HEADER HYDROLASE 28-AUG-08 3EBQ TITLE CRYSTAL STRUCTURE OF HUMAN PPPDE1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MOLECULE: PPPDE1 (PERMUTED PAPAIN FOLD PEPTIDASES OF DSRNA COMPND 3 VIRUSES AND EUKARYOTES 1), UPF0326 PROTEIN FAM152B; COMPND 4 CHAIN: A; COMPND 5 EC: 3.4.22.-; COMPND 6 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: FAM152B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS(DE3)-V2R; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A-LIC KEYWDS PEPTIDASE, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, KEYWDS 2 HYDROLASE, THIOL PROTEASE, UBL CONJUGATION PATHWAY EXPDTA X-RAY DIFFRACTION AUTHOR J.R.WALKER,M.AKUTSU,L.QIU,Y.LI,Y.SLESSAREV,C.BOUNTRA,J.WEIGELT, AUTHOR 2 C.H.ARROWSMITH,A.M.EDWARDS,A.BOTCHKAREV,S.DHE-PAGANON,STRUCTURAL AUTHOR 3 GENOMICS CONSORTIUM (SGC) REVDAT 4 21-FEB-24 3EBQ 1 REMARK REVDAT 3 25-OCT-17 3EBQ 1 REMARK REVDAT 2 24-FEB-09 3EBQ 1 VERSN REVDAT 1 04-NOV-08 3EBQ 0 JRNL AUTH J.R.WALKER,M.AKUTSU,L.QIU,Y.LI,Y.SLESSAREV,J.WEIGELT, JRNL AUTH 2 C.BOUNTRA,C.H.ARROWSMITH,A.M.EDWARDS,A.BOCHKAREV, JRNL AUTH 3 S.DHE-PAGANON JRNL TITL STRUCTURE OF HUMAN PPPDE1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 28.04 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 12727 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) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 670 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) : 770 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.27 REMARK 3 BIN R VALUE (WORKING SET) : 0.2540 REMARK 3 BIN FREE R VALUE SET COUNT : 46 REMARK 3 BIN FREE R VALUE : 0.2590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1109 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 63 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.57 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.32000 REMARK 3 B22 (A**2) : 0.32000 REMARK 3 B33 (A**2) : -0.64000 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): 0.168 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.162 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.097 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.625 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.918 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1155 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1576 ; 1.630 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 147 ; 6.323 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 48 ;33.969 ;24.375 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 180 ;12.825 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;21.889 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 177 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 887 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 518 ; 0.218 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 804 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 75 ; 0.151 ; 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): 25 ; 0.205 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.147 ; 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): 746 ; 1.012 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1178 ; 1.505 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 463 ; 2.439 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 398 ; 3.524 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 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 5 A 20 REMARK 3 ORIGIN FOR THE GROUP (A): 5.9348 23.9228 74.4846 REMARK 3 T TENSOR REMARK 3 T11: 0.0501 T22: -0.0067 REMARK 3 T33: 0.0820 T12: 0.0117 REMARK 3 T13: 0.0141 T23: 0.0446 REMARK 3 L TENSOR REMARK 3 L11: 1.8947 L22: 2.6352 REMARK 3 L33: 2.2949 L12: 1.0382 REMARK 3 L13: 1.8435 L23: 1.3436 REMARK 3 S TENSOR REMARK 3 S11: 0.0861 S12: 0.0550 S13: 0.0871 REMARK 3 S21: 0.2786 S22: 0.2006 S23: 0.3448 REMARK 3 S31: -0.1588 S32: -0.0602 S33: -0.2867 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 21 A 25 REMARK 3 ORIGIN FOR THE GROUP (A): 23.0351 29.9387 85.9019 REMARK 3 T TENSOR REMARK 3 T11: 0.0705 T22: 0.1086 REMARK 3 T33: 0.0743 T12: 0.0504 REMARK 3 T13: -0.1265 T23: -0.1262 REMARK 3 L TENSOR REMARK 3 L11: 20.3053 L22: 26.5129 REMARK 3 L33: 7.2556 L12: -7.8928 REMARK 3 L13: -12.0466 L23: 3.0861 REMARK 3 S TENSOR REMARK 3 S11: -0.3741 S12: -1.2688 S13: 1.9282 REMARK 3 S21: 0.1269 S22: 1.2173 S23: -0.0706 REMARK 3 S31: -0.7058 S32: 1.2899 S33: -0.8432 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 26 A 33 REMARK 3 ORIGIN FOR THE GROUP (A): 28.3416 25.0012 84.2223 REMARK 3 T TENSOR REMARK 3 T11: -0.0583 T22: 0.0339 REMARK 3 T33: 0.1053 T12: 0.1320 REMARK 3 T13: -0.0763 T23: -0.1150 REMARK 3 L TENSOR REMARK 3 L11: 26.3048 L22: 6.3756 REMARK 3 L33: 18.6530 L12: 3.2024 REMARK 3 L13: 12.4962 L23: -7.2033 REMARK 3 S TENSOR REMARK 3 S11: 0.2872 S12: -0.0306 S13: -0.7117 REMARK 3 S21: -0.3030 S22: 0.1164 S23: -0.4979 REMARK 3 S31: 0.2304 S32: -0.2830 S33: -0.4036 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 34 A 49 REMARK 3 ORIGIN FOR THE GROUP (A): 5.1337 20.3147 76.1654 REMARK 3 T TENSOR REMARK 3 T11: 0.0540 T22: -0.0020 REMARK 3 T33: 0.0653 T12: 0.0521 REMARK 3 T13: 0.0285 T23: 0.0180 REMARK 3 L TENSOR REMARK 3 L11: 2.1220 L22: 2.8161 REMARK 3 L33: 3.6695 L12: 1.6215 REMARK 3 L13: 2.2487 L23: 0.2937 REMARK 3 S TENSOR REMARK 3 S11: -0.0573 S12: 0.2387 S13: -0.1391 REMARK 3 S21: 0.4598 S22: 0.2243 S23: 0.3363 REMARK 3 S31: -0.2233 S32: 0.0837 S33: -0.1670 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 50 A 61 REMARK 3 ORIGIN FOR THE GROUP (A): 1.1676 14.2520 80.9382 REMARK 3 T TENSOR REMARK 3 T11: 0.0881 T22: 0.0275 REMARK 3 T33: 0.0050 T12: 0.0456 REMARK 3 T13: 0.1226 T23: 0.0102 REMARK 3 L TENSOR REMARK 3 L11: 5.3640 L22: 16.3524 REMARK 3 L33: 1.8114 L12: -7.3295 REMARK 3 L13: 0.8323 L23: -2.6246 REMARK 3 S TENSOR REMARK 3 S11: 0.2334 S12: -0.4397 S13: 0.1255 REMARK 3 S21: 0.6978 S22: 0.2246 S23: 0.2519 REMARK 3 S31: 0.0047 S32: -0.1944 S33: -0.4580 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 62 A 74 REMARK 3 ORIGIN FOR THE GROUP (A): 5.2077 25.7047 77.7944 REMARK 3 T TENSOR REMARK 3 T11: 0.1352 T22: -0.0220 REMARK 3 T33: 0.0319 T12: 0.0949 REMARK 3 T13: 0.0950 T23: -0.0067 REMARK 3 L TENSOR REMARK 3 L11: 3.3182 L22: 3.4768 REMARK 3 L33: 2.0195 L12: 0.6128 REMARK 3 L13: 1.2168 L23: 0.5708 REMARK 3 S TENSOR REMARK 3 S11: -0.2518 S12: -0.1727 S13: 0.2446 REMARK 3 S21: 0.4018 S22: 0.1937 S23: 0.4717 REMARK 3 S31: -0.4923 S32: -0.0474 S33: 0.0581 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 84 REMARK 3 ORIGIN FOR THE GROUP (A): -4.0107 13.8703 64.4783 REMARK 3 T TENSOR REMARK 3 T11: -0.0404 T22: 0.0151 REMARK 3 T33: 0.1674 T12: -0.0400 REMARK 3 T13: -0.1331 T23: 0.0845 REMARK 3 L TENSOR REMARK 3 L11: 6.7228 L22: 21.7011 REMARK 3 L33: 9.8657 L12: 8.5420 REMARK 3 L13: -8.1400 L23: -10.0160 REMARK 3 S TENSOR REMARK 3 S11: -0.3878 S12: 0.4638 S13: 0.3570 REMARK 3 S21: -0.4585 S22: 0.4114 S23: 0.9150 REMARK 3 S31: 0.1312 S32: -0.2856 S33: -0.0236 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 85 A 95 REMARK 3 ORIGIN FOR THE GROUP (A): 0.5441 4.6456 72.3535 REMARK 3 T TENSOR REMARK 3 T11: 0.0285 T22: -0.0090 REMARK 3 T33: 0.1261 T12: -0.0241 REMARK 3 T13: 0.0213 T23: 0.0336 REMARK 3 L TENSOR REMARK 3 L11: 5.3334 L22: 3.7771 REMARK 3 L33: 3.0885 L12: -3.0819 REMARK 3 L13: 1.1470 L23: -0.6046 REMARK 3 S TENSOR REMARK 3 S11: 0.0003 S12: -0.0545 S13: -0.0111 REMARK 3 S21: 0.3691 S22: -0.0375 S23: 0.3647 REMARK 3 S31: -0.0784 S32: -0.1465 S33: 0.0373 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 96 A 100 REMARK 3 ORIGIN FOR THE GROUP (A): 7.0407 2.9260 80.2089 REMARK 3 T TENSOR REMARK 3 T11: 0.1112 T22: -0.0393 REMARK 3 T33: 0.0826 T12: 0.0182 REMARK 3 T13: 0.0142 T23: 0.0519 REMARK 3 L TENSOR REMARK 3 L11: 9.6367 L22: 0.9107 REMARK 3 L33: 20.0269 L12: 2.6643 REMARK 3 L13: 2.9501 L23: 2.6402 REMARK 3 S TENSOR REMARK 3 S11: 0.0544 S12: -0.2610 S13: -0.6124 REMARK 3 S21: 0.2046 S22: 0.0070 S23: -0.2683 REMARK 3 S31: 0.4929 S32: -0.5087 S33: -0.0614 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 101 A 117 REMARK 3 ORIGIN FOR THE GROUP (A): 12.0055 11.3313 75.6696 REMARK 3 T TENSOR REMARK 3 T11: 0.0623 T22: 0.0102 REMARK 3 T33: 0.0645 T12: 0.0364 REMARK 3 T13: -0.0160 T23: -0.0133 REMARK 3 L TENSOR REMARK 3 L11: 1.1694 L22: 1.9608 REMARK 3 L33: 5.0890 L12: 0.6262 REMARK 3 L13: 1.8223 L23: -0.9363 REMARK 3 S TENSOR REMARK 3 S11: 0.0681 S12: 0.0750 S13: -0.0635 REMARK 3 S21: 0.1088 S22: 0.1034 S23: -0.0230 REMARK 3 S31: 0.0403 S32: 0.1140 S33: -0.1716 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 118 A 130 REMARK 3 ORIGIN FOR THE GROUP (A): 12.7360 17.5768 67.7251 REMARK 3 T TENSOR REMARK 3 T11: 0.0420 T22: 0.0191 REMARK 3 T33: 0.0540 T12: -0.0024 REMARK 3 T13: -0.0004 T23: 0.0002 REMARK 3 L TENSOR REMARK 3 L11: 1.6877 L22: 3.0418 REMARK 3 L33: 2.7084 L12: 1.6146 REMARK 3 L13: 1.2302 L23: 0.6540 REMARK 3 S TENSOR REMARK 3 S11: -0.0340 S12: 0.0889 S13: 0.1304 REMARK 3 S21: -0.1582 S22: 0.1158 S23: -0.1109 REMARK 3 S31: 0.1003 S32: 0.0997 S33: -0.0818 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 131 A 136 REMARK 3 ORIGIN FOR THE GROUP (A): 24.0058 16.0224 79.7725 REMARK 3 T TENSOR REMARK 3 T11: -0.0299 T22: 0.0087 REMARK 3 T33: 0.0585 T12: 0.0412 REMARK 3 T13: -0.0065 T23: -0.0472 REMARK 3 L TENSOR REMARK 3 L11: 48.3659 L22: 2.9292 REMARK 3 L33: 44.7416 L12: -0.4071 REMARK 3 L13: 38.1660 L23: -6.8624 REMARK 3 S TENSOR REMARK 3 S11: 0.4768 S12: -1.1502 S13: 0.0473 REMARK 3 S21: -0.7116 S22: -0.6942 S23: -0.0288 REMARK 3 S31: 0.1175 S32: -0.5030 S33: 0.2175 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 137 A 142 REMARK 3 ORIGIN FOR THE GROUP (A): 29.2673 15.0818 86.2384 REMARK 3 T TENSOR REMARK 3 T11: -0.0466 T22: 0.1455 REMARK 3 T33: -0.0358 T12: 0.0685 REMARK 3 T13: -0.0250 T23: -0.0012 REMARK 3 L TENSOR REMARK 3 L11: 16.8977 L22: 12.0185 REMARK 3 L33: 37.8990 L12: 3.1146 REMARK 3 L13: 8.7682 L23: -6.7310 REMARK 3 S TENSOR REMARK 3 S11: -0.6033 S12: -0.2784 S13: -0.2600 REMARK 3 S21: -0.0620 S22: 0.6090 S23: -0.6827 REMARK 3 S31: -0.0361 S32: 0.0669 S33: -0.0056 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 143 A 148 REMARK 3 ORIGIN FOR THE GROUP (A): 23.3726 9.8209 90.7349 REMARK 3 T TENSOR REMARK 3 T11: 0.1827 T22: 0.1969 REMARK 3 T33: -0.1041 T12: -0.1682 REMARK 3 T13: -0.0843 T23: -0.0309 REMARK 3 L TENSOR REMARK 3 L11: 2.7444 L22: 1.8051 REMARK 3 L33: 57.5202 L12: 0.9405 REMARK 3 L13: -7.4406 L23: -9.9917 REMARK 3 S TENSOR REMARK 3 S11: -0.2792 S12: -1.8648 S13: -0.3102 REMARK 3 S21: -1.3119 S22: -0.0820 S23: -1.5859 REMARK 3 S31: 2.6264 S32: -2.8016 S33: 0.3613 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B REMARK 3 FACTORS. ANISOU RECORD CONTAINS SUMOF TLS AND RESIDUAL U FACTORS. REMARK 4 REMARK 4 3EBQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-AUG-08. REMARK 100 THE DEPOSITION ID IS D_1000049124. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.6 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 FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13493 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06800 REMARK 200 FOR THE DATA SET : 45.2100 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 (%) : 87.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.64600 REMARK 200 FOR SHELL : 2.570 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE, RESOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: MERCURY DERIVATIVE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 4000, 0.1 M SODIUM, ACETATE, REMARK 280 0.1 M TRIS HCL PH 4.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K. CRYSTALS WERE SOAKED OVERNIGHT IN 0.01 M REMARK 280 THIMEROSAL TO CREATE THE MERCURY DERIVATIVE. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 92.11950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 20.81250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 20.81250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 138.17925 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 20.81250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 20.81250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 46.05975 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 20.81250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 20.81250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 138.17925 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 20.81250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 20.81250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 46.05975 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 92.11950 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 GLU A 2 REMARK 465 PRO A 3 REMARK 465 PRO A 4 REMARK 465 ASP A 149 REMARK 465 SER A 150 REMARK 465 ILE A 151 REMARK 465 GLN A 152 REMARK 465 ILE A 153 REMARK 465 GLN A 154 REMARK 465 PRO A 155 REMARK 465 PRO A 156 REMARK 465 GLY A 157 REMARK 465 GLY A 158 REMARK 465 SER A 159 REMARK 465 SER A 160 REMARK 465 VAL A 161 REMARK 465 GLY A 162 REMARK 465 ARG A 163 REMARK 465 PRO A 164 REMARK 465 ASN A 165 REMARK 465 GLY A 166 REMARK 465 GLN A 167 REMARK 465 SER A 168 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 31 CG CD CE NZ REMARK 470 ARG A 145 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD1 ASP A 130 O HOH A 249 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 LEU A 148 C LEU A 148 O 0.176 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 94 -75.46 -127.07 REMARK 500 HIS A 106 75.80 -151.85 REMARK 500 ASN A 107 -168.26 -117.66 REMARK 500 ASN A 107 -169.25 -117.66 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 HG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG A 202 DBREF 3EBQ A 1 168 UNP Q6ICB0 F152B_HUMAN 1 168 SEQADV 3EBQ GLY A -1 UNP Q6ICB0 EXPRESSION TAG SEQADV 3EBQ SER A 0 UNP Q6ICB0 EXPRESSION TAG SEQRES 1 A 170 GLY SER MET GLU PRO PRO ASN LEU TYR PRO VAL LYS LEU SEQRES 2 A 170 TYR VAL TYR ASP LEU SER LYS GLY LEU ALA ARG ARG LEU SEQRES 3 A 170 SER PRO ILE MET LEU GLY LYS GLN LEU GLU GLY ILE TRP SEQRES 4 A 170 HIS THR SER ILE VAL VAL HIS LYS ASP GLU PHE PHE PHE SEQRES 5 A 170 GLY SER GLY GLY ILE SER SER CYS PRO PRO GLY GLY THR SEQRES 6 A 170 LEU LEU GLY PRO PRO ASP SER VAL VAL ASP VAL GLY SER SEQRES 7 A 170 THR GLU VAL THR GLU GLU ILE PHE LEU GLU TYR LEU SER SEQRES 8 A 170 SER LEU GLY GLU SER LEU PHE ARG GLY GLU ALA TYR ASN SEQRES 9 A 170 LEU PHE GLU HIS ASN CYS ASN THR PHE SER ASN GLU VAL SEQRES 10 A 170 ALA GLN PHE LEU THR GLY ARG LYS ILE PRO SER TYR ILE SEQRES 11 A 170 THR ASP LEU PRO SER GLU VAL LEU SER THR PRO PHE GLY SEQRES 12 A 170 GLN ALA LEU ARG PRO LEU LEU ASP SER ILE GLN ILE GLN SEQRES 13 A 170 PRO PRO GLY GLY SER SER VAL GLY ARG PRO ASN GLY GLN SEQRES 14 A 170 SER HET HG A 201 1 HET HG A 202 2 HETNAM HG MERCURY (II) ION FORMUL 2 HG 2(HG 2+) FORMUL 4 HOH *63(H2 O) HELIX 1 1 GLY A 19 GLY A 30 1 12 HELIX 2 2 THR A 80 GLU A 93 1 14 HELIX 3 3 ARG A 97 TYR A 101 5 5 HELIX 4 4 ASN A 107 GLY A 121 1 15 HELIX 5 5 PRO A 125 ASP A 130 1 6 HELIX 6 6 ASP A 130 SER A 137 1 8 HELIX 7 7 THR A 138 ARG A 145 1 8 SHEET 1 A 5 SER A 56 CYS A 58 0 SHEET 2 A 5 ASP A 46 PHE A 49 -1 N GLU A 47 O CYS A 58 SHEET 3 A 5 TRP A 37 VAL A 43 -1 N ILE A 41 O PHE A 48 SHEET 4 A 5 TYR A 7 ASP A 15 -1 N TYR A 14 O HIS A 38 SHEET 5 A 5 SER A 70 THR A 77 -1 O SER A 70 N VAL A 13 SITE 1 AC1 2 CYS A 58 GLY A 62 SITE 1 AC2 2 HIS A 38 CYS A 108 CRYST1 41.625 41.625 184.239 90.00 90.00 90.00 P 43 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 0.024024 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024024 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005428 0.00000