HEADER HYDROLASE/IMMUNE SYSTEM 01-DEC-15 5F21 TITLE HUMAN CD38 IN COMPLEX WITH NANOBODY MU375 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADP-RIBOSYL CYCLASE/CYCLIC ADP-RIBOSE HYDROLASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ECTODOMAIN, UNP RESIDUES 46-300; COMPND 5 SYNONYM: CD38; COMPND 6 EC: 3.2.2.6; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: NANOBODY MU375; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CD38; SOURCE 6 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: PICHIA PASTORIS; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: X33; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PPICZALPHA; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 14 ORGANISM_TAXID: 9844; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 16 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 19 EXPRESSION_SYSTEM_PLASMID: PHEN2 KEYWDS CD38, ADP-RIBOSYL CYCLASE, CYCLIC ADP-RIBOSE, X-CRYSTALLOGRAPHY, KEYWDS 2 CALCIUM SIGNALING, NANOBODY, MU375, HYDROLASE-IMMUNE SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Q.HAO,H.ZHANG REVDAT 2 08-NOV-23 5F21 1 REMARK REVDAT 1 15-JUN-16 5F21 0 JRNL AUTH T.LI,S.QI,M.UNGER,Y.N.HOU,Q.W.DENG,J.LIU,C.M.LAM,X.W.WANG, JRNL AUTH 2 D.XIN,P.ZHANG,F.KOCH-NOLTE,Q.HAO,H.ZHANG,H.C.LEE,Y.J.ZHAO JRNL TITL IMMUNO-TARGETING THE MULTIFUNCTIONAL CD38 USING NANOBODY JRNL REF SCI REP V. 6 27055 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 27251573 JRNL DOI 10.1038/SREP27055 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 28138 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) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1499 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1290 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 59.76 REMARK 3 BIN R VALUE (WORKING SET) : 0.1550 REMARK 3 BIN FREE R VALUE SET COUNT : 66 REMARK 3 BIN FREE R VALUE : 0.1930 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2855 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 273 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.26000 REMARK 3 B22 (A**2) : 0.96000 REMARK 3 B33 (A**2) : -1.22000 REMARK 3 B12 (A**2) : 0.00000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.139 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.093 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.148 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2957 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2750 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4012 ; 1.303 ; 1.945 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6345 ; 0.906 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 362 ; 6.047 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 134 ;38.986 ;24.030 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 511 ;13.588 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;15.977 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 445 ; 0.076 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3309 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 681 ; 0.001 ; 0.020 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): 1448 ; 0.728 ; 1.200 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1447 ; 0.722 ; 1.200 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1804 ; 0.883 ; 1.792 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 5707 ; 0.944 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 90 ;24.384 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 5823 ; 4.150 ; 5.000 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 : 12 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 49 A 70 REMARK 3 ORIGIN FOR THE GROUP (A): 41.9250 -7.6960 60.8160 REMARK 3 T TENSOR REMARK 3 T11: 0.0228 T22: 0.0703 REMARK 3 T33: 0.1895 T12: 0.0143 REMARK 3 T13: 0.0125 T23: 0.0934 REMARK 3 L TENSOR REMARK 3 L11: 4.0635 L22: 1.5948 REMARK 3 L33: 3.7141 L12: -0.2366 REMARK 3 L13: 1.3711 L23: -1.4554 REMARK 3 S TENSOR REMARK 3 S11: -0.0908 S12: -0.2509 S13: 0.0911 REMARK 3 S21: 0.1540 S22: 0.1435 S23: 0.1700 REMARK 3 S31: -0.1456 S32: -0.1320 S33: -0.0527 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 71 A 117 REMARK 3 ORIGIN FOR THE GROUP (A): 47.6090 -11.4570 50.3810 REMARK 3 T TENSOR REMARK 3 T11: 0.0211 T22: 0.1015 REMARK 3 T33: 0.1584 T12: -0.0229 REMARK 3 T13: -0.0045 T23: 0.0608 REMARK 3 L TENSOR REMARK 3 L11: 3.3714 L22: 1.5642 REMARK 3 L33: 4.8711 L12: -1.0688 REMARK 3 L13: 2.4715 L23: -1.9019 REMARK 3 S TENSOR REMARK 3 S11: -0.0541 S12: 0.3177 S13: -0.1125 REMARK 3 S21: -0.1013 S22: 0.0565 S23: -0.0073 REMARK 3 S31: 0.0166 S32: -0.0502 S33: -0.0024 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 118 A 144 REMARK 3 ORIGIN FOR THE GROUP (A): 48.7920 9.9750 48.1550 REMARK 3 T TENSOR REMARK 3 T11: 0.0498 T22: 0.0906 REMARK 3 T33: 0.1821 T12: -0.0194 REMARK 3 T13: 0.0038 T23: 0.1130 REMARK 3 L TENSOR REMARK 3 L11: 6.1446 L22: 4.1233 REMARK 3 L33: 5.7371 L12: -1.4728 REMARK 3 L13: 0.2060 L23: 0.2768 REMARK 3 S TENSOR REMARK 3 S11: -0.0443 S12: -0.0303 S13: 0.0130 REMARK 3 S21: 0.0626 S22: 0.2902 S23: 0.3646 REMARK 3 S31: 0.0098 S32: -0.3511 S33: -0.2460 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 145 A 193 REMARK 3 ORIGIN FOR THE GROUP (A): 51.7050 -7.6150 61.4260 REMARK 3 T TENSOR REMARK 3 T11: 0.0411 T22: 0.0722 REMARK 3 T33: 0.1744 T12: -0.0101 REMARK 3 T13: -0.0091 T23: 0.0693 REMARK 3 L TENSOR REMARK 3 L11: 2.8055 L22: 2.6123 REMARK 3 L33: 2.0131 L12: -0.2102 REMARK 3 L13: -0.1269 L23: -1.9921 REMARK 3 S TENSOR REMARK 3 S11: 0.0062 S12: -0.2744 S13: 0.0417 REMARK 3 S21: 0.1467 S22: 0.0224 S23: -0.0307 REMARK 3 S31: -0.1286 S32: 0.0699 S33: -0.0286 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 194 A 276 REMARK 3 ORIGIN FOR THE GROUP (A): 62.8700 11.7180 50.1040 REMARK 3 T TENSOR REMARK 3 T11: 0.0184 T22: 0.0710 REMARK 3 T33: 0.1060 T12: -0.0116 REMARK 3 T13: -0.0030 T23: 0.0400 REMARK 3 L TENSOR REMARK 3 L11: 1.8077 L22: 3.4505 REMARK 3 L33: 3.1743 L12: -0.1429 REMARK 3 L13: -0.7679 L23: -0.4719 REMARK 3 S TENSOR REMARK 3 S11: 0.0147 S12: -0.2165 S13: -0.0136 REMARK 3 S21: 0.1684 S22: 0.0126 S23: -0.2867 REMARK 3 S31: -0.0901 S32: 0.1907 S33: -0.0273 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 277 A 300 REMARK 3 ORIGIN FOR THE GROUP (A): 45.1660 27.2790 48.2880 REMARK 3 T TENSOR REMARK 3 T11: 0.1598 T22: 0.1316 REMARK 3 T33: 0.1771 T12: 0.1101 REMARK 3 T13: 0.1384 T23: 0.0917 REMARK 3 L TENSOR REMARK 3 L11: 1.8466 L22: 4.8680 REMARK 3 L33: 5.7013 L12: 1.3756 REMARK 3 L13: 0.2417 L23: -3.6009 REMARK 3 S TENSOR REMARK 3 S11: -0.0006 S12: -0.0399 S13: 0.2556 REMARK 3 S21: 0.7466 S22: 0.5653 S23: 0.7919 REMARK 3 S31: -0.6444 S32: -0.8202 S33: -0.5647 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 : B 3 B 11 REMARK 3 ORIGIN FOR THE GROUP (A): 62.1580 33.1300 30.8890 REMARK 3 T TENSOR REMARK 3 T11: 0.0184 T22: 0.0729 REMARK 3 T33: 0.1383 T12: 0.0207 REMARK 3 T13: 0.0170 T23: 0.0337 REMARK 3 L TENSOR REMARK 3 L11: 2.1073 L22: 22.0359 REMARK 3 L33: 14.4552 L12: 2.4979 REMARK 3 L13: -1.9670 L23: -14.2467 REMARK 3 S TENSOR REMARK 3 S11: 0.0357 S12: -0.1199 S13: -0.2918 REMARK 3 S21: -0.1172 S22: -0.0750 S23: -0.3047 REMARK 3 S31: 0.2453 S32: 0.3500 S33: 0.0392 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 12 B 22 REMARK 3 ORIGIN FOR THE GROUP (A): 57.1660 43.4800 25.1440 REMARK 3 T TENSOR REMARK 3 T11: 0.1060 T22: 0.0193 REMARK 3 T33: 0.0895 T12: 0.0123 REMARK 3 T13: 0.0325 T23: 0.0202 REMARK 3 L TENSOR REMARK 3 L11: 2.6633 L22: 24.1801 REMARK 3 L33: 1.6208 L12: -1.9792 REMARK 3 L13: 1.0642 L23: -2.7011 REMARK 3 S TENSOR REMARK 3 S11: -0.0603 S12: 0.0931 S13: 0.2806 REMARK 3 S21: -0.5961 S22: 0.0044 S23: -0.5174 REMARK 3 S31: -0.2330 S32: 0.0351 S33: 0.0559 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 23 B 44 REMARK 3 ORIGIN FOR THE GROUP (A): 56.0370 33.1590 39.2990 REMARK 3 T TENSOR REMARK 3 T11: 0.0878 T22: 0.0832 REMARK 3 T33: 0.1098 T12: 0.0291 REMARK 3 T13: -0.0028 T23: 0.0162 REMARK 3 L TENSOR REMARK 3 L11: 1.7803 L22: 7.9645 REMARK 3 L33: 3.3324 L12: 1.2378 REMARK 3 L13: -1.5664 L23: -2.5819 REMARK 3 S TENSOR REMARK 3 S11: 0.0202 S12: -0.1992 S13: 0.0236 REMARK 3 S21: 0.5105 S22: 0.0734 S23: -0.1230 REMARK 3 S31: -0.3434 S32: 0.1023 S33: -0.0936 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 45 B 87 REMARK 3 ORIGIN FOR THE GROUP (A): 49.1120 37.0570 34.2780 REMARK 3 T TENSOR REMARK 3 T11: 0.0544 T22: 0.0854 REMARK 3 T33: 0.1456 T12: 0.0645 REMARK 3 T13: 0.0507 T23: 0.0596 REMARK 3 L TENSOR REMARK 3 L11: 3.0941 L22: 4.5707 REMARK 3 L33: 4.2491 L12: 1.3523 REMARK 3 L13: -0.0035 L23: -2.3914 REMARK 3 S TENSOR REMARK 3 S11: 0.0114 S12: -0.0025 S13: 0.0040 REMARK 3 S21: 0.2203 S22: 0.2853 S23: 0.2003 REMARK 3 S31: -0.2479 S32: -0.4517 S33: -0.2967 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 88 B 104 REMARK 3 ORIGIN FOR THE GROUP (A): 56.4180 42.3590 35.6630 REMARK 3 T TENSOR REMARK 3 T11: 0.0991 T22: 0.0636 REMARK 3 T33: 0.0937 T12: 0.0375 REMARK 3 T13: -0.0018 T23: -0.0220 REMARK 3 L TENSOR REMARK 3 L11: 1.5329 L22: 5.6926 REMARK 3 L33: 6.2483 L12: 1.4901 REMARK 3 L13: -1.6707 L23: -4.5512 REMARK 3 S TENSOR REMARK 3 S11: -0.0096 S12: -0.1752 S13: 0.2471 REMARK 3 S21: 0.3793 S22: 0.2105 S23: 0.2369 REMARK 3 S31: -0.4967 S32: -0.1799 S33: -0.2009 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 105 B 120 REMARK 3 ORIGIN FOR THE GROUP (A): 62.1330 36.9550 37.1580 REMARK 3 T TENSOR REMARK 3 T11: 0.0503 T22: 0.1845 REMARK 3 T33: 0.1707 T12: -0.0577 REMARK 3 T13: -0.0523 T23: 0.0993 REMARK 3 L TENSOR REMARK 3 L11: 5.4407 L22: 9.1302 REMARK 3 L33: 6.6857 L12: 1.1999 REMARK 3 L13: -4.8662 L23: -5.0424 REMARK 3 S TENSOR REMARK 3 S11: 0.0027 S12: -0.6859 S13: -0.2672 REMARK 3 S21: 0.3268 S22: -0.8162 S23: -0.9783 REMARK 3 S31: -0.2196 S32: 0.9653 S33: 0.8135 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 5F21 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-DEC-15. REMARK 100 THE DEPOSITION ID IS D_1000215871. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97852 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31133 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.61400 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: 1YH3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 0.1 M BIS REMARK 280 -TRIS, 25%(W/V) PEG3350, PH 5.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 22.57450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.73800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.83300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.73800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.57450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.83300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 TRP A 46 REMARK 465 ARG A 47 REMARK 465 GLN A 48 REMARK 465 GLY A 246 REMARK 465 ARG A 247 REMARK 465 GLU A 248 REMARK 465 ASP A 249 REMARK 465 ASP B 1 REMARK 465 VAL B 2 REMARK 465 THR B 74 REMARK 465 GLY B 75 REMARK 465 ASP B 76 REMARK 465 ASN B 77 REMARK 465 SER B 121 REMARK 465 GLU B 122 REMARK 465 PRO B 123 REMARK 465 LYS B 124 REMARK 465 THR B 125 REMARK 465 PRO B 126 REMARK 465 LYS B 127 REMARK 465 PRO B 128 REMARK 465 GLN B 129 REMARK 465 PRO B 130 REMARK 465 ALA B 131 REMARK 465 ALA B 132 REMARK 465 ALA B 133 REMARK 465 HIS B 134 REMARK 465 HIS B 135 REMARK 465 HIS B 136 REMARK 465 HIS B 137 REMARK 465 HIS B 138 REMARK 465 HIS B 139 REMARK 465 GLY B 140 REMARK 465 ALA B 141 REMARK 465 ALA B 142 REMARK 465 GLU B 143 REMARK 465 GLN B 144 REMARK 465 LYS B 145 REMARK 465 LEU B 146 REMARK 465 ILE B 147 REMARK 465 SER B 148 REMARK 465 GLU B 149 REMARK 465 GLU B 150 REMARK 465 ASP B 151 REMARK 465 LEU B 152 REMARK 465 ASN B 153 REMARK 465 GLY B 154 REMARK 465 ALA B 155 REMARK 465 ALA B 156 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 ILE A 128 45.02 -150.00 REMARK 500 ASP A 179 -67.61 -107.01 REMARK 500 ASN A 182 58.90 -92.75 REMARK 500 ASP A 202 -120.37 59.78 REMARK 500 GLU A 233 -61.56 75.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5F1O RELATED DB: PDB REMARK 900 HUMAN CD38 IN COMPLEX WITH NANOBODY MU551 REMARK 900 RELATED ID: 5F1K RELATED DB: PDB REMARK 900 HUMAN CD38 IN COMPLEX WITH NANOBODY MU1053 DBREF 5F21 A 46 300 UNP P28907 CD38_HUMAN 46 300 DBREF 5F21 B 1 156 PDB 5F21 5F21 1 156 SEQADV 5F21 THR A 49 UNP P28907 GLN 49 ENGINEERED MUTATION SEQADV 5F21 ASP A 100 UNP P28907 ASN 100 ENGINEERED MUTATION SEQADV 5F21 ASP A 164 UNP P28907 ASN 164 ENGINEERED MUTATION SEQADV 5F21 ASP A 209 UNP P28907 ASN 209 ENGINEERED MUTATION SEQADV 5F21 ASP A 219 UNP P28907 ASN 219 ENGINEERED MUTATION SEQRES 1 A 255 TRP ARG GLN THR TRP SER GLY PRO GLY THR THR LYS ARG SEQRES 2 A 255 PHE PRO GLU THR VAL LEU ALA ARG CYS VAL LYS TYR THR SEQRES 3 A 255 GLU ILE HIS PRO GLU MET ARG HIS VAL ASP CYS GLN SER SEQRES 4 A 255 VAL TRP ASP ALA PHE LYS GLY ALA PHE ILE SER LYS HIS SEQRES 5 A 255 PRO CYS ASP ILE THR GLU GLU ASP TYR GLN PRO LEU MET SEQRES 6 A 255 LYS LEU GLY THR GLN THR VAL PRO CYS ASN LYS ILE LEU SEQRES 7 A 255 LEU TRP SER ARG ILE LYS ASP LEU ALA HIS GLN PHE THR SEQRES 8 A 255 GLN VAL GLN ARG ASP MET PHE THR LEU GLU ASP THR LEU SEQRES 9 A 255 LEU GLY TYR LEU ALA ASP ASP LEU THR TRP CYS GLY GLU SEQRES 10 A 255 PHE ASP THR SER LYS ILE ASN TYR GLN SER CYS PRO ASP SEQRES 11 A 255 TRP ARG LYS ASP CYS SER ASN ASN PRO VAL SER VAL PHE SEQRES 12 A 255 TRP LYS THR VAL SER ARG ARG PHE ALA GLU ALA ALA CYS SEQRES 13 A 255 ASP VAL VAL HIS VAL MET LEU ASP GLY SER ARG SER LYS SEQRES 14 A 255 ILE PHE ASP LYS ASP SER THR PHE GLY SER VAL GLU VAL SEQRES 15 A 255 HIS ASN LEU GLN PRO GLU LYS VAL GLN THR LEU GLU ALA SEQRES 16 A 255 TRP VAL ILE HIS GLY GLY ARG GLU ASP SER ARG ASP LEU SEQRES 17 A 255 CYS GLN ASP PRO THR ILE LYS GLU LEU GLU SER ILE ILE SEQRES 18 A 255 SER LYS ARG ASN ILE GLN PHE SER CYS LYS ASN ILE TYR SEQRES 19 A 255 ARG PRO ASP LYS PHE LEU GLN CYS VAL LYS ASN PRO GLU SEQRES 20 A 255 ASP SER SER CYS THR SER GLU ILE SEQRES 1 B 156 ASP VAL GLN LEU GLN GLU SER GLY GLY GLY SER VAL GLN SEQRES 2 B 156 ALA GLY GLY SER LEU THR LEU SER CYS THR ALA SER GLY SEQRES 3 B 156 LEU LEU PHE ARG LEU ALA SER MET GLY TRP TYR ARG GLN SEQRES 4 B 156 ALA PRO GLY LYS GLU ARG GLU LEU ILE ALA THR ILE THR SEQRES 5 B 156 VAL GLY GLY LYS THR ASN TYR LYS ASP SER VAL GLN GLY SEQRES 6 B 156 ARG PHE ILE ILE THR ARG ASP ASN THR GLY ASP ASN THR SEQRES 7 B 156 LYS SER THR VAL THR LEU GLN MET ASN ARG LEU LYS PRO SEQRES 8 B 156 GLU ASP THR ALA VAL TYR TYR CYS ASN THR ALA SER PRO SEQRES 9 B 156 ALA VAL GLY ALA ASP THR TRP GLY GLN GLY THR ARG VAL SEQRES 10 B 156 THR VAL SER SER GLU PRO LYS THR PRO LYS PRO GLN PRO SEQRES 11 B 156 ALA ALA ALA HIS HIS HIS HIS HIS HIS GLY ALA ALA GLU SEQRES 12 B 156 GLN LYS LEU ILE SER GLU GLU ASP LEU ASN GLY ALA ALA HET SO4 A 401 5 HET SO4 A 402 5 HET GOL A 403 6 HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *273(H2 O) HELIX 1 AA1 ARG A 58 HIS A 74 1 17 HELIX 2 AA2 PRO A 75 ARG A 78 5 4 HELIX 3 AA3 ASP A 81 ILE A 94 1 14 HELIX 4 AA4 GLU A 103 ASP A 105 5 3 HELIX 5 AA5 TYR A 106 GLY A 113 1 8 HELIX 6 AA6 ILE A 128 GLN A 139 1 12 HELIX 7 AA7 THR A 144 ASP A 147 5 4 HELIX 8 AA8 THR A 148 ASP A 155 1 8 HELIX 9 AA9 ASN A 183 ALA A 199 1 17 HELIX 10 AB1 SER A 220 VAL A 225 1 6 HELIX 11 AB2 GLU A 226 LEU A 230 5 5 HELIX 12 AB3 ASP A 252 GLN A 255 5 4 HELIX 13 AB4 ASP A 256 ARG A 269 1 14 HELIX 14 AB5 ARG A 280 ASN A 290 1 11 HELIX 15 AB6 ASP A 293 THR A 297 5 5 HELIX 16 AB7 GLY B 26 ALA B 32 1 7 HELIX 17 AB8 LYS B 90 THR B 94 5 5 SHEET 1 AA1 2 GLY A 52 PRO A 53 0 SHEET 2 AA1 2 SER A 172 CYS A 173 -1 O CYS A 173 N GLY A 52 SHEET 1 AA2 4 LEU A 123 SER A 126 0 SHEET 2 AA2 4 ASP A 202 ASP A 209 1 O HIS A 205 N LEU A 124 SHEET 3 AA2 4 VAL A 235 ILE A 243 1 O TRP A 241 N VAL A 206 SHEET 4 AA2 4 GLN A 272 ILE A 278 1 O LYS A 276 N VAL A 242 SHEET 1 AA3 4 LEU B 4 SER B 7 0 SHEET 2 AA3 4 LEU B 18 SER B 25 -1 O SER B 21 N SER B 7 SHEET 3 AA3 4 LYS B 79 MET B 86 -1 O SER B 80 N ALA B 24 SHEET 4 AA3 4 PHE B 67 ASP B 72 -1 N ILE B 68 O GLN B 85 SHEET 1 AA4 6 GLY B 10 VAL B 12 0 SHEET 2 AA4 6 THR B 115 VAL B 119 1 O THR B 118 N GLY B 10 SHEET 3 AA4 6 ALA B 95 THR B 101 -1 N TYR B 97 O THR B 115 SHEET 4 AA4 6 MET B 34 GLN B 39 -1 N TYR B 37 O TYR B 98 SHEET 5 AA4 6 GLU B 46 ILE B 51 -1 O GLU B 46 N ARG B 38 SHEET 6 AA4 6 THR B 57 TYR B 59 -1 O ASN B 58 N THR B 50 SSBOND 1 CYS A 67 CYS A 82 1555 1555 2.11 SSBOND 2 CYS A 99 CYS A 180 1555 1555 2.07 SSBOND 3 CYS A 119 CYS A 201 1555 1555 2.05 SSBOND 4 CYS A 160 CYS A 173 1555 1555 2.09 SSBOND 5 CYS A 254 CYS A 275 1555 1555 2.10 SSBOND 6 CYS A 287 CYS A 296 1555 1555 2.04 SSBOND 7 CYS B 22 CYS B 99 1555 1555 2.10 SITE 1 AC1 9 TRP A 125 SER A 126 ARG A 127 SER A 220 SITE 2 AC1 9 THR A 221 PHE A 222 HOH A 511 HOH A 535 SITE 3 AC1 9 HOH A 586 SITE 1 AC2 5 LYS A 214 ARG A 280 PRO A 281 ASP A 282 SITE 2 AC2 5 LYS A 283 SITE 1 AC3 10 ASP A 100 ILE A 101 THR A 102 SER A 166 SITE 2 AC3 10 ILE A 168 ASN A 182 HOH A 506 HOH A 510 SITE 3 AC3 10 HOH A 515 HOH A 543 CRYST1 45.149 69.666 123.476 90.00 90.00 90.00 P 21 21 21 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 0.022149 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014354 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008099 0.00000