PDB Short entry for 5J3E HEADER NUCLEAR PROTEIN/DNA 30-MAR-16 5J3E TITLE CRYSTAL STRUCTURE OF HUMAN THYN1 PROTEIN IN COMPLEX WITH 5- TITLE 2 METHYLCYTOSINE CONTAINING DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: THYMOCYTE NUCLEAR PROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: THYMOCYTE PROTEIN THY28; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5-METHYLCYTOSINE CONTAINING DNA; COMPND 8 CHAIN: C, D, E, F; COMPND 9 SYNONYM: 5-METHYLCYTOSINE CONTAINING DNA; COMPND 10 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: THYN1, THY28, HSPC144, MDS012, MY0054; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-V3R-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28-MHL; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 OTHER_DETAILS: SYNTHESIZED BY IDTDNA KEYWDS PROTEIN-DNA COMPLEX, MODIFIED DNA, 5-METHYLCYTOSINE CONTAINING DNA, KEYWDS 2 STRUCTURAL GENOMICS CONSORTIUM, SGC, NUCLEAR PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.HALABELIAN,W.TEMPEL,Y.LI,C.BOUNTRA,A.M.EDWARDS,C.H.ARROWSMITH, AUTHOR 2 STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 1 20-APR-16 5J3E 0 JRNL AUTH L.HALABELIAN,W.TEMPEL,Y.LI,C.BOUNTRA,A.M.EDWARDS, JRNL AUTH 2 C.H.ARROWSMITH JRNL TITL CRYSTAL STRUCTURE OF HUMAN THYN1 PROTEIN IN COMPLEX WITH JRNL TITL 2 5-METHYLCYTOSINE CONTAINING DNA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.51 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 18559 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) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 941 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1356 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.93 REMARK 3 BIN R VALUE (WORKING SET) : 0.3430 REMARK 3 BIN FREE R VALUE SET COUNT : 85 REMARK 3 BIN FREE R VALUE : 0.4200 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2728 REMARK 3 NUCLEIC ACID ATOMS : 976 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 10 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.43000 REMARK 3 B22 (A**2) : -1.17000 REMARK 3 B33 (A**2) : 1.54000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.34000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.572 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.296 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.294 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 32.564 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3942 ; 0.015 ; 0.017 REMARK 3 BOND LENGTHS OTHERS (A): 3137 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5550 ; 1.379 ; 1.737 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7259 ; 1.078 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 341 ; 6.787 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 135 ;36.806 ;24.370 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 471 ;14.834 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ; 9.410 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 547 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3767 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 891 ; 0.002 ; 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): 1370 ; 0.863 ; 2.142 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1369 ; 0.859 ; 2.140 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1709 ; 1.466 ; 3.209 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): 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 218 A 222 2 REMARK 3 1 B 218 B 222 2 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 37 ; 0.020 ; 0.500 REMARK 3 TIGHT THERMAL 1 A (A**2): 30 ; 3.070 ; 0.500 REMARK 3 MEDIUM THERMAL 1 A (A**2): 37 ; 3.360 ; 2.000 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 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 53 A 224 REMARK 3 ORIGIN FOR THE GROUP (A): -18.5018 13.9421 -48.0560 REMARK 3 T TENSOR REMARK 3 T11: 0.2917 T22: 0.1453 REMARK 3 T33: 0.2618 T12: 0.0190 REMARK 3 T13: 0.1167 T23: -0.0166 REMARK 3 L TENSOR REMARK 3 L11: 2.9126 L22: 2.1566 REMARK 3 L33: 5.1837 L12: -0.3452 REMARK 3 L13: -1.7657 L23: -0.8142 REMARK 3 S TENSOR REMARK 3 S11: -0.0401 S12: 0.4160 S13: -0.0125 REMARK 3 S21: -0.3068 S22: -0.0925 S23: 0.0133 REMARK 3 S31: 0.0630 S32: 0.0353 S33: 0.1325 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 : B 54 B 224 REMARK 3 ORIGIN FOR THE GROUP (A): -39.7289 10.3239 -6.3277 REMARK 3 T TENSOR REMARK 3 T11: 0.2569 T22: 0.0204 REMARK 3 T33: 0.5197 T12: -0.0379 REMARK 3 T13: 0.3457 T23: -0.0760 REMARK 3 L TENSOR REMARK 3 L11: 3.6210 L22: 2.7956 REMARK 3 L33: 4.5242 L12: -1.0565 REMARK 3 L13: -2.6863 L23: 1.6201 REMARK 3 S TENSOR REMARK 3 S11: -0.2003 S12: -0.0004 S13: -0.1105 REMARK 3 S21: 0.1735 S22: -0.1905 S23: 0.5308 REMARK 3 S31: 0.2996 S32: -0.1509 S33: 0.3908 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 : C 1 C 12 REMARK 3 ORIGIN FOR THE GROUP (A): -53.3247 28.8705 -15.3184 REMARK 3 T TENSOR REMARK 3 T11: 0.1348 T22: 0.5077 REMARK 3 T33: 0.7770 T12: 0.0452 REMARK 3 T13: 0.1177 T23: -0.0994 REMARK 3 L TENSOR REMARK 3 L11: 7.1109 L22: 2.1841 REMARK 3 L33: 0.3497 L12: -2.1820 REMARK 3 L13: 1.5288 L23: -0.4889 REMARK 3 S TENSOR REMARK 3 S11: 0.1138 S12: 0.2336 S13: -0.0097 REMARK 3 S21: 0.0552 S22: -0.1073 S23: 0.2153 REMARK 3 S31: -0.0146 S32: -0.0318 S33: -0.0064 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 : D 1 D 12 REMARK 3 ORIGIN FOR THE GROUP (A): -52.9952 27.5560 -15.5761 REMARK 3 T TENSOR REMARK 3 T11: 0.2355 T22: 0.4732 REMARK 3 T33: 0.6812 T12: -0.0320 REMARK 3 T13: -0.0743 T23: -0.0584 REMARK 3 L TENSOR REMARK 3 L11: 11.8755 L22: 0.9305 REMARK 3 L33: 0.4135 L12: -0.1477 REMARK 3 L13: -0.2666 L23: -0.6012 REMARK 3 S TENSOR REMARK 3 S11: 0.0190 S12: 0.2273 S13: -0.0316 REMARK 3 S21: 0.0973 S22: -0.0866 S23: -0.0451 REMARK 3 S31: -0.1134 S32: 0.0183 S33: 0.0675 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 1 E 12 REMARK 3 ORIGIN FOR THE GROUP (A): -7.1853 30.2953 -38.0110 REMARK 3 T TENSOR REMARK 3 T11: 0.1856 T22: 0.5313 REMARK 3 T33: 0.4932 T12: -0.0340 REMARK 3 T13: -0.0615 T23: 0.0534 REMARK 3 L TENSOR REMARK 3 L11: 11.3982 L22: 1.0184 REMARK 3 L33: 0.2666 L12: 1.4224 REMARK 3 L13: -0.0695 L23: 0.0397 REMARK 3 S TENSOR REMARK 3 S11: -0.4252 S12: 0.2902 S13: 1.1335 REMARK 3 S21: -0.1362 S22: 0.2068 S23: 0.1805 REMARK 3 S31: -0.1367 S32: 0.1623 S33: 0.2184 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 : F 1 F 12 REMARK 3 ORIGIN FOR THE GROUP (A): -7.0288 31.7500 -38.2000 REMARK 3 T TENSOR REMARK 3 T11: 0.1629 T22: 0.5647 REMARK 3 T33: 0.4252 T12: 0.0326 REMARK 3 T13: -0.0074 T23: 0.0784 REMARK 3 L TENSOR REMARK 3 L11: 10.8256 L22: 1.0976 REMARK 3 L33: 0.4992 L12: 0.5455 REMARK 3 L13: -0.9682 L23: 0.6106 REMARK 3 S TENSOR REMARK 3 S11: -0.0739 S12: 0.3648 S13: 0.1270 REMARK 3 S21: 0.0591 S22: 0.0266 S23: 0.0468 REMARK 3 S31: 0.0234 S32: -0.0061 S33: 0.0473 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: MOLECULAR REPLACEMENT REMARK 4 REMARK 4 5J3E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000219880. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97929 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.9 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19516 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 43.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.72900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 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: 3EOP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRISODIUM CITRATE, 0.2M NACL, 30% REMARK 280 PEG3350, PH 5.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 36.61600 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, E, F 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 ARG A 3 REMARK 465 PRO A 4 REMARK 465 ARG A 5 REMARK 465 LYS A 6 REMARK 465 ARG A 7 REMARK 465 LEU A 8 REMARK 465 ALA A 9 REMARK 465 GLY A 10 REMARK 465 THR A 11 REMARK 465 SER A 12 REMARK 465 GLY A 13 REMARK 465 SER A 14 REMARK 465 ASP A 15 REMARK 465 LYS A 16 REMARK 465 GLY A 17 REMARK 465 LEU A 18 REMARK 465 SER A 19 REMARK 465 GLY A 20 REMARK 465 LYS A 21 REMARK 465 ARG A 22 REMARK 465 THR A 23 REMARK 465 LYS A 24 REMARK 465 THR A 25 REMARK 465 GLU A 26 REMARK 465 ASN A 27 REMARK 465 SER A 28 REMARK 465 GLY A 29 REMARK 465 GLU A 30 REMARK 465 ALA A 31 REMARK 465 LEU A 32 REMARK 465 ALA A 33 REMARK 465 LYS A 34 REMARK 465 VAL A 35 REMARK 465 GLU A 36 REMARK 465 ASP A 37 REMARK 465 SER A 38 REMARK 465 ASN A 39 REMARK 465 PRO A 40 REMARK 465 GLN A 41 REMARK 465 LYS A 42 REMARK 465 THR A 43 REMARK 465 SER A 44 REMARK 465 ALA A 45 REMARK 465 THR A 46 REMARK 465 LYS A 47 REMARK 465 ASN A 48 REMARK 465 CYS A 49 REMARK 465 LEU A 50 REMARK 465 LYS A 51 REMARK 465 ASN A 52 REMARK 465 SER A 225 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 ARG B 3 REMARK 465 PRO B 4 REMARK 465 ARG B 5 REMARK 465 LYS B 6 REMARK 465 ARG B 7 REMARK 465 LEU B 8 REMARK 465 ALA B 9 REMARK 465 GLY B 10 REMARK 465 THR B 11 REMARK 465 SER B 12 REMARK 465 GLY B 13 REMARK 465 SER B 14 REMARK 465 ASP B 15 REMARK 465 LYS B 16 REMARK 465 GLY B 17 REMARK 465 LEU B 18 REMARK 465 SER B 19 REMARK 465 GLY B 20 REMARK 465 LYS B 21 REMARK 465 ARG B 22 REMARK 465 THR B 23 REMARK 465 LYS B 24 REMARK 465 THR B 25 REMARK 465 GLU B 26 REMARK 465 ASN B 27 REMARK 465 SER B 28 REMARK 465 GLY B 29 REMARK 465 GLU B 30 REMARK 465 ALA B 31 REMARK 465 LEU B 32 REMARK 465 ALA B 33 REMARK 465 LYS B 34 REMARK 465 VAL B 35 REMARK 465 GLU B 36 REMARK 465 ASP B 37 REMARK 465 SER B 38 REMARK 465 ASN B 39 REMARK 465 PRO B 40 REMARK 465 GLN B 41 REMARK 465 LYS B 42 REMARK 465 THR B 43 REMARK 465 SER B 44 REMARK 465 ALA B 45 REMARK 465 THR B 46 REMARK 465 LYS B 47 REMARK 465 ASN B 48 REMARK 465 CYS B 49 REMARK 465 LEU B 50 REMARK 465 LYS B 51 REMARK 465 ASN B 52 REMARK 465 LEU B 53 REMARK 465 SER B 225 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 LEU A 53 CG CD1 CD2 REMARK 470 GLU A 68 CG CD OE1 OE2 REMARK 470 LYS A 69 CG CD CE NZ REMARK 470 LYS A 85 CE NZ REMARK 470 LYS A 142 CG CD CE NZ REMARK 470 LYS A 152 CG CD CE NZ REMARK 470 ASP A 154 CG OD1 OD2 REMARK 470 LYS A 170 CG CD CE NZ REMARK 470 LYS A 193 NZ REMARK 470 ARG A 200 NE CZ NH1 NH2 REMARK 470 LYS A 222 CG CD CE NZ REMARK 470 GLU A 223 CG CD OE1 OE2 REMARK 470 SER B 54 OG REMARK 470 GLU B 68 CD OE1 OE2 REMARK 470 LYS B 69 CE NZ REMARK 470 LYS B 85 CG CD CE NZ REMARK 470 LYS B 106 CG CD CE NZ REMARK 470 LYS B 119 CG CD CE NZ REMARK 470 GLU B 120 OE1 OE2 REMARK 470 LYS B 131 CG CD CE NZ REMARK 470 LYS B 142 CG CD CE NZ REMARK 470 LYS B 152 CG CD CE NZ REMARK 470 GLU B 153 CG CD OE1 OE2 REMARK 470 LYS B 170 CG CD CE NZ REMARK 470 LYS B 179 CD CE NZ REMARK 470 ARG B 200 CZ NH1 NH2 REMARK 470 GLU B 223 CD OE1 OE2 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 LYS A 69 44.78 39.44 REMARK 500 HIS A 146 38.37 -98.13 REMARK 500 ASN A 155 85.27 -153.74 REMARK 500 GLU B 120 67.16 -118.34 REMARK 500 PRO B 135 129.55 -38.83 REMARK 500 ARG B 202 58.04 -110.47 REMARK 500 REMARK 500 REMARK: NULL DBREF 5J3E A 1 225 UNP Q9P016 THYN1_HUMAN 1 225 DBREF 5J3E B 1 225 UNP Q9P016 THYN1_HUMAN 1 225 DBREF 5J3E C 1 12 PDB 5J3E 5J3E 1 12 DBREF 5J3E D 1 12 PDB 5J3E 5J3E 1 12 DBREF 5J3E E 1 12 PDB 5J3E 5J3E 1 12 DBREF 5J3E F 1 12 PDB 5J3E 5J3E 1 12 SEQRES 1 A 225 MET SER ARG PRO ARG LYS ARG LEU ALA GLY THR SER GLY SEQRES 2 A 225 SER ASP LYS GLY LEU SER GLY LYS ARG THR LYS THR GLU SEQRES 3 A 225 ASN SER GLY GLU ALA LEU ALA LYS VAL GLU ASP SER ASN SEQRES 4 A 225 PRO GLN LYS THR SER ALA THR LYS ASN CYS LEU LYS ASN SEQRES 5 A 225 LEU SER SER HIS TRP LEU MET LYS SER GLU PRO GLU SER SEQRES 6 A 225 ARG LEU GLU LYS GLY VAL ASP VAL LYS PHE SER ILE GLU SEQRES 7 A 225 ASP LEU LYS ALA GLN PRO LYS GLN THR THR CYS TRP ASP SEQRES 8 A 225 GLY VAL ARG ASN TYR GLN ALA ARG ASN PHE LEU ARG ALA SEQRES 9 A 225 MET LYS LEU GLY GLU GLU ALA PHE PHE TYR HIS SER ASN SEQRES 10 A 225 CYS LYS GLU PRO GLY ILE ALA GLY LEU MET LYS ILE VAL SEQRES 11 A 225 LYS GLU ALA TYR PRO ASP HIS THR GLN PHE GLU LYS ASN SEQRES 12 A 225 ASN PRO HIS TYR ASP PRO SER SER LYS GLU ASP ASN PRO SEQRES 13 A 225 LYS TRP SER MET VAL ASP VAL GLN PHE VAL ARG MET MET SEQRES 14 A 225 LYS ARG PHE ILE PRO LEU ALA GLU LEU LYS SER TYR HIS SEQRES 15 A 225 GLN ALA HIS LYS ALA THR GLY GLY PRO LEU LYS ASN MET SEQRES 16 A 225 VAL LEU PHE THR ARG GLN ARG LEU SER ILE GLN PRO LEU SEQRES 17 A 225 THR GLN GLU GLU PHE ASP PHE VAL LEU SER LEU GLU GLU SEQRES 18 A 225 LYS GLU PRO SER SEQRES 1 B 225 MET SER ARG PRO ARG LYS ARG LEU ALA GLY THR SER GLY SEQRES 2 B 225 SER ASP LYS GLY LEU SER GLY LYS ARG THR LYS THR GLU SEQRES 3 B 225 ASN SER GLY GLU ALA LEU ALA LYS VAL GLU ASP SER ASN SEQRES 4 B 225 PRO GLN LYS THR SER ALA THR LYS ASN CYS LEU LYS ASN SEQRES 5 B 225 LEU SER SER HIS TRP LEU MET LYS SER GLU PRO GLU SER SEQRES 6 B 225 ARG LEU GLU LYS GLY VAL ASP VAL LYS PHE SER ILE GLU SEQRES 7 B 225 ASP LEU LYS ALA GLN PRO LYS GLN THR THR CYS TRP ASP SEQRES 8 B 225 GLY VAL ARG ASN TYR GLN ALA ARG ASN PHE LEU ARG ALA SEQRES 9 B 225 MET LYS LEU GLY GLU GLU ALA PHE PHE TYR HIS SER ASN SEQRES 10 B 225 CYS LYS GLU PRO GLY ILE ALA GLY LEU MET LYS ILE VAL SEQRES 11 B 225 LYS GLU ALA TYR PRO ASP HIS THR GLN PHE GLU LYS ASN SEQRES 12 B 225 ASN PRO HIS TYR ASP PRO SER SER LYS GLU ASP ASN PRO SEQRES 13 B 225 LYS TRP SER MET VAL ASP VAL GLN PHE VAL ARG MET MET SEQRES 14 B 225 LYS ARG PHE ILE PRO LEU ALA GLU LEU LYS SER TYR HIS SEQRES 15 B 225 GLN ALA HIS LYS ALA THR GLY GLY PRO LEU LYS ASN MET SEQRES 16 B 225 VAL LEU PHE THR ARG GLN ARG LEU SER ILE GLN PRO LEU SEQRES 17 B 225 THR GLN GLU GLU PHE ASP PHE VAL LEU SER LEU GLU GLU SEQRES 18 B 225 LYS GLU PRO SER SEQRES 1 C 12 DG DC DC DA DA 5CM DG DT DT DG DG DC SEQRES 1 D 12 DG DC DC DA DA 5CM DG DT DT DG DG DC SEQRES 1 E 12 DG DC DC DA DA 5CM DG DT DT DG DG DC SEQRES 1 F 12 DG DC DC DA DA 5CM DG DT DT DG DG DC HET 5CM C 6 20 HET 5CM D 6 20 HET 5CM E 6 20 HET 5CM F 6 20 HET UNX A 301 1 HET UNX A 302 1 HET UNX A 303 1 HET UNX B 301 1 HET UNX B 302 1 HET UNX B 303 1 HET UNX B 304 1 HET UNX B 305 1 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM UNX UNKNOWN ATOM OR ION FORMUL 3 5CM 4(C10 H16 N3 O7 P) FORMUL 7 UNX 8(X) FORMUL 15 HOH *10(H2 O) HELIX 1 AA1 SER A 76 GLN A 83 1 8 HELIX 2 AA2 ASN A 95 MET A 105 1 11 HELIX 3 AA3 HIS A 137 GLU A 141 5 5 HELIX 4 AA4 LEU A 175 GLY A 189 1 15 HELIX 5 AA5 MET A 195 ARG A 200 1 6 HELIX 6 AA6 THR A 209 GLU A 220 1 12 HELIX 7 AA7 SER B 76 ALA B 82 1 7 HELIX 8 AA8 GLN B 83 LYS B 85 5 3 HELIX 9 AA9 ASN B 95 MET B 105 1 11 HELIX 10 AB1 HIS B 137 GLU B 141 5 5 HELIX 11 AB2 LEU B 175 GLY B 189 1 15 HELIX 12 AB3 GLY B 190 ASN B 194 5 5 HELIX 13 AB4 MET B 195 ARG B 200 1 6 HELIX 14 AB5 THR B 209 GLU B 220 1 12 SHEET 1 AA1 6 THR A 87 CYS A 89 0 SHEET 2 AA1 6 SER A 159 PRO A 174 -1 O VAL A 163 N THR A 88 SHEET 3 AA1 6 GLY A 122 PRO A 135 -1 N LEU A 126 O ARG A 167 SHEET 4 AA1 6 GLU A 110 HIS A 115 -1 N ALA A 111 O MET A 127 SHEET 5 AA1 6 HIS A 56 SER A 61 1 N SER A 61 O TYR A 114 SHEET 6 AA1 6 ILE A 205 LEU A 208 -1 O LEU A 208 N HIS A 56 SHEET 1 AA2 2 LEU A 67 GLU A 68 0 SHEET 2 AA2 2 VAL A 71 ASP A 72 -1 O VAL A 71 N GLU A 68 SHEET 1 AA3 6 THR B 87 CYS B 89 0 SHEET 2 AA3 6 SER B 159 PRO B 174 -1 O VAL B 163 N THR B 88 SHEET 3 AA3 6 GLY B 122 PRO B 135 -1 N VAL B 130 O ASP B 162 SHEET 4 AA3 6 GLU B 110 HIS B 115 -1 N HIS B 115 O GLY B 122 SHEET 5 AA3 6 HIS B 56 SER B 61 1 N TRP B 57 O PHE B 112 SHEET 6 AA3 6 ILE B 205 LEU B 208 -1 O GLN B 206 N LEU B 58 SHEET 1 AA4 2 LEU B 67 GLU B 68 0 SHEET 2 AA4 2 VAL B 71 ASP B 72 -1 O VAL B 71 N GLU B 68 LINK O3' DA C 5 P 5CM C 6 1555 1555 1.57 LINK O3' 5CM C 6 P DG C 7 1555 1555 1.62 LINK O3' DA D 5 P 5CM D 6 1555 1555 1.62 LINK O3' 5CM D 6 P DG D 7 1555 1555 1.61 LINK O3' DA E 5 P 5CM E 6 1555 1555 1.60 LINK O3' 5CM E 6 P DG E 7 1555 1555 1.63 LINK O3' DA F 5 P 5CM F 6 1555 1555 1.59 LINK O3' 5CM F 6 P DG F 7 1555 1555 1.60 CRYST1 40.327 73.232 108.201 90.00 91.18 90.00 P 1 21 1 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 0.024797 0.000000 0.000512 0.00000 SCALE2 0.000000 0.013655 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009244 0.00000