HEADER HYDROLASE 02-AUG-18 6H8M TITLE CRYSTAL STRUCTURE OF THE THIRD SRCR DOMAIN OF MURINE NEUROTRYPSIN. COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROTRYPSIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: BRAIN-SPECIFIC SERINE PROTEASE 3,BSSP-3,MOTOPSIN,SERINE COMPND 5 PROTEASE 12; COMPND 6 EC: 3.4.21.-; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: THE FIRST TWO RESIDUES OF THE PROVIDED SEQUENCE (GS) COMPND 9 HAVE BEEN INTRODUCED DURING GENERATION OF THE RECOMBINANT PROTEIN COMPND 10 (TAG RESIDUES). THE LAST FIVE RESIDUES (KKASS) ARE FLEXIBLE. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: PRSS12, BSSP3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SHUFFLE T7; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PCIOX KEYWDS NEUROTRYPSIN, EXTRACELLULAR PROTEASE, SRCR DOMAIN, CRD DOMAIN, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.CANCIANI,F.FORNERIS REVDAT 3 17-JAN-24 6H8M 1 REMARK REVDAT 2 27-MAR-19 6H8M 1 JRNL REVDAT 1 20-FEB-19 6H8M 0 JRNL AUTH A.CANCIANI,G.CATUCCI,F.FORNERIS JRNL TITL STRUCTURAL CHARACTERIZATION OF THE THIRD SCAVENGER RECEPTOR JRNL TITL 2 CYSTEINE-RICH DOMAIN OF MURINE NEUROTRYPSIN. JRNL REF PROTEIN SCI. V. 28 746 2019 JRNL REFN ESSN 1469-896X JRNL PMID 30748049 JRNL DOI 10.1002/PRO.3587 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0230 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.58 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 32795 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1725 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2397 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.3630 REMARK 3 BIN FREE R VALUE SET COUNT : 112 REMARK 3 BIN FREE R VALUE : 0.4120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1654 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 85 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.91000 REMARK 3 B22 (A**2) : -0.40000 REMARK 3 B33 (A**2) : -2.50000 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): 0.085 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.085 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.075 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.836 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1701 ; 0.016 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 1479 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2291 ; 1.699 ; 1.655 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3478 ; 1.040 ; 1.658 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 214 ; 7.230 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 100 ;32.103 ;22.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 291 ;15.489 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;17.399 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 207 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1972 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 316 ; 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): 859 ; 3.660 ; 4.163 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 858 ; 3.660 ; 4.156 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1072 ; 5.540 ; 6.201 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1073 ; 5.538 ; 6.210 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 842 ; 4.041 ; 4.631 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 840 ; 4.009 ; 4.610 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1219 ; 6.146 ; 6.738 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1830 ; 8.747 ;47.282 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1822 ; 8.761 ;47.226 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 1 107 B 1 107 3063 0.14 0.05 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 1 A 7 REMARK 3 ORIGIN FOR THE GROUP (A): 30.4754 36.3493 12.6859 REMARK 3 T TENSOR REMARK 3 T11: 0.0150 T22: 0.0267 REMARK 3 T33: 0.0365 T12: -0.0074 REMARK 3 T13: 0.0059 T23: 0.0067 REMARK 3 L TENSOR REMARK 3 L11: 4.9290 L22: 3.6931 REMARK 3 L33: 10.0321 L12: 1.9781 REMARK 3 L13: -4.3129 L23: -4.7869 REMARK 3 S TENSOR REMARK 3 S11: 0.1305 S12: 0.1411 S13: 0.3154 REMARK 3 S21: 0.0487 S22: 0.0848 S23: -0.0034 REMARK 3 S31: -0.0706 S32: -0.0078 S33: -0.2153 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 8 A 13 REMARK 3 ORIGIN FOR THE GROUP (A): 24.3350 31.2753 23.6738 REMARK 3 T TENSOR REMARK 3 T11: 0.0396 T22: 0.1314 REMARK 3 T33: 0.1904 T12: 0.0104 REMARK 3 T13: 0.0726 T23: -0.0118 REMARK 3 L TENSOR REMARK 3 L11: 12.2691 L22: 11.0367 REMARK 3 L33: 10.9105 L12: -9.7771 REMARK 3 L13: -7.2911 L23: 1.2315 REMARK 3 S TENSOR REMARK 3 S11: -0.1726 S12: -0.1129 S13: -0.2261 REMARK 3 S21: 0.4251 S22: 0.5393 S23: 0.6264 REMARK 3 S31: -0.2586 S32: -0.6336 S33: -0.3667 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 14 A 51 REMARK 3 ORIGIN FOR THE GROUP (A): 34.9860 36.2470 17.5111 REMARK 3 T TENSOR REMARK 3 T11: 0.0477 T22: 0.0399 REMARK 3 T33: 0.0835 T12: -0.0395 REMARK 3 T13: 0.0030 T23: -0.0211 REMARK 3 L TENSOR REMARK 3 L11: 2.6888 L22: 2.8754 REMARK 3 L33: 4.4992 L12: -1.0712 REMARK 3 L13: 1.5714 L23: -1.9307 REMARK 3 S TENSOR REMARK 3 S11: -0.1648 S12: 0.0754 S13: 0.3649 REMARK 3 S21: 0.0551 S22: -0.0496 S23: -0.2220 REMARK 3 S31: -0.3466 S32: 0.2168 S33: 0.2144 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 52 A 59 REMARK 3 ORIGIN FOR THE GROUP (A): 36.6808 27.4390 24.3596 REMARK 3 T TENSOR REMARK 3 T11: 0.0143 T22: 0.0474 REMARK 3 T33: 0.0224 T12: -0.0065 REMARK 3 T13: 0.0098 T23: -0.0268 REMARK 3 L TENSOR REMARK 3 L11: 4.1175 L22: 7.1761 REMARK 3 L33: 2.9670 L12: -2.2642 REMARK 3 L13: 0.4127 L23: -1.4859 REMARK 3 S TENSOR REMARK 3 S11: -0.1300 S12: 0.0404 S13: -0.0225 REMARK 3 S21: 0.0410 S22: 0.0295 S23: 0.0067 REMARK 3 S31: 0.0786 S32: 0.0474 S33: 0.1005 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 60 A 69 REMARK 3 ORIGIN FOR THE GROUP (A): 37.1893 27.2860 9.6713 REMARK 3 T TENSOR REMARK 3 T11: 0.1128 T22: 0.1854 REMARK 3 T33: 0.0757 T12: 0.0438 REMARK 3 T13: 0.0702 T23: -0.0167 REMARK 3 L TENSOR REMARK 3 L11: 3.2411 L22: 6.3041 REMARK 3 L33: 9.4548 L12: 0.7961 REMARK 3 L13: 2.8175 L23: -4.6600 REMARK 3 S TENSOR REMARK 3 S11: 0.1374 S12: 0.6265 S13: 0.0001 REMARK 3 S21: -0.4843 S22: -0.0657 S23: -0.0415 REMARK 3 S31: 0.3844 S32: 0.4268 S33: -0.0717 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 70 A 74 REMARK 3 ORIGIN FOR THE GROUP (A): 46.2331 40.1611 17.3720 REMARK 3 T TENSOR REMARK 3 T11: 0.0910 T22: 0.1791 REMARK 3 T33: 0.4111 T12: -0.0805 REMARK 3 T13: -0.0829 T23: 0.1410 REMARK 3 L TENSOR REMARK 3 L11: 3.7672 L22: 9.8740 REMARK 3 L33: 8.0497 L12: -0.4884 REMARK 3 L13: -1.1022 L23: 8.5302 REMARK 3 S TENSOR REMARK 3 S11: 0.1824 S12: 0.4371 S13: 0.2241 REMARK 3 S21: -0.2712 S22: 0.1400 S23: -0.8166 REMARK 3 S31: -0.4444 S32: 0.2562 S33: -0.3224 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 75 A 82 REMARK 3 ORIGIN FOR THE GROUP (A): 37.9727 45.9629 17.2572 REMARK 3 T TENSOR REMARK 3 T11: 0.2551 T22: 0.1097 REMARK 3 T33: 0.3936 T12: -0.1616 REMARK 3 T13: -0.2108 T23: 0.1648 REMARK 3 L TENSOR REMARK 3 L11: 5.4515 L22: 3.2071 REMARK 3 L33: 12.3755 L12: 1.3065 REMARK 3 L13: -1.7153 L23: 1.0893 REMARK 3 S TENSOR REMARK 3 S11: -0.6964 S12: 0.5945 S13: 1.0954 REMARK 3 S21: 0.1314 S22: -0.0039 S23: -0.0050 REMARK 3 S31: -0.4195 S32: 0.2147 S33: 0.7003 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 83 A 106 REMARK 3 ORIGIN FOR THE GROUP (A): 41.8351 31.8213 16.8137 REMARK 3 T TENSOR REMARK 3 T11: 0.1174 T22: 0.1969 REMARK 3 T33: 0.1371 T12: 0.0175 REMARK 3 T13: 0.0485 T23: -0.0139 REMARK 3 L TENSOR REMARK 3 L11: 1.4920 L22: 7.0529 REMARK 3 L33: 3.3345 L12: -0.5473 REMARK 3 L13: 2.1588 L23: 0.3901 REMARK 3 S TENSOR REMARK 3 S11: -0.0966 S12: 0.4041 S13: 0.1440 REMARK 3 S21: -0.3043 S22: 0.0263 S23: -0.8241 REMARK 3 S31: -0.1617 S32: 0.6327 S33: 0.0704 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 1 B 13 REMARK 3 ORIGIN FOR THE GROUP (A): 43.3493 22.1110 27.4675 REMARK 3 T TENSOR REMARK 3 T11: 0.1043 T22: 0.2075 REMARK 3 T33: 0.0944 T12: 0.0245 REMARK 3 T13: 0.0320 T23: -0.0134 REMARK 3 L TENSOR REMARK 3 L11: 3.3533 L22: 6.5115 REMARK 3 L33: 0.4946 L12: -0.3863 REMARK 3 L13: 0.2816 L23: -1.4387 REMARK 3 S TENSOR REMARK 3 S11: -0.0549 S12: 0.1095 S13: -0.0578 REMARK 3 S21: -0.2223 S22: -0.0263 S23: -0.1379 REMARK 3 S31: 0.1230 S32: 0.1395 S33: 0.0813 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 14 B 44 REMARK 3 ORIGIN FOR THE GROUP (A): 44.0791 16.1882 33.8923 REMARK 3 T TENSOR REMARK 3 T11: 0.1907 T22: 0.1722 REMARK 3 T33: 0.1132 T12: 0.0861 REMARK 3 T13: 0.0022 T23: 0.0111 REMARK 3 L TENSOR REMARK 3 L11: 4.0651 L22: 4.1134 REMARK 3 L33: 1.2712 L12: 2.1607 REMARK 3 L13: 0.8485 L23: 0.4774 REMARK 3 S TENSOR REMARK 3 S11: 0.1035 S12: -0.2619 S13: -0.5221 REMARK 3 S21: 0.4411 S22: -0.0829 S23: -0.3107 REMARK 3 S31: 0.4031 S32: 0.1993 S33: -0.0206 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 45 B 68 REMARK 3 ORIGIN FOR THE GROUP (A): 44.9679 21.5585 34.9922 REMARK 3 T TENSOR REMARK 3 T11: 0.0793 T22: 0.1420 REMARK 3 T33: 0.0240 T12: 0.0366 REMARK 3 T13: -0.0262 T23: -0.0209 REMARK 3 L TENSOR REMARK 3 L11: 4.5103 L22: 3.6791 REMARK 3 L33: 4.1356 L12: 0.7775 REMARK 3 L13: 0.9451 L23: -0.0403 REMARK 3 S TENSOR REMARK 3 S11: 0.0219 S12: -0.2267 S13: -0.1608 REMARK 3 S21: 0.4502 S22: -0.0008 S23: -0.2156 REMARK 3 S31: 0.2768 S32: 0.2979 S33: -0.0211 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 69 B 79 REMARK 3 ORIGIN FOR THE GROUP (A): 50.7512 8.4710 35.3155 REMARK 3 T TENSOR REMARK 3 T11: 0.3319 T22: 0.3320 REMARK 3 T33: 0.5603 T12: 0.1619 REMARK 3 T13: -0.1004 T23: 0.1001 REMARK 3 L TENSOR REMARK 3 L11: 5.6995 L22: 13.1826 REMARK 3 L33: 1.8343 L12: -1.6823 REMARK 3 L13: 2.7088 L23: 1.7951 REMARK 3 S TENSOR REMARK 3 S11: 0.2816 S12: -0.5289 S13: -0.9031 REMARK 3 S21: 0.8112 S22: 0.1201 S23: -0.1034 REMARK 3 S31: 0.3088 S32: -0.2530 S33: -0.4017 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 80 B 106 REMARK 3 ORIGIN FOR THE GROUP (A): 44.6092 15.0161 39.1863 REMARK 3 T TENSOR REMARK 3 T11: 0.3812 T22: 0.4294 REMARK 3 T33: 0.3800 T12: 0.0106 REMARK 3 T13: -0.1288 T23: 0.1701 REMARK 3 L TENSOR REMARK 3 L11: 2.9451 L22: 4.1416 REMARK 3 L33: 4.6349 L12: -0.6738 REMARK 3 L13: 0.5341 L23: 1.1324 REMARK 3 S TENSOR REMARK 3 S11: 0.1616 S12: -0.6567 S13: -0.8194 REMARK 3 S21: 0.9222 S22: -0.2724 S23: -0.1909 REMARK 3 S31: 0.7597 S32: 0.3129 S33: 0.1108 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 REMARK 4 REMARK 4 6H8M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1200011261. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.983 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34576 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 42.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 2.84000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.500 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: 1BY2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 3350, 0.1 M TRI-SOIDIUM REMARK 280 CITRATE, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 28.87600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.26300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.45100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.26300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.87600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.45100 REMARK 290 SMTRY3 4 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 GLY A 381 REMARK 465 SER A 382 REMARK 465 LYS A 490 REMARK 465 LYS A 491 REMARK 465 ALA A 492 REMARK 465 SER A 493 REMARK 465 SER A 494 REMARK 465 GLY B 381 REMARK 465 SER B 382 REMARK 465 LYS B 490 REMARK 465 LYS B 491 REMARK 465 ALA B 492 REMARK 465 SER B 493 REMARK 465 SER B 494 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 452 87.98 -151.54 REMARK 500 ILE A 470 75.28 -118.32 REMARK 500 HIS A 473 67.48 63.77 REMARK 500 ASP B 469 -72.35 -38.06 REMARK 500 REMARK 500 REMARK: NULL DBREF 6H8M A 383 494 UNP O08762 NETR_MOUSE 383 494 DBREF 6H8M B 383 494 UNP O08762 NETR_MOUSE 383 494 SEQADV 6H8M GLY A 381 UNP O08762 EXPRESSION TAG SEQADV 6H8M SER A 382 UNP O08762 EXPRESSION TAG SEQADV 6H8M GLY B 381 UNP O08762 EXPRESSION TAG SEQADV 6H8M SER B 382 UNP O08762 EXPRESSION TAG SEQRES 1 A 114 GLY SER GLY PHE PRO ILE ARG LEU VAL ASP GLY GLU ASN SEQRES 2 A 114 LYS LYS GLU GLY ARG VAL GLU VAL PHE VAL ASN GLY GLN SEQRES 3 A 114 TRP GLY THR ILE CYS ASP ASP GLY TRP THR ASP LYS HIS SEQRES 4 A 114 ALA ALA VAL ILE CYS ARG GLN LEU GLY TYR LYS GLY PRO SEQRES 5 A 114 ALA ARG ALA ARG THR MET ALA TYR PHE GLY GLU GLY LYS SEQRES 6 A 114 GLY PRO ILE HIS MET ASP ASN VAL LYS CYS THR GLY ASN SEQRES 7 A 114 GLU LYS ALA LEU ALA ASP CYS VAL LYS GLN ASP ILE GLY SEQRES 8 A 114 ARG HIS ASN CYS ARG HIS SER GLU ASP ALA GLY VAL ILE SEQRES 9 A 114 CYS ASP TYR LEU GLU LYS LYS ALA SER SER SEQRES 1 B 114 GLY SER GLY PHE PRO ILE ARG LEU VAL ASP GLY GLU ASN SEQRES 2 B 114 LYS LYS GLU GLY ARG VAL GLU VAL PHE VAL ASN GLY GLN SEQRES 3 B 114 TRP GLY THR ILE CYS ASP ASP GLY TRP THR ASP LYS HIS SEQRES 4 B 114 ALA ALA VAL ILE CYS ARG GLN LEU GLY TYR LYS GLY PRO SEQRES 5 B 114 ALA ARG ALA ARG THR MET ALA TYR PHE GLY GLU GLY LYS SEQRES 6 B 114 GLY PRO ILE HIS MET ASP ASN VAL LYS CYS THR GLY ASN SEQRES 7 B 114 GLU LYS ALA LEU ALA ASP CYS VAL LYS GLN ASP ILE GLY SEQRES 8 B 114 ARG HIS ASN CYS ARG HIS SER GLU ASP ALA GLY VAL ILE SEQRES 9 B 114 CYS ASP TYR LEU GLU LYS LYS ALA SER SER FORMUL 3 HOH *85(H2 O) HELIX 1 AA1 THR A 416 LEU A 427 1 12 HELIX 2 AA2 ALA A 461 CYS A 465 5 5 HELIX 3 AA3 ARG A 476 ASP A 480 5 5 HELIX 4 AA4 THR B 416 LEU B 427 1 12 HELIX 5 AA5 ALA B 461 CYS B 465 5 5 HELIX 6 AA6 ARG B 476 ASP B 480 5 5 SHEET 1 AA1 4 ILE A 386 ASP A 390 0 SHEET 2 AA1 4 GLU A 396 VAL A 403 -1 O ARG A 398 N VAL A 389 SHEET 3 AA1 4 GLY A 482 CYS A 485 -1 O VAL A 483 N GLY A 397 SHEET 4 AA1 4 ALA A 433 ARG A 436 -1 N ARG A 436 O GLY A 482 SHEET 1 AA2 4 ILE A 386 ASP A 390 0 SHEET 2 AA2 4 GLU A 396 VAL A 403 -1 O ARG A 398 N VAL A 389 SHEET 3 AA2 4 GLN A 406 ILE A 410 -1 O GLY A 408 N VAL A 401 SHEET 4 AA2 4 ILE A 448 MET A 450 1 O HIS A 449 N THR A 409 SHEET 1 AA3 2 VAL A 453 LYS A 454 0 SHEET 2 AA3 2 VAL A 466 LYS A 467 -1 O VAL A 466 N LYS A 454 SHEET 1 AA4 4 ILE B 386 ASP B 390 0 SHEET 2 AA4 4 GLU B 396 VAL B 403 -1 O ARG B 398 N VAL B 389 SHEET 3 AA4 4 GLY B 482 CYS B 485 -1 O VAL B 483 N GLY B 397 SHEET 4 AA4 4 ALA B 433 ARG B 436 -1 N ARG B 436 O GLY B 482 SHEET 1 AA5 4 ILE B 386 ASP B 390 0 SHEET 2 AA5 4 GLU B 396 VAL B 403 -1 O ARG B 398 N VAL B 389 SHEET 3 AA5 4 GLN B 406 ILE B 410 -1 O GLY B 408 N VAL B 401 SHEET 4 AA5 4 ILE B 448 MET B 450 1 O HIS B 449 N THR B 409 SSBOND 1 CYS A 411 CYS A 475 1555 1555 2.16 SSBOND 2 CYS A 424 CYS A 485 1555 1555 2.04 SSBOND 3 CYS A 455 CYS A 465 1555 1555 2.19 SSBOND 4 CYS B 411 CYS B 475 1555 1555 2.11 SSBOND 5 CYS B 424 CYS B 485 1555 1555 2.01 SSBOND 6 CYS B 455 CYS B 465 1555 1555 2.14 CRYST1 57.752 62.902 84.526 90.00 90.00 90.00 P 21 21 21 8 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 0.017315 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015898 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011831 0.00000