HEADER TRANSFERASE 07-AUG-15 5D49 TITLE STRUCTURAL BASIS FOR A NEW TEMPLATED ACTIVITY BY TERMINAL TITLE 2 DEOXYNUCLEOTIDYL TRANSFERASE: IMPLICATIONS FOR V(D)J RECOMBINATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*AP*AP*AP*AP*AP*C)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (5'-D(*TP*TP*TP*TP*TP*GP*GP*C)-3'); COMPND 11 CHAIN: C, D; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: DNA (5'-D(*AP*AP*AP*AP*A)-3'); COMPND 15 CHAIN: E; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: DNTT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 17 ORGANISM_TAXID: 32630; SOURCE 18 MOL_ID: 4; SOURCE 19 SYNTHETIC: YES; SOURCE 20 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 21 ORGANISM_TAXID: 32630 KEYWDS TDT, SYNAPSIS, DOUBLE STRAND BREAKS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.LOC'H,S.ROSARIO,M.DELARUE REVDAT 4 10-JAN-24 5D49 1 LINK REVDAT 3 14-SEP-16 5D49 1 JRNL REVDAT 2 17-AUG-16 5D49 1 JRNL REVDAT 1 27-JUL-16 5D49 0 JRNL AUTH J.LOC'H,S.ROSARIO,M.DELARUE JRNL TITL STRUCTURAL BASIS FOR A NEW TEMPLATED ACTIVITY BY TERMINAL JRNL TITL 2 DEOXYNUCLEOTIDYL TRANSFERASE: IMPLICATIONS FOR V(D)J JRNL TITL 3 RECOMBINATION. JRNL REF STRUCTURE V. 24 1452 2016 JRNL REFN ISSN 0969-2126 JRNL PMID 27499438 JRNL DOI 10.1016/J.STR.2016.06.014 REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.4 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.02 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 34590 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) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1729 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 17 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.99 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.05 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.38 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 3034 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2653 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2882 REMARK 3 BIN R VALUE (WORKING SET) : 0.2628 REMARK 3 BIN FREE R VALUE : 0.3154 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.01 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 152 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2826 REMARK 3 NUCLEIC ACID ATOMS : 540 REMARK 3 HETEROGEN ATOMS : 37 REMARK 3 SOLVENT ATOMS : 573 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.07 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.13850 REMARK 3 B22 (A**2) : -6.60450 REMARK 3 B33 (A**2) : -1.53400 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.64970 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.298 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.203 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.174 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.181 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.165 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 3525 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 4858 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1168 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 73 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 453 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 3525 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 1 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 451 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 4370 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.00 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.09 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 18.29 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): 54.8057 2.4316 34.3210 REMARK 3 T TENSOR REMARK 3 T11: -0.0770 T22: -0.0385 REMARK 3 T33: 0.0021 T12: 0.0245 REMARK 3 T13: -0.0359 T23: 0.0386 REMARK 3 L TENSOR REMARK 3 L11: 0.4954 L22: 0.5411 REMARK 3 L33: 0.4392 L12: -0.0390 REMARK 3 L13: 0.0657 L23: 0.2896 REMARK 3 S TENSOR REMARK 3 S11: 0.0674 S12: -0.0360 S13: -0.0228 REMARK 3 S21: -0.0468 S22: -0.0592 S23: -0.0800 REMARK 3 S31: 0.0406 S32: 0.0245 S33: -0.0081 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|* } REMARK 3 ORIGIN FOR THE GROUP (A): 58.8658 24.6317 41.4195 REMARK 3 T TENSOR REMARK 3 T11: 0.0042 T22: -0.0387 REMARK 3 T33: 0.0322 T12: -0.0540 REMARK 3 T13: -0.0145 T23: 0.0068 REMARK 3 L TENSOR REMARK 3 L11: 0.1654 L22: 0.3300 REMARK 3 L33: 0.1459 L12: -0.2470 REMARK 3 L13: 0.0676 L23: -0.3054 REMARK 3 S TENSOR REMARK 3 S11: 0.0003 S12: -0.0069 S13: -0.0015 REMARK 3 S21: -0.0004 S22: 0.0001 S23: 0.0021 REMARK 3 S31: -0.0047 S32: 0.0012 S33: -0.0003 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { C|* } REMARK 3 ORIGIN FOR THE GROUP (A): 58.1769 17.9845 34.7308 REMARK 3 T TENSOR REMARK 3 T11: -0.0461 T22: -0.0107 REMARK 3 T33: 0.0546 T12: -0.0159 REMARK 3 T13: -0.0127 T23: 0.0384 REMARK 3 L TENSOR REMARK 3 L11: 0.4854 L22: 0.0205 REMARK 3 L33: 0.1468 L12: 0.0276 REMARK 3 L13: 0.3928 L23: -0.8420 REMARK 3 S TENSOR REMARK 3 S11: 0.0049 S12: -0.0182 S13: -0.0082 REMARK 3 S21: -0.0143 S22: -0.0049 S23: -0.0039 REMARK 3 S31: -0.0147 S32: 0.0139 S33: 0.0000 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: { D|* } REMARK 3 ORIGIN FOR THE GROUP (A): 54.7475 11.0008 13.7026 REMARK 3 T TENSOR REMARK 3 T11: 0.0398 T22: 0.0070 REMARK 3 T33: -0.0476 T12: 0.0400 REMARK 3 T13: -0.0388 T23: 0.0343 REMARK 3 L TENSOR REMARK 3 L11: 0.0952 L22: 0.1059 REMARK 3 L33: 0.0216 L12: -0.3685 REMARK 3 L13: -0.0660 L23: -0.0855 REMARK 3 S TENSOR REMARK 3 S11: -0.0024 S12: 0.0166 S13: 0.0048 REMARK 3 S21: -0.0058 S22: 0.0127 S23: 0.0305 REMARK 3 S31: -0.0132 S32: 0.0105 S33: -0.0104 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: { E|* } REMARK 3 ORIGIN FOR THE GROUP (A): 57.8103 3.7117 8.5151 REMARK 3 T TENSOR REMARK 3 T11: 0.0379 T22: 0.0329 REMARK 3 T33: -0.0723 T12: 0.0136 REMARK 3 T13: -0.0645 T23: 0.0216 REMARK 3 L TENSOR REMARK 3 L11: 0.1122 L22: 0.1641 REMARK 3 L33: 0.3435 L12: 0.0418 REMARK 3 L13: -0.1397 L23: 0.0610 REMARK 3 S TENSOR REMARK 3 S11: -0.0003 S12: 0.0054 S13: -0.0128 REMARK 3 S21: -0.0050 S22: 0.0009 S23: 0.0040 REMARK 3 S31: 0.0009 S32: -0.0066 S33: -0.0006 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5D49 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212648. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUL-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978570 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34690 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 44.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : 0.10000 REMARK 200 FOR THE DATA SET : 8.9900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.69200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.260 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: 1JMS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22-28% PEG 4000, 100-300 MM LITHIUM REMARK 280 SULFATE AND 100 MM TRIS, PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 28.27500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.12500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 28.27500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 37.12500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: PENTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -73.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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 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 D 111 LIES ON A SPECIAL POSITION. 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 111 REMARK 465 GLY A 112 REMARK 465 SER A 113 REMARK 465 SER A 114 REMARK 465 HIS A 115 REMARK 465 HIS A 116 REMARK 465 HIS A 117 REMARK 465 HIS A 118 REMARK 465 HIS A 119 REMARK 465 HIS A 120 REMARK 465 SER A 121 REMARK 465 SER A 122 REMARK 465 GLY A 123 REMARK 465 LEU A 124 REMARK 465 VAL A 125 REMARK 465 PRO A 126 REMARK 465 ARG A 127 REMARK 465 GLY A 128 REMARK 465 SER A 129 REMARK 465 HIS A 130 REMARK 465 MET A 131 REMARK 465 SER A 132 REMARK 465 PRO A 133 REMARK 465 SER A 134 REMARK 465 PRO A 135 REMARK 465 VAL A 136 REMARK 465 PRO A 137 REMARK 465 GLY A 138 REMARK 465 SER A 139 REMARK 465 GLN A 140 REMARK 465 ASN A 141 REMARK 465 VAL A 142 REMARK 465 PRO A 143 REMARK 465 ALA A 144 REMARK 465 PRO A 145 REMARK 465 ALA A 146 REMARK 465 VAL A 147 REMARK 465 SER A 417 REMARK 465 GLU A 418 REMARK 465 LYS A 419 REMARK 465 SER A 420 REMARK 465 GLY A 421 REMARK 465 GLN A 422 REMARK 465 GLN A 423 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 148 CG CD CE NZ REMARK 470 LYS A 149 CD CE NZ REMARK 470 GLU A 177 CD OE1 OE2 REMARK 470 GLU A 185 CD OE1 OE2 REMARK 470 LYS A 209 CG CD CE NZ REMARK 470 ASP A 219 OD1 OD2 REMARK 470 GLU A 233 CD OE1 OE2 REMARK 470 LYS A 238 CG CD CE NZ REMARK 470 ARG A 268 NE CZ NH1 NH2 REMARK 470 LYS A 281 CE NZ REMARK 470 ARG A 284 CD NE CZ NH1 NH2 REMARK 470 GLU A 317 CD OE1 OE2 REMARK 470 HIS A 342 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 387 CG CD CE NZ REMARK 470 LYS A 389 CD CE NZ REMARK 470 VAL A 395 CG1 CG2 REMARK 470 HIS A 416 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 424 CG CD OE1 OE2 REMARK 470 LYS A 469 CE NZ REMARK 470 DC B 6 O3' REMARK 470 DC C 8 O3' REMARK 470 DC D 8 O3' 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 DA B 4 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT C 2 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DC C 8 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT D 5 O4' - C1' - N1 ANGL. DEV. = 2.6 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 THR A 331 -156.20 -112.25 REMARK 500 ASN A 509 31.07 -83.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1155 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH A1156 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH A1157 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH A1158 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH A1159 DISTANCE = 6.10 ANGSTROMS REMARK 525 HOH A1160 DISTANCE = 6.69 ANGSTROMS REMARK 525 HOH A1161 DISTANCE = 6.76 ANGSTROMS REMARK 525 HOH A1162 DISTANCE = 6.79 ANGSTROMS REMARK 525 HOH A1163 DISTANCE = 7.38 ANGSTROMS REMARK 525 HOH A1164 DISTANCE = 7.55 ANGSTROMS REMARK 525 HOH A1165 DISTANCE = 8.71 ANGSTROMS REMARK 525 HOH A1166 DISTANCE = 11.27 ANGSTROMS REMARK 525 HOH B 135 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH B 136 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH B 137 DISTANCE = 6.27 ANGSTROMS REMARK 525 HOH E 116 DISTANCE = 6.54 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 602 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 253 O REMARK 620 2 VAL A 255 O 87.4 REMARK 620 3 VAL A 258 O 94.6 94.0 REMARK 620 4 HOH A1003 O 83.4 85.4 177.9 REMARK 620 5 DG C 6 OP1 166.3 102.9 93.8 88.3 REMARK 620 6 HOH C 104 O 89.4 174.0 81.2 99.3 81.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 601 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 343 OD1 REMARK 620 2 ASP A 345 OD2 92.0 REMARK 620 3 SO4 A 603 O4 172.4 95.0 REMARK 620 4 HOH A 720 O 80.7 92.0 96.1 REMARK 620 5 HOH A 852 O 82.2 172.4 91.1 91.9 REMARK 620 6 DC C 8 OP1 87.4 88.4 95.7 168.2 86.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 608 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5D46 RELATED DB: PDB DBREF 5D49 A 132 510 UNP Q3UZ80 Q3UZ80_MOUSE 132 510 DBREF 5D49 B 1 6 PDB 5D49 5D49 1 6 DBREF 5D49 C 1 8 PDB 5D49 5D49 1 8 DBREF 5D49 D 1 8 PDB 5D49 5D49 1 8 DBREF 5D49 E 1 5 PDB 5D49 5D49 1 5 SEQADV 5D49 MET A 111 UNP Q3UZ80 INITIATING METHIONINE SEQADV 5D49 GLY A 112 UNP Q3UZ80 EXPRESSION TAG SEQADV 5D49 SER A 113 UNP Q3UZ80 EXPRESSION TAG SEQADV 5D49 SER A 114 UNP Q3UZ80 EXPRESSION TAG SEQADV 5D49 HIS A 115 UNP Q3UZ80 EXPRESSION TAG SEQADV 5D49 HIS A 116 UNP Q3UZ80 EXPRESSION TAG SEQADV 5D49 HIS A 117 UNP Q3UZ80 EXPRESSION TAG SEQADV 5D49 HIS A 118 UNP Q3UZ80 EXPRESSION TAG SEQADV 5D49 HIS A 119 UNP Q3UZ80 EXPRESSION TAG SEQADV 5D49 HIS A 120 UNP Q3UZ80 EXPRESSION TAG SEQADV 5D49 SER A 121 UNP Q3UZ80 EXPRESSION TAG SEQADV 5D49 SER A 122 UNP Q3UZ80 EXPRESSION TAG SEQADV 5D49 GLY A 123 UNP Q3UZ80 EXPRESSION TAG SEQADV 5D49 LEU A 124 UNP Q3UZ80 EXPRESSION TAG SEQADV 5D49 VAL A 125 UNP Q3UZ80 EXPRESSION TAG SEQADV 5D49 PRO A 126 UNP Q3UZ80 EXPRESSION TAG SEQADV 5D49 ARG A 127 UNP Q3UZ80 EXPRESSION TAG SEQADV 5D49 GLY A 128 UNP Q3UZ80 EXPRESSION TAG SEQADV 5D49 SER A 129 UNP Q3UZ80 EXPRESSION TAG SEQADV 5D49 HIS A 130 UNP Q3UZ80 EXPRESSION TAG SEQADV 5D49 MET A 131 UNP Q3UZ80 EXPRESSION TAG SEQRES 1 A 400 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 400 LEU VAL PRO ARG GLY SER HIS MET SER PRO SER PRO VAL SEQRES 3 A 400 PRO GLY SER GLN ASN VAL PRO ALA PRO ALA VAL LYS LYS SEQRES 4 A 400 ILE SER GLN TYR ALA CYS GLN ARG ARG THR THR LEU ASN SEQRES 5 A 400 ASN TYR ASN GLN LEU PHE THR ASP ALA LEU ASP ILE LEU SEQRES 6 A 400 ALA GLU ASN ASP GLU LEU ARG GLU ASN GLU GLY SER CYS SEQRES 7 A 400 LEU ALA PHE MET ARG ALA SER SER VAL LEU LYS SER LEU SEQRES 8 A 400 PRO PHE PRO ILE THR SER MET LYS ASP THR GLU GLY ILE SEQRES 9 A 400 PRO CYS LEU GLY ASP LYS VAL LYS SER ILE ILE GLU GLY SEQRES 10 A 400 ILE ILE GLU ASP GLY GLU SER SER GLU ALA LYS ALA VAL SEQRES 11 A 400 LEU ASN ASP GLU ARG TYR LYS SER PHE LYS LEU PHE THR SEQRES 12 A 400 SER VAL PHE GLY VAL GLY LEU LYS THR ALA GLU LYS TRP SEQRES 13 A 400 PHE ARG MET GLY PHE ARG THR LEU SER LYS ILE GLN SER SEQRES 14 A 400 ASP LYS SER LEU ARG PHE THR GLN MET GLN LYS ALA GLY SEQRES 15 A 400 PHE LEU TYR TYR GLU ASP LEU VAL SER CYS VAL ASN ARG SEQRES 16 A 400 PRO GLU ALA GLU ALA VAL SER MET LEU VAL LYS GLU ALA SEQRES 17 A 400 VAL VAL THR PHE LEU PRO ASP ALA LEU VAL THR MET THR SEQRES 18 A 400 GLY GLY PHE ARG ARG GLY LYS MET THR GLY HIS ASP VAL SEQRES 19 A 400 ASP PHE LEU ILE THR SER PRO GLU ALA THR GLU ASP GLU SEQRES 20 A 400 GLU GLN GLN LEU LEU HIS LYS VAL THR ASP PHE TRP LYS SEQRES 21 A 400 GLN GLN GLY LEU LEU LEU TYR CYS ASP ILE LEU GLU SER SEQRES 22 A 400 THR PHE GLU LYS PHE LYS GLN PRO SER ARG LYS VAL ASP SEQRES 23 A 400 ALA LEU ASP HIS PHE GLN LYS CYS PHE LEU ILE LEU LYS SEQRES 24 A 400 LEU ASP HIS GLY ARG VAL HIS SER GLU LYS SER GLY GLN SEQRES 25 A 400 GLN GLU GLY LYS GLY TRP LYS ALA ILE ARG VAL ASP LEU SEQRES 26 A 400 VAL MET CYS PRO TYR ASP ARG ARG ALA PHE ALA LEU LEU SEQRES 27 A 400 GLY TRP THR GLY SER ARG GLN PHE GLU ARG ASP LEU ARG SEQRES 28 A 400 ARG TYR ALA THR HIS GLU ARG LYS MET MET LEU ASP ASN SEQRES 29 A 400 HIS ALA LEU TYR ASP ARG THR LYS ARG VAL PHE LEU GLU SEQRES 30 A 400 ALA GLU SER GLU GLU GLU ILE PHE ALA HIS LEU GLY LEU SEQRES 31 A 400 ASP TYR ILE GLU PRO TRP GLU ARG ASN ALA SEQRES 1 B 6 DA DA DA DA DA DC SEQRES 1 C 8 DT DT DT DT DT DG DG DC SEQRES 1 D 8 DT DT DT DT DT DG DG DC SEQRES 1 E 5 DA DA DA DA DA HET MG A 601 1 HET NA A 602 1 HET SO4 A 603 5 HET SO4 A 604 5 HET ACT A 605 4 HET ACT A 606 4 HET ACT A 607 4 HET PG4 A 608 13 HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM SO4 SULFATE ION HETNAM ACT ACETATE ION HETNAM PG4 TETRAETHYLENE GLYCOL FORMUL 6 MG MG 2+ FORMUL 7 NA NA 1+ FORMUL 8 SO4 2(O4 S 2-) FORMUL 10 ACT 3(C2 H3 O2 1-) FORMUL 13 PG4 C8 H18 O5 FORMUL 14 HOH *573(H2 O) HELIX 1 AA1 TYR A 153 ARG A 157 5 5 HELIX 2 AA2 ASN A 165 ARG A 182 1 18 HELIX 3 AA3 ASN A 184 SER A 200 1 17 HELIX 4 AA4 SER A 207 GLU A 212 5 6 HELIX 5 AA5 GLY A 218 GLY A 232 1 15 HELIX 6 AA6 SER A 234 ASN A 242 1 9 HELIX 7 AA7 ASP A 243 SER A 254 1 12 HELIX 8 AA8 GLY A 259 MET A 269 1 11 HELIX 9 AA9 THR A 273 ASP A 280 1 8 HELIX 10 AB1 THR A 286 TYR A 295 1 10 HELIX 11 AB2 TYR A 295 SER A 301 1 7 HELIX 12 AB3 ARG A 305 LEU A 323 1 19 HELIX 13 AB4 GLY A 332 ARG A 336 1 5 HELIX 14 AB5 THR A 354 GLN A 372 1 19 HELIX 15 AB6 GLU A 386 GLN A 390 5 5 HELIX 16 AB7 GLY A 413 VAL A 415 5 3 HELIX 17 AB8 PRO A 439 ASP A 441 5 3 HELIX 18 AB9 ARG A 442 GLY A 452 1 11 HELIX 19 AC1 SER A 453 LYS A 469 1 17 HELIX 20 AC2 SER A 490 LEU A 498 1 9 HELIX 21 AC3 GLU A 504 ARG A 508 5 5 SHEET 1 AA1 2 VAL A 303 ASN A 304 0 SHEET 2 AA1 2 THR A 340 GLY A 341 -1 O GLY A 341 N VAL A 303 SHEET 1 AA2 5 LEU A 327 THR A 331 0 SHEET 2 AA2 5 VAL A 344 THR A 349 -1 O THR A 349 N LEU A 327 SHEET 3 AA2 5 TRP A 428 MET A 437 1 O VAL A 436 N ILE A 348 SHEET 4 AA2 5 GLN A 402 ASP A 411 -1 N GLN A 402 O MET A 437 SHEET 5 AA2 5 LEU A 375 LEU A 381 -1 N LEU A 381 O LYS A 403 SHEET 1 AA3 3 MET A 470 LEU A 472 0 SHEET 2 AA3 3 LEU A 477 ASP A 479 -1 O TYR A 478 N MET A 471 SHEET 3 AA3 3 VAL A 484 PHE A 485 -1 O VAL A 484 N ASP A 479 LINK O THR A 253 NA NA A 602 1555 1555 2.46 LINK O VAL A 255 NA NA A 602 1555 1555 2.38 LINK O VAL A 258 NA NA A 602 1555 1555 2.34 LINK OD1 ASP A 343 MG MG A 601 1555 1555 2.17 LINK OD2 ASP A 345 MG MG A 601 1555 1555 2.07 LINK MG MG A 601 O4 SO4 A 603 1555 1555 2.12 LINK MG MG A 601 O HOH A 720 1555 1555 2.21 LINK MG MG A 601 O HOH A 852 1555 1555 2.29 LINK MG MG A 601 OP1 DC C 8 1555 1555 1.93 LINK NA NA A 602 O HOH A1003 1555 1555 2.61 LINK NA NA A 602 OP1 DG C 6 1555 1555 2.41 LINK NA NA A 602 O HOH C 104 1555 1555 2.51 CISPEP 1 GLN A 390 PRO A 391 0 0.83 CISPEP 2 GLY A 452 SER A 453 0 -3.85 SITE 1 AC1 6 ASP A 343 ASP A 345 SO4 A 603 HOH A 720 SITE 2 AC1 6 HOH A 852 DC C 8 SITE 1 AC2 6 THR A 253 VAL A 255 VAL A 258 HOH A1003 SITE 2 AC2 6 DG C 6 HOH C 104 SITE 1 AC3 11 GLY A 332 GLY A 333 ARG A 336 ASP A 345 SITE 2 AC3 11 MG A 601 HOH A 756 HOH A 777 HOH A 852 SITE 3 AC3 11 HOH A 944 DC C 8 HOH C 107 SITE 1 AC4 2 GLY A 425 LYS A 426 SITE 1 AC5 4 ASN A 184 GLY A 186 SER A 187 HOH A 848 SITE 1 AC6 4 LYS A 338 MET A 339 THR A 340 HOH A 796 SITE 1 AC7 2 GLY A 213 LYS A 222 SITE 1 AC8 4 PRO A 324 ASP A 325 GLU A 352 HOH A 770 CRYST1 56.550 74.250 126.150 90.00 101.84 90.00 C 1 2 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 0.017683 0.000000 0.003707 0.00000 SCALE2 0.000000 0.013468 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008099 0.00000