.1475 REMARK 3 L13: 0.2331 L23: 0.3286 REMARK 3 S TENSOR REMARK 3 S11: 0.0136 S12: 0.0370 S13: 0.0311 REMARK 3 S21: 0.0981 S22: -0.0617 S23: -0.2162 REMARK 3 S31: 0.0370 S32: 0.0689 S33: 0.0482 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 : B 504 B 524 REMARK 3 ORIGIN FOR THE GROUP (A): 31.8995 -31.3835 41.7556 REMARK 3 T TENSOR REMARK 3 T11: 0.2090 T22: 0.1597 REMARK 3 T33: 0.0394 T12: 0.0021 REMARK 3 T13: -0.0758 T23: 0.0218 REMARK 3 L TENSOR REMARK 3 L11: 1.9329 L22: 1.6989 REMARK 3 L33: 0.4341 L12: 0.3775 REMARK 3 L13: -0.3921 L23: 0.6810 REMARK 3 S TENSOR REMARK 3 S11: 0.1263 S12: -0.0858 S13: -0.0879 REMARK 3 S21: 0.2168 S22: -0.0704 S23: -0.2010 REMARK 3 S31: 0.0519 S32: -0.0050 S33: -0.0559 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 : B 525 B 548 REMARK 3 ORIGIN FOR THE GROUP (A): 28.1626 -32.6307 32.4330 REMARK 3 T TENSOR REMARK 3 T11: 0.1335 T22: 0.1742 REMARK 3 T33: 0.0563 T12: -0.0117 REMARK 3 T13: 0.0117 T23: 0.0011 REMARK 3 L TENSOR REMARK 3 L11: 0.7570 L22: 1.7796 REMARK 3 L33: 0.5129 L12: -0.8709 REMARK 3 L13: -0.2902 L23: 0.0469 REMARK 3 S TENSOR REMARK 3 S11: 0.0473 S12: 0.0396 S13: 0.1303 REMARK 3 S21: -0.0385 S22: -0.0130 S23: -0.0351 REMARK 3 S31: 0.1065 S32: -0.0623 S33: -0.0342 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL PLUS MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 7XTM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1300029562. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53654 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.470 REMARK 200 RESOLUTION RANGE LOW (A) : 39.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.52600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 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: ALPHAFOLD2 MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES-NAOH, PH 7.0, 12%(W/V) REMARK 280 PEG20000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 32.23300 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 388 REMARK 465 GLY A 389 REMARK 465 SER A 390 REMARK 465 SER A 391 REMARK 465 HIS A 392 REMARK 465 HIS A 393 REMARK 465 HIS A 394 REMARK 465 HIS A 395 REMARK 465 HIS A 396 REMARK 465 HIS A 397 REMARK 465 SER A 398 REMARK 465 SER A 399 REMARK 465 GLY A 400 REMARK 465 LEU A 401 REMARK 465 VAL A 402 REMARK 465 PRO A 403 REMARK 465 ARG A 404 REMARK 465 GLY A 405 REMARK 465 SER A 406 REMARK 465 HIS A 407 REMARK 465 MET A 408 REMARK 465 GLU A 548 REMARK 465 LYS A 549 REMARK 465 LYS A 550 REMARK 465 THR A 551 REMARK 465 MET B 388 REMARK 465 GLY B 389 REMARK 465 SER B 390 REMARK 465 SER B 391 REMARK 465 HIS B 392 REMARK 465 HIS B 393 REMARK 465 HIS B 394 REMARK 465 HIS B 395 REMARK 465 HIS B 396 REMARK 465 HIS B 397 REMARK 465 SER B 398 REMARK 465 SER B 399 REMARK 465 GLY B 400 REMARK 465 LEU B 401 REMARK 465 VAL B 402 REMARK 465 PRO B 403 REMARK 465 ARG B 404 REMARK 465 GLY B 405 REMARK 465 SER B 406 REMARK 465 HIS B 407 REMARK 465 MET B 408 REMARK 465 LYS B 549 REMARK 465 LYS B 550 REMARK 465 THR B 551 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 ARG A 471 NE - CZ - NH2 ANGL. DEV. = -3.1 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 TYR B 430 -123.09 43.86 REMARK 500 REMARK 500 REMARK: NULL DBREF 7XTM A 388 551 PDB 7XTM 7XTM 388 551 DBREF 7XTM B 388 551 PDB 7XTM 7XTM 388 551 SEQRES 1 A 164 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 164 LEU VAL PRO ARG GLY SER HIS MET GLN SER TYR PHE PRO SEQRES 3 A 164 HIS GLN ASN PRO PRO ALA GLN LYS ILE THR THR THR ILE SEQRES 4 A 164 GLU ASP TYR TYR GLN HIS SER ILE GLN ASN ALA TYR GLU SEQRES 5 A 164 GLY ILE ASP PHE PHE TRP GLY LYS LYS PRO LYS LYS GLY SEQRES 6 A 164 ASP THR LEU GLU PHE TRP TYR GLY ARG PRO LEU GLN ILE SEQRES 7 A 164 LYS ARG VAL THR PHE ARG SER GLY ASN ALA GLU HIS ILE SEQRES 8 A 164 THR ASP GLN PHE TYR ASN THR VAL VAL GLU VAL LEU PRO SEQRES 9 A 164 ALA PHE GLY ASP ASN ASN PHE THR THR ILE LEU HIS PHE SEQRES 10 A 164 ASP GLU PHE GLY LEU ALA ASP GLY ASP VAL GLU GLU GLU SEQRES 11 A 164 PHE SER LEU VAL LYS ALA ILE ARG LEU ARG VAL ASN ALA SEQRES 12 A 164 ASP SER LYS TYR TRP VAL ILE LEU SER GLU ILE TYR ILE SEQRES 13 A 164 GLN THR PRO ASP GLU LYS LYS THR SEQRES 1 B 164 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 164 LEU VAL PRO ARG GLY SER HIS MET GLN SER TYR PHE PRO SEQRES 3 B 164 HIS GLN ASN PRO PRO ALA GLN LYS ILE THR THR THR ILE SEQRES 4 B 164 GLU ASP TYR TYR GLN HIS SER ILE GLN ASN ALA TYR GLU SEQRES 5 B 164 GLY ILE ASP PHE PHE TRP GLY LYS LYS PRO LYS LYS GLY SEQRES 6 B 164 ASP THR LEU GLU PHE TRP TYR GLY ARG PRO LEU GLN ILE SEQRES 7 B 164 LYS ARG VAL THR PHE ARG SER GLY ASN ALA GLU HIS ILE SEQRES 8 B 164 THR ASP GLN PHE TYR ASN THR VAL VAL GLU VAL LEU PRO SEQRES 9 B 164 ALA PHE GLY ASP ASN ASN PHE THR THR ILE LEU HIS PHE SEQRES 10 B 164 ASP GLU PHE GLY LEU ALA ASP GLY ASP VAL GLU GLU GLU SEQRES 11 B 164 PHE SER LEU VAL LYS ALA ILE ARG LEU ARG VAL ASN ALA SEQRES 12 B 164 ASP SER LYS TYR TRP VAL ILE LEU SER GLU ILE TYR ILE SEQRES 13 B 164 GLN THR PRO ASP GLU LYS LYS THR HET MES A 601 12 HET EDO A 602 4 HET EDO B 601 4 HET EDO B 602 4 HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 MES C6 H13 N O4 S FORMUL 4 EDO 3(C2 H6 O2) FORMUL 7 HOH *152(H2 O) HELIX 1 AA1 SER A 433 GLU A 439 1 7 HELIX 2 AA2 GLU A 515 PHE A 518 5 4 HELIX 3 AA3 SER B 433 GLU B 439 1 7 HELIX 4 AA4 GLU B 515 PHE B 518 5 4 SHEET 1 AA1 5 LYS A 421 THR A 424 0 SHEET 2 AA1 5 THR A 454 GLN A 464 -1 O TRP A 458 N LYS A 421 SHEET 3 AA1 5 LEU A 520 VAL A 528 -1 O ILE A 524 N PHE A 457 SHEET 4 AA1 5 THR A 485 PRO A 491 -1 N LEU A 490 O LYS A 522 SHEET 5 AA1 5 THR A 499 HIS A 503 -1 O ILE A 501 N VAL A 487 SHEET 1 AA2 4 PHE A 444 GLY A 446 0 SHEET 2 AA2 4 VAL A 536 GLN A 544 -1 O VAL A 536 N GLY A 446 SHEET 3 AA2 4 ARG A 467 SER A 472 -1 N ARG A 471 O GLU A 540 SHEET 4 AA2 4 LEU A 509 ASP A 513 -1 O ALA A 510 N PHE A 470 SHEET 1 AA3 5 LYS B 421 THR B 424 0 SHEET 2 AA3 5 THR B 454 GLN B 464 -1 O TRP B 458 N LYS B 421 SHEET 3 AA3 5 LEU B 520 VAL B 528 -1 O ILE B 524 N PHE B 457 SHEET 4 AA3 5 THR B 485 PRO B 491 -1 N LEU B 490 O LYS B 522 SHEET 5 AA3 5 THR B 499 HIS B 503 -1 O ILE B 501 N VAL B 487 SHEET 1 AA4 4 PHE B 444 GLY B 446 0 SHEET 2 AA4 4 VAL B 536 GLN B 544 -1 O VAL B 536 N GLY B 446 SHEET 3 AA4 4 ARG B 467 SER B 472 -1 N ARG B 471 O GLU B 540 SHEET 4 AA4 4 LEU B 509 ASP B 513 -1 O ALA B 510 N PHE B 470 CRYST1 32.733 64.466 78.810 90.00 95.09 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.030550 0.000000 0.002722 0.00000 SCALE2 0.000000 0.015512 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012739 0.00000