HEADER PROTEIN FIBRIL 18-JUL-08 3DVI TITLE CRYSTAL STRUCTURE OF KAPPA 1 AMYLOIDOGENIC LIGHT CHAIN VARIABLE DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOIDOGENIC LIGHT CHAIN VARIABLE DOMAIN AL-103; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MUTANT OF VK1 O18/O8 GERMLINE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 GOLD (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET12A KEYWDS AL, LIGHT CHAIN AMYLOIDOSIS, AMYLOID, IMMUNOGLOBULIN, LIGHT CHAIN, KEYWDS 2 LIGHT CHAIN VARIABLE DOMAIN, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR J.R.THOMPSON,E.G.RANDLES,M.RAMIREZ-ALVARADO REVDAT 3 30-AUG-23 3DVI 1 REMARK REVDAT 2 26-MAY-09 3DVI 1 JRNL REVDAT 1 12-MAY-09 3DVI 0 JRNL AUTH E.G.RANDLES,J.R.THOMPSON,D.J.MARTIN,M.RAMIREZ-ALVARADO JRNL TITL STRUCTURAL ALTERATIONS WITHIN NATIVE AMYLOIDOGENIC JRNL TITL 2 IMMUNOGLOBULIN LIGHT CHAINS. JRNL REF J.MOL.BIOL. V. 389 199 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19361523 JRNL DOI 10.1016/J.JMB.2009.04.010 REMARK 2 REMARK 2 RESOLUTION. 1.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 103.14 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.1 REMARK 3 NUMBER OF REFLECTIONS : 16194 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) : 0.189 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.200 REMARK 3 FREE R VALUE TEST SET COUNT : 534 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) : 1.53 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.58 REMARK 3 REFLECTION IN BIN (WORKING SET) : 387 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 842 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 201 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.40000 REMARK 3 B22 (A**2) : -0.40000 REMARK 3 B33 (A**2) : 0.80000 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): 0.129 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.105 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.064 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.714 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 947 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1306 ; 1.880 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 127 ; 7.148 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 38 ;37.390 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 152 ;14.452 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 3 ;17.859 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 145 ; 0.146 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 747 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 504 ; 0.218 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 659 ; 0.310 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 158 ; 0.168 ; 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): 28 ; 0.196 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 25 ; 0.199 ; 0.200 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): 623 ; 1.879 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 997 ; 2.529 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 376 ; 3.605 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 309 ; 4.760 ; 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): 999 ; 2.128 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 202 ; 9.015 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 916 ; 4.064 ; 3.000 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 : 14 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 0 A 3 REMARK 3 ORIGIN FOR THE GROUP (A): -13.2253 2.4271 -8.6704 REMARK 3 T TENSOR REMARK 3 T11: 0.2426 T22: 0.0973 REMARK 3 T33: -0.0547 T12: -0.1350 REMARK 3 T13: -0.0735 T23: 0.0321 REMARK 3 L TENSOR REMARK 3 L11: 7.5459 L22: 36.5432 REMARK 3 L33: 2.0938 L12: 10.7456 REMARK 3 L13: 3.9536 L23: 6.3201 REMARK 3 S TENSOR REMARK 3 S11: -0.2391 S12: 0.5799 S13: -0.1365 REMARK 3 S21: -1.0332 S22: 0.0465 S23: -0.3801 REMARK 3 S31: 0.0402 S32: 0.2453 S33: 0.1926 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 4 A 11 REMARK 3 ORIGIN FOR THE GROUP (A): -6.7109 14.1510 2.0674 REMARK 3 T TENSOR REMARK 3 T11: 0.1486 T22: 0.0931 REMARK 3 T33: 0.0067 T12: -0.0544 REMARK 3 T13: -0.0212 T23: 0.0083 REMARK 3 L TENSOR REMARK 3 L11: 7.2230 L22: 9.3141 REMARK 3 L33: 0.4879 L12: 4.8210 REMARK 3 L13: 1.6153 L23: 0.1992 REMARK 3 S TENSOR REMARK 3 S11: -0.4708 S12: 0.0140 S13: 0.2217 REMARK 3 S21: -0.6582 S22: 0.4873 S23: 0.0498 REMARK 3 S31: -0.1558 S32: 0.0328 S33: -0.0165 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 12 A 26 REMARK 3 ORIGIN FOR THE GROUP (A): -7.1787 14.2579 10.0844 REMARK 3 T TENSOR REMARK 3 T11: 0.0528 T22: 0.0485 REMARK 3 T33: 0.0160 T12: -0.0007 REMARK 3 T13: -0.0148 T23: -0.0201 REMARK 3 L TENSOR REMARK 3 L11: 2.0757 L22: 3.4206 REMARK 3 L33: 3.2148 L12: 2.0330 REMARK 3 L13: 1.9526 L23: 1.9065 REMARK 3 S TENSOR REMARK 3 S11: -0.1350 S12: 0.0373 S13: 0.1557 REMARK 3 S21: -0.1799 S22: 0.1359 S23: 0.0825 REMARK 3 S31: -0.0736 S32: 0.0593 S33: -0.0009 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 27 A 33 REMARK 3 ORIGIN FOR THE GROUP (A): -16.4484 -1.1758 1.6972 REMARK 3 T TENSOR REMARK 3 T11: 0.0877 T22: 0.0515 REMARK 3 T33: 0.0439 T12: -0.0526 REMARK 3 T13: -0.0365 T23: 0.0379 REMARK 3 L TENSOR REMARK 3 L11: 5.9543 L22: 5.3249 REMARK 3 L33: 8.0542 L12: -0.9380 REMARK 3 L13: 1.8202 L23: -1.6203 REMARK 3 S TENSOR REMARK 3 S11: -0.2106 S12: 0.2162 S13: 0.1732 REMARK 3 S21: -0.4715 S22: 0.1856 S23: 0.4576 REMARK 3 S31: -0.0998 S32: -0.1794 S33: 0.0250 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 34 A 39 REMARK 3 ORIGIN FOR THE GROUP (A): -0.9001 3.7250 6.6498 REMARK 3 T TENSOR REMARK 3 T11: 0.0271 T22: 0.0348 REMARK 3 T33: 0.0962 T12: 0.0051 REMARK 3 T13: 0.0070 T23: -0.0650 REMARK 3 L TENSOR REMARK 3 L11: 5.5003 L22: 1.8488 REMARK 3 L33: 4.8926 L12: 2.4731 REMARK 3 L13: 1.1759 L23: 1.6849 REMARK 3 S TENSOR REMARK 3 S11: 0.0452 S12: 0.1806 S13: -0.4980 REMARK 3 S21: 0.0835 S22: 0.3727 S23: -0.5707 REMARK 3 S31: 0.0943 S32: 0.3380 S33: -0.4179 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 40 A 45 REMARK 3 ORIGIN FOR THE GROUP (A): 7.0152 2.7653 5.6910 REMARK 3 T TENSOR REMARK 3 T11: -0.0377 T22: 0.2702 REMARK 3 T33: 0.1494 T12: 0.0417 REMARK 3 T13: -0.0447 T23: -0.2323 REMARK 3 L TENSOR REMARK 3 L11: 20.5846 L22: 9.8980 REMARK 3 L33: 20.2964 L12: 2.1678 REMARK 3 L13: -8.4278 L23: -0.5046 REMARK 3 S TENSOR REMARK 3 S11: 0.5588 S12: 0.1099 S13: 0.0029 REMARK 3 S21: 0.0425 S22: 0.3187 S23: -0.6311 REMARK 3 S31: -0.0890 S32: 1.9475 S33: -0.8775 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 46 A 51 REMARK 3 ORIGIN FOR THE GROUP (A): -6.6630 -0.9618 10.7413 REMARK 3 T TENSOR REMARK 3 T11: 0.1176 T22: 0.0130 REMARK 3 T33: 0.0611 T12: -0.0106 REMARK 3 T13: -0.0547 T23: 0.0036 REMARK 3 L TENSOR REMARK 3 L11: 5.2024 L22: 8.3180 REMARK 3 L33: 1.2618 L12: 5.5960 REMARK 3 L13: 0.1988 L23: 1.9117 REMARK 3 S TENSOR REMARK 3 S11: 0.2483 S12: -0.1908 S13: -0.6653 REMARK 3 S21: 0.7693 S22: -0.0464 S23: -0.7179 REMARK 3 S31: 0.1386 S32: -0.0191 S33: -0.2020 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 52 A 56 REMARK 3 ORIGIN FOR THE GROUP (A): -6.2976 -3.4339 15.5895 REMARK 3 T TENSOR REMARK 3 T11: 0.2207 T22: 0.0392 REMARK 3 T33: 0.0139 T12: -0.0092 REMARK 3 T13: -0.0682 T23: 0.0375 REMARK 3 L TENSOR REMARK 3 L11: 20.1985 L22: 5.3739 REMARK 3 L33: 6.8262 L12: -7.6876 REMARK 3 L13: 9.9293 L23: -4.9462 REMARK 3 S TENSOR REMARK 3 S11: -0.1972 S12: -0.2644 S13: -0.3472 REMARK 3 S21: 0.7557 S22: 0.1131 S23: -0.2538 REMARK 3 S31: 0.1754 S32: -0.0651 S33: 0.0841 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 57 A 69 REMARK 3 ORIGIN FOR THE GROUP (A): -7.8446 4.5614 14.6061 REMARK 3 T TENSOR REMARK 3 T11: 0.0983 T22: 0.0588 REMARK 3 T33: 0.0170 T12: 0.0044 REMARK 3 T13: -0.0013 T23: 0.0104 REMARK 3 L TENSOR REMARK 3 L11: 3.5413 L22: 3.3237 REMARK 3 L33: 3.3552 L12: 0.9705 REMARK 3 L13: 1.7004 L23: 0.7202 REMARK 3 S TENSOR REMARK 3 S11: 0.0463 S12: -0.2265 S13: -0.0387 REMARK 3 S21: 0.2632 S22: 0.0139 S23: -0.0970 REMARK 3 S31: 0.0384 S32: -0.0028 S33: -0.0602 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 70 A 78 REMARK 3 ORIGIN FOR THE GROUP (A): -7.9309 10.1395 12.8104 REMARK 3 T TENSOR REMARK 3 T11: 0.0590 T22: 0.0578 REMARK 3 T33: 0.0314 T12: 0.0127 REMARK 3 T13: 0.0122 T23: -0.0162 REMARK 3 L TENSOR REMARK 3 L11: 6.9490 L22: 5.8998 REMARK 3 L33: 7.6803 L12: 4.2568 REMARK 3 L13: 5.6187 L23: 4.1237 REMARK 3 S TENSOR REMARK 3 S11: -0.0437 S12: -0.1726 S13: 0.1922 REMARK 3 S21: 0.0444 S22: 0.0904 S23: -0.0469 REMARK 3 S31: -0.0352 S32: 0.0063 S33: -0.0467 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 79 A 91 REMARK 3 ORIGIN FOR THE GROUP (A): -1.1365 6.5690 7.8624 REMARK 3 T TENSOR REMARK 3 T11: 0.0330 T22: 0.0674 REMARK 3 T33: 0.0705 T12: 0.0022 REMARK 3 T13: 0.0173 T23: -0.0546 REMARK 3 L TENSOR REMARK 3 L11: 2.6285 L22: 4.1259 REMARK 3 L33: 2.3830 L12: 2.1570 REMARK 3 L13: 1.1269 L23: 1.3861 REMARK 3 S TENSOR REMARK 3 S11: -0.2076 S12: 0.1829 S13: -0.1780 REMARK 3 S21: -0.1431 S22: 0.4089 S23: -0.4809 REMARK 3 S31: -0.1048 S32: 0.2677 S33: -0.2012 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 92 A 98 REMARK 3 ORIGIN FOR THE GROUP (A): -11.1224 -4.8879 -4.8564 REMARK 3 T TENSOR REMARK 3 T11: 0.0538 T22: 0.1251 REMARK 3 T33: 0.0373 T12: -0.0426 REMARK 3 T13: 0.0066 T23: -0.0599 REMARK 3 L TENSOR REMARK 3 L11: 3.7014 L22: 8.3856 REMARK 3 L33: 9.4111 L12: 3.4947 REMARK 3 L13: 2.7236 L23: 1.6044 REMARK 3 S TENSOR REMARK 3 S11: 0.0598 S12: 0.3412 S13: -0.0188 REMARK 3 S21: -0.2029 S22: 0.0356 S23: 0.1269 REMARK 3 S31: -0.3027 S32: 0.1638 S33: -0.0955 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 99 A 104 REMARK 3 ORIGIN FOR THE GROUP (A): -2.6476 9.6392 0.5232 REMARK 3 T TENSOR REMARK 3 T11: 0.0611 T22: 0.0792 REMARK 3 T33: 0.0252 T12: -0.0381 REMARK 3 T13: 0.0468 T23: -0.0559 REMARK 3 L TENSOR REMARK 3 L11: 9.1843 L22: 11.5102 REMARK 3 L33: 9.2345 L12: 9.0440 REMARK 3 L13: 1.9391 L23: -0.6669 REMARK 3 S TENSOR REMARK 3 S11: -0.4748 S12: 0.5838 S13: -0.2505 REMARK 3 S21: -0.6149 S22: 0.6426 S23: -0.4685 REMARK 3 S31: 0.0607 S32: 0.1617 S33: -0.1678 REMARK 3 REMARK 3 TLS GROUP : 14 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 105 A 108 REMARK 3 ORIGIN FOR THE GROUP (A): 3.8134 19.2289 10.4790 REMARK 3 T TENSOR REMARK 3 T11: 0.0771 T22: 0.0680 REMARK 3 T33: 0.0714 T12: -0.0127 REMARK 3 T13: -0.0011 T23: -0.1123 REMARK 3 L TENSOR REMARK 3 L11: 15.0933 L22: 38.9459 REMARK 3 L33: 10.4892 L12: -2.1155 REMARK 3 L13: -4.9826 L23: 8.4777 REMARK 3 S TENSOR REMARK 3 S11: -0.0001 S12: -0.3965 S13: 1.0706 REMARK 3 S21: 0.1069 S22: 1.0499 S23: -1.5938 REMARK 3 S31: -1.1113 S32: 0.7206 S33: -1.0497 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 3DVI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048540. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5241 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : OSMIC VARIMAX OPTICS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16734 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530 REMARK 200 RESOLUTION RANGE LOW (A) : 103.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 200 DATA REDUNDANCY : 16.62 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 35.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.36500 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: PDB ENTRY 2Q20 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN: 1.26 MM. MOTHER LIQUOR: 15% REMARK 280 W/V POLYETHYLENE GLYCOL 8000, 0.05 M MAGNESIUM ACETATE, 0.1 M REMARK 280 SODIUM ACETATE, 0.1 M TRIS BUFFER, PH 5.4, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.67800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 23.51000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 23.51000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.83900 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 23.51000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 23.51000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 77.51700 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 23.51000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 23.51000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.83900 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 23.51000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 23.51000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 77.51700 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 51.67800 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: 1340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 292 LIES ON A SPECIAL POSITION. 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 LEU A 78 CA - CB - CG ANGL. DEV. = 13.8 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 SER A 30 -131.38 45.19 REMARK 500 ALA A 51 -38.16 74.09 REMARK 500 ALA A 84 174.48 177.20 REMARK 500 TYR A 91 36.36 -142.61 REMARK 500 ASN A 93 -126.36 54.17 REMARK 500 PRO A 95 157.17 -48.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ILE A 107 LYS A 108 148.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Q20 RELATED DB: PDB REMARK 900 RELATED ID: 2Q1E RELATED DB: PDB DBREF 3DVI A 0 108 PDB 3DVI 3DVI 0 108 SEQRES 1 A 109 THR ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER SEQRES 2 A 109 ALA SER VAL GLY ASP ARG VAL THR ILE THR CYS GLN ALA SEQRES 3 A 109 SER GLN ASP ILE SER ASN TYR LEU ILE TRP TYR GLN GLN SEQRES 4 A 109 LYS PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR ASP ALA SEQRES 5 A 109 SER ASN LEU GLU THR GLY VAL PRO SER ARG PHE SER GLY SEQRES 6 A 109 SER GLY SER GLY THR ASP PHE THR PHE THR ILE SER SER SEQRES 7 A 109 LEU GLN PRO GLU ASP ILE ALA THR TYR TYR CYS GLN GLN SEQRES 8 A 109 TYR HIS ASN LEU PRO PRO TYR THR PHE GLY PRO GLY THR SEQRES 9 A 109 LYS LEU GLU ILE LYS FORMUL 2 HOH *201(H2 O) HELIX 1 1 GLN A 79 ILE A 83 5 5 SHEET 1 A 4 MET A 4 SER A 7 0 SHEET 2 A 4 VAL A 19 ALA A 25 -1 O THR A 22 N SER A 7 SHEET 3 A 4 ASP A 70 ILE A 75 -1 O PHE A 73 N ILE A 21 SHEET 4 A 4 PHE A 62 SER A 65 -1 N SER A 63 O THR A 74 SHEET 1 B 6 SER A 10 ALA A 13 0 SHEET 2 B 6 THR A 103 ILE A 107 1 O LYS A 104 N LEU A 11 SHEET 3 B 6 ALA A 84 GLN A 90 -1 N ALA A 84 O LEU A 105 SHEET 4 B 6 LEU A 33 GLN A 38 -1 N TYR A 36 O TYR A 87 SHEET 5 B 6 LYS A 45 TYR A 49 -1 O LYS A 45 N GLN A 37 SHEET 6 B 6 ASN A 53 LEU A 54 -1 O ASN A 53 N TYR A 49 SSBOND 1 CYS A 23 CYS A 88 1555 1555 2.10 CISPEP 1 SER A 7 PRO A 8 0 -10.20 CISPEP 2 SER A 7 PRO A 8 0 6.55 CISPEP 3 PRO A 95 PRO A 96 0 6.36 CRYST1 47.020 47.020 103.356 90.00 90.00 90.00 P 41 21 2 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 0.021268 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021268 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009675 0.00000