PDB Short entry for 5J39 HEADER TRANSCRIPTION 30-MAR-16 5J39 TITLE CRYSTAL STRUCTURE OF THE EXTENDED TUDOR DOMAIN FROM TDRD2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUDOR AND KH DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 309-498; COMPND 5 SYNONYM: TUDOR DOMAIN-CONTAINING PROTEIN 2; 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: TDRKH, TDRD2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-V2R-PRARE3; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28MHL KEYWDS TUDOR DOMAIN, STRUCTURAL GENOMICS CONSORTIUM, SGC, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR H.ZHANG,W.TEMPEL,A.DONG,C.BOUNTRA,C.H.ARROWSMITH,A.M.EDWARDS,J.MIN, AUTHOR 2 STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 8 27-SEP-23 5J39 1 REMARK REVDAT 7 11-DEC-19 5J39 1 REMARK REVDAT 6 15-AUG-18 5J39 1 REMARK REVDAT 5 06-DEC-17 5J39 1 JRNL REVDAT 4 22-NOV-17 5J39 1 JRNL REVDAT 3 15-NOV-17 5J39 1 JRNL REVDAT 2 09-AUG-17 5J39 1 REMARK REVDAT 1 13-APR-16 5J39 0 JRNL AUTH H.ZHANG,K.LIU,N.IZUMI,H.HUANG,D.DING,Z.NI,S.S.SIDHU,C.CHEN, JRNL AUTH 2 Y.TOMARI,J.MIN JRNL TITL STRUCTURAL BASIS FOR ARGININE METHYLATION-INDEPENDENT JRNL TITL 2 RECOGNITION OF PIWIL1 BY TDRD2. JRNL REF PROC. NATL. ACAD. SCI. V. 114 12483 2017 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 29118143 JRNL DOI 10.1073/PNAS.1711486114 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER-TNT 2.10.2 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SMART,VONRHEIN,WOMACK, REMARK 3 : MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.11 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 30630 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : THIN SHELLS (SFTOOLS) REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.110 REMARK 3 FREE R VALUE TEST SET COUNT : 1872 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 : 15 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.27 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2984 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2047 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2799 REMARK 3 BIN R VALUE (WORKING SET) : 0.2023 REMARK 3 BIN FREE R VALUE : 0.2402 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 185 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 : 2980 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 83 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.80900 REMARK 3 B22 (A**2) : 4.21350 REMARK 3 B33 (A**2) : 2.59550 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -8.22150 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.151 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.136 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.156 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.139 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 : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 3154 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 4327 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1019 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 64 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 481 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 3154 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 407 ; 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 : 3413 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.11 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.62 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 17.10 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: {A|301 - 339} REMARK 3 ORIGIN FOR THE GROUP (A): 25.2502 11.0506 110.8162 REMARK 3 T TENSOR REMARK 3 T11: 0.0982 T22: -0.0832 REMARK 3 T33: -0.0443 T12: 0.0292 REMARK 3 T13: 0.1101 T23: 0.0211 REMARK 3 L TENSOR REMARK 3 L11: 0.8357 L22: 1.9012 REMARK 3 L33: 3.5842 L12: 0.1125 REMARK 3 L13: -0.0490 L23: -1.5767 REMARK 3 S TENSOR REMARK 3 S11: -0.0545 S12: -0.1149 S13: 0.2489 REMARK 3 S21: 0.1051 S22: 0.0905 S23: 0.2024 REMARK 3 S31: -0.1742 S32: -0.1883 S33: -0.0360 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: {A|340 - 414} REMARK 3 ORIGIN FOR THE GROUP (A): 26.6533 5.3151 92.8569 REMARK 3 T TENSOR REMARK 3 T11: 0.0881 T22: -0.1025 REMARK 3 T33: -0.1327 T12: -0.0335 REMARK 3 T13: 0.0241 T23: 0.0211 REMARK 3 L TENSOR REMARK 3 L11: 1.1723 L22: 5.3822 REMARK 3 L33: 1.4288 L12: 0.1918 REMARK 3 L13: -0.9848 L23: 0.0524 REMARK 3 S TENSOR REMARK 3 S11: -0.0813 S12: 0.2710 S13: 0.0166 REMARK 3 S21: -0.5233 S22: 0.1748 S23: 0.4343 REMARK 3 S31: 0.0171 S32: -0.1091 S33: -0.0935 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: {A|415 - 497} REMARK 3 ORIGIN FOR THE GROUP (A): 19.8275 2.4555 120.2710 REMARK 3 T TENSOR REMARK 3 T11: 0.0195 T22: -0.1070 REMARK 3 T33: -0.1402 T12: 0.0128 REMARK 3 T13: 0.1082 T23: 0.0272 REMARK 3 L TENSOR REMARK 3 L11: 1.1676 L22: 3.8956 REMARK 3 L33: 4.6134 L12: 0.0662 REMARK 3 L13: 0.0366 L23: -2.5151 REMARK 3 S TENSOR REMARK 3 S11: 0.0068 S12: 0.0650 S13: 0.0395 REMARK 3 S21: 0.3787 S22: 0.2219 S23: 0.3402 REMARK 3 S31: -0.3390 S32: -0.3764 S33: -0.2286 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: {B|301 - 344} REMARK 3 ORIGIN FOR THE GROUP (A): 8.1387 7.5303 56.8198 REMARK 3 T TENSOR REMARK 3 T11: 0.1630 T22: -0.1556 REMARK 3 T33: -0.0631 T12: 0.0196 REMARK 3 T13: 0.0913 T23: -0.0252 REMARK 3 L TENSOR REMARK 3 L11: 0.1674 L22: 1.1138 REMARK 3 L33: 2.5133 L12: -0.0677 REMARK 3 L13: -0.9056 L23: 0.6565 REMARK 3 S TENSOR REMARK 3 S11: 0.0191 S12: -0.0708 S13: -0.1051 REMARK 3 S21: 0.0793 S22: 0.0687 S23: -0.1245 REMARK 3 S31: 0.1362 S32: 0.0150 S33: -0.0879 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: {B|345 - 414} REMARK 3 ORIGIN FOR THE GROUP (A): 17.4076 14.7117 44.8373 REMARK 3 T TENSOR REMARK 3 T11: 0.0759 T22: -0.1035 REMARK 3 T33: -0.0598 T12: 0.0040 REMARK 3 T13: 0.0912 T23: -0.0149 REMARK 3 L TENSOR REMARK 3 L11: 1.2726 L22: 4.8212 REMARK 3 L33: 2.1766 L12: 0.2226 REMARK 3 L13: -0.0646 L23: -0.7016 REMARK 3 S TENSOR REMARK 3 S11: -0.0601 S12: 0.2639 S13: 0.0028 REMARK 3 S21: -0.1435 S22: 0.0408 S23: -0.4974 REMARK 3 S31: 0.0561 S32: 0.1618 S33: 0.0194 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: {B|415 - 496} REMARK 3 ORIGIN FOR THE GROUP (A): 3.8086 16.1801 70.2308 REMARK 3 T TENSOR REMARK 3 T11: 0.1147 T22: -0.1249 REMARK 3 T33: -0.1311 T12: -0.0087 REMARK 3 T13: 0.0990 T23: -0.0071 REMARK 3 L TENSOR REMARK 3 L11: 0.9807 L22: 2.7396 REMARK 3 L33: 1.9819 L12: -0.2728 REMARK 3 L13: -0.8430 L23: 0.8752 REMARK 3 S TENSOR REMARK 3 S11: -0.0283 S12: -0.1400 S13: -0.0185 REMARK 3 S21: 0.0417 S22: -0.0353 S23: 0.0007 REMARK 3 S31: 0.1215 S32: 0.1737 S33: 0.0636 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE WAS SOLVED BY MOLECULAR REMARK 3 REPLACEMENT (PHASER SOFTWARE) AND A MODEL BUILD AUTOMATICALLY REMARK 3 (ARP/WARP) USING DATA FROM AN ISOMORPHOUS CRYSTAL. FURTHER REMARK 3 REFINEMENT WAS PERFORMED WITH THE PROGRAMS REFMAC AND REMARK 3 AUTOBUSTER. TLS GROUPS WERE DEFINED BY THE TLSMD SERVER. MODEL REMARK 3 GEOMETRY WAS VALIDATED WITH PHENIX.MOLPROBITY. NOT RESOLVED IN REMARK 3 THIS VERSION OF THE MODEL: PEAKS IN THE ANOMALOUS DIFFERENCE REMARK 3 FOURIER MAP NEAR RESIDUES Y371/F391/D393 ARE CURRENTLY MODELED REMARK 3 AS CACODYLATE IONS, BUT POSITIVE DIFFERENCE DENSITY COINCIDES REMARK 3 WITH HIGH B-FACTORS FOR THE ION MODELED NEAR TDRD2 CHAIN A. REMARK 3 ORIENTATION AND IDENTITY OF THESE IONS REMAIN IN QUESTION. REMARK 4 REMARK 4 5J39 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000219875. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JAN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97957 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.23 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30647 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 53.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 1.11400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600 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: 3FDR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG-8000, 0.2 M MAGNESIUM REMARK 280 CHLORIDE, 0.1 SODIUM CACODYLATE. A PUTATIVE PEPTIDE LIGAND WAS REMARK 280 ADDED TO THE PROTEIN BUT NOT FOUND DURING CRYSTAL STRUCTURE REMARK 280 ANALYSIS., PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 291K 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 26.89900 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 291 REMARK 465 HIS A 292 REMARK 465 HIS A 293 REMARK 465 HIS A 294 REMARK 465 HIS A 295 REMARK 465 HIS A 296 REMARK 465 HIS A 297 REMARK 465 SER A 298 REMARK 465 SER A 299 REMARK 465 ASN A 476 REMARK 465 GLY A 477 REMARK 465 ASP A 498 REMARK 465 MET B 291 REMARK 465 HIS B 292 REMARK 465 HIS B 293 REMARK 465 HIS B 294 REMARK 465 HIS B 295 REMARK 465 HIS B 296 REMARK 465 HIS B 297 REMARK 465 SER B 298 REMARK 465 SER B 299 REMARK 465 GLY B 462 REMARK 465 ILE B 463 REMARK 465 ASP B 498 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 GLY A 300 N REMARK 470 LEU A 331 CD1 CD2 REMARK 470 ASP A 334 CG OD1 OD2 REMARK 470 GLN A 342 CG CD OE1 NE2 REMARK 470 GLU A 345 CG CD OE1 OE2 REMARK 470 ASN A 346 CG OD1 ND2 REMARK 470 VAL A 348 CG1 CG2 REMARK 470 ASP A 351 CG OD1 OD2 REMARK 470 THR A 353 OG1 CG2 REMARK 470 HIS A 355 CE1 NE2 REMARK 470 THR A 366 OG1 CG2 REMARK 470 GLU A 380 CG CD OE1 OE2 REMARK 470 ASP A 396 OD1 OD2 REMARK 470 LYS A 400 CG CD CE NZ REMARK 470 ARG A 423 NH1 NH2 REMARK 470 ASP A 429 CG OD1 OD2 REMARK 470 GLN A 430 OE1 NE2 REMARK 470 GLU A 433 CD OE1 OE2 REMARK 470 GLU A 434 CG CD OE1 OE2 REMARK 470 ARG A 441 NH1 NH2 REMARK 470 LYS A 449 CG CD CE NZ REMARK 470 LYS A 454 NZ REMARK 470 GLN A 460 OE1 NE2 REMARK 470 THR A 461 OG1 CG2 REMARK 470 ILE A 463 CG1 CG2 CD1 REMARK 470 SER A 464 OG REMARK 470 LYS A 468 NZ REMARK 470 SER A 475 C O CB OG REMARK 470 LYS A 478 N CB CG CD CE NZ REMARK 470 GLU A 494 CD OE1 OE2 REMARK 470 GLU A 497 CG CD OE1 OE2 REMARK 470 GLY B 300 N REMARK 470 ASN B 303 OD1 ND2 REMARK 470 SER B 328 OG REMARK 470 LEU B 331 CG CD1 CD2 REMARK 470 ASP B 334 OD1 OD2 REMARK 470 ASN B 346 CG OD1 ND2 REMARK 470 VAL B 348 CG1 CG2 REMARK 470 ASP B 351 CG OD1 OD2 REMARK 470 GLU B 380 CG CD OE1 OE2 REMARK 470 LYS B 400 CD CE NZ REMARK 470 ASP B 429 CG OD1 OD2 REMARK 470 GLN B 430 CG CD OE1 NE2 REMARK 470 GLU B 432 CD OE1 OE2 REMARK 470 GLU B 433 CD OE1 OE2 REMARK 470 GLU B 434 CG CD OE1 OE2 REMARK 470 LYS B 454 NZ REMARK 470 GLN B 460 CG CD OE1 NE2 REMARK 470 THR B 461 C O CB OG1 CG2 REMARK 470 SER B 464 OG REMARK 470 LYS B 468 NZ REMARK 470 SER B 475 OG REMARK 470 ASN B 476 OD1 ND2 REMARK 470 LYS B 478 CG CD CE NZ REMARK 470 LYS B 479 CG CD CE NZ REMARK 470 GLU B 485 CD OE1 OE2 REMARK 470 GLU B 497 CG 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 HIS A 320 89.73 -155.60 REMARK 500 ASP A 351 50.93 -93.37 REMARK 500 ASN B 346 18.02 58.98 REMARK 500 ASN B 476 -140.93 61.57 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 CAC A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CAC B 501 DBREF 5J39 A 309 498 UNP Q9Y2W6 TDRKH_HUMAN 309 498 DBREF 5J39 B 309 498 UNP Q9Y2W6 TDRKH_HUMAN 309 498 SEQADV 5J39 MET A 291 UNP Q9Y2W6 INITIATING METHIONINE SEQADV 5J39 HIS A 292 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 HIS A 293 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 HIS A 294 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 HIS A 295 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 HIS A 296 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 HIS A 297 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 SER A 298 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 SER A 299 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 GLY A 300 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 ARG A 301 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 GLU A 302 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 ASN A 303 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 LEU A 304 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 TYR A 305 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 PHE A 306 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 GLN A 307 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 GLY A 308 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 MET B 291 UNP Q9Y2W6 INITIATING METHIONINE SEQADV 5J39 HIS B 292 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 HIS B 293 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 HIS B 294 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 HIS B 295 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 HIS B 296 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 HIS B 297 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 SER B 298 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 SER B 299 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 GLY B 300 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 ARG B 301 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 GLU B 302 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 ASN B 303 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 LEU B 304 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 TYR B 305 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 PHE B 306 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 GLN B 307 UNP Q9Y2W6 EXPRESSION TAG SEQADV 5J39 GLY B 308 UNP Q9Y2W6 EXPRESSION TAG SEQRES 1 A 208 MET HIS HIS HIS HIS HIS HIS SER SER GLY ARG GLU ASN SEQRES 2 A 208 LEU TYR PHE GLN GLY GLU VAL TYR VAL SER ALA SER GLU SEQRES 3 A 208 HIS PRO ASN HIS PHE TRP ILE GLN ILE VAL GLY SER ARG SEQRES 4 A 208 SER LEU GLN LEU ASP LYS LEU VAL ASN GLU MET THR GLN SEQRES 5 A 208 HIS TYR GLU ASN SER VAL PRO GLU ASP LEU THR VAL HIS SEQRES 6 A 208 VAL GLY ASP ILE VAL ALA ALA PRO LEU PRO THR ASN GLY SEQRES 7 A 208 SER TRP TYR ARG ALA ARG VAL LEU GLY THR LEU GLU ASN SEQRES 8 A 208 GLY ASN LEU ASP LEU TYR PHE VAL ASP PHE GLY ASP ASN SEQRES 9 A 208 GLY ASP CYS PRO LEU LYS ASP LEU ARG ALA LEU ARG SER SEQRES 10 A 208 ASP PHE LEU SER LEU PRO PHE GLN ALA ILE GLU CYS SER SEQRES 11 A 208 LEU ALA ARG ILE ALA PRO SER GLY ASP GLN TRP GLU GLU SEQRES 12 A 208 GLU ALA LEU ASP GLU PHE ASP ARG LEU THR HIS CYS ALA SEQRES 13 A 208 ASP TRP LYS PRO LEU VAL ALA LYS ILE SER SER TYR VAL SEQRES 14 A 208 GLN THR GLY ILE SER THR TRP PRO LYS ILE TYR LEU TYR SEQRES 15 A 208 ASP THR SER ASN GLY LYS LYS LEU ASP ILE GLY LEU GLU SEQRES 16 A 208 LEU VAL HIS LYS GLY TYR ALA ILE GLU LEU PRO GLU ASP SEQRES 1 B 208 MET HIS HIS HIS HIS HIS HIS SER SER GLY ARG GLU ASN SEQRES 2 B 208 LEU TYR PHE GLN GLY GLU VAL TYR VAL SER ALA SER GLU SEQRES 3 B 208 HIS PRO ASN HIS PHE TRP ILE GLN ILE VAL GLY SER ARG SEQRES 4 B 208 SER LEU GLN LEU ASP LYS LEU VAL ASN GLU MET THR GLN SEQRES 5 B 208 HIS TYR GLU ASN SER VAL PRO GLU ASP LEU THR VAL HIS SEQRES 6 B 208 VAL GLY ASP ILE VAL ALA ALA PRO LEU PRO THR ASN GLY SEQRES 7 B 208 SER TRP TYR ARG ALA ARG VAL LEU GLY THR LEU GLU ASN SEQRES 8 B 208 GLY ASN LEU ASP LEU TYR PHE VAL ASP PHE GLY ASP ASN SEQRES 9 B 208 GLY ASP CYS PRO LEU LYS ASP LEU ARG ALA LEU ARG SER SEQRES 10 B 208 ASP PHE LEU SER LEU PRO PHE GLN ALA ILE GLU CYS SER SEQRES 11 B 208 LEU ALA ARG ILE ALA PRO SER GLY ASP GLN TRP GLU GLU SEQRES 12 B 208 GLU ALA LEU ASP GLU PHE ASP ARG LEU THR HIS CYS ALA SEQRES 13 B 208 ASP TRP LYS PRO LEU VAL ALA LYS ILE SER SER TYR VAL SEQRES 14 B 208 GLN THR GLY ILE SER THR TRP PRO LYS ILE TYR LEU TYR SEQRES 15 B 208 ASP THR SER ASN GLY LYS LYS LEU ASP ILE GLY LEU GLU SEQRES 16 B 208 LEU VAL HIS LYS GLY TYR ALA ILE GLU LEU PRO GLU ASP HET CAC A 501 5 HET UNX A 502 1 HET UNX A 503 1 HET UNX A 504 1 HET UNX A 505 1 HET UNX A 506 1 HET UNX A 507 1 HET UNX A 508 1 HET CAC B 501 5 HET UNX B 502 1 HET UNX B 503 1 HET UNX B 504 1 HET UNX B 505 1 HET UNX B 506 1 HET UNX B 507 1 HET UNX B 508 1 HET UNX B 509 1 HET UNX B 510 1 HET UNX B 511 1 HET UNX B 512 1 HETNAM CAC CACODYLATE ION HETNAM UNX UNKNOWN ATOM OR ION HETSYN CAC DIMETHYLARSINATE FORMUL 3 CAC 2(C2 H6 AS O2 1-) FORMUL 4 UNX 18(X) FORMUL 23 HOH *83(H2 O) HELIX 1 AA1 GLY A 327 GLU A 345 1 19 HELIX 2 AA2 PRO A 398 LEU A 402 5 5 HELIX 3 AA3 ARG A 406 SER A 411 5 6 HELIX 4 AA4 GLU A 432 HIS A 444 1 13 HELIX 5 AA5 ILE A 482 LYS A 489 1 8 HELIX 6 AA6 GLY B 327 GLU B 345 1 19 HELIX 7 AA7 PRO B 398 LEU B 402 5 5 HELIX 8 AA8 ARG B 406 LEU B 410 5 5 HELIX 9 AA9 GLU B 432 HIS B 444 1 13 HELIX 10 AB1 ILE B 482 LYS B 489 1 8 SHEET 1 AA1 7 LEU A 480 ASP A 481 0 SHEET 2 AA1 7 SER A 464 ASP A 473 -1 N ASP A 473 O LEU A 480 SHEET 3 AA1 7 LEU A 451 THR A 461 -1 N SER A 456 O LYS A 468 SHEET 4 AA1 7 GLN A 307 HIS A 317 -1 N GLY A 308 O ALA A 453 SHEET 5 AA1 7 HIS A 320 ILE A 325 -1 O HIS A 320 N HIS A 317 SHEET 6 AA1 7 ILE A 417 LEU A 421 -1 O CYS A 419 N PHE A 321 SHEET 7 AA1 7 SER A 464 ASP A 473 1 O ILE A 469 N SER A 420 SHEET 1 AA2 5 ASN A 394 CYS A 397 0 SHEET 2 AA2 5 LEU A 384 PHE A 388 -1 N LEU A 384 O CYS A 397 SHEET 3 AA2 5 TRP A 370 THR A 378 -1 N LEU A 376 O ASP A 385 SHEET 4 AA2 5 ILE A 359 PRO A 363 -1 N VAL A 360 O ALA A 373 SHEET 5 AA2 5 ARG A 403 ALA A 404 -1 O ARG A 403 N ALA A 361 SHEET 1 AA3 2 ILE A 424 PRO A 426 0 SHEET 2 AA3 2 ALA A 492 GLU A 494 -1 O ILE A 493 N ALA A 425 SHEET 1 AA4 7 LEU B 480 ASP B 481 0 SHEET 2 AA4 7 TRP B 466 ASP B 473 -1 N ASP B 473 O LEU B 480 SHEET 3 AA4 7 LEU B 451 VAL B 459 -1 N SER B 456 O LYS B 468 SHEET 4 AA4 7 GLN B 307 HIS B 317 -1 N GLY B 308 O ALA B 453 SHEET 5 AA4 7 HIS B 320 ILE B 325 -1 O TRP B 322 N ALA B 314 SHEET 6 AA4 7 ILE B 417 LEU B 421 -1 O CYS B 419 N PHE B 321 SHEET 7 AA4 7 TRP B 466 ASP B 473 1 O ILE B 469 N SER B 420 SHEET 1 AA5 5 ASN B 394 CYS B 397 0 SHEET 2 AA5 5 LEU B 384 PHE B 388 -1 N LEU B 384 O CYS B 397 SHEET 3 AA5 5 TRP B 370 THR B 378 -1 N GLY B 377 O ASP B 385 SHEET 4 AA5 5 ILE B 359 PRO B 363 -1 N ALA B 362 O TYR B 371 SHEET 5 AA5 5 ARG B 403 ALA B 404 -1 O ARG B 403 N ALA B 361 SHEET 1 AA6 2 ILE B 424 PRO B 426 0 SHEET 2 AA6 2 ALA B 492 GLU B 494 -1 O ILE B 493 N ALA B 425 SITE 1 AC1 4 LEU A 364 TYR A 371 PHE A 391 ASP A 393 SITE 1 AC2 5 LEU B 364 TYR B 371 PHE B 388 PHE B 391 SITE 2 AC2 5 ASP B 393 CRYST1 36.692 53.798 108.063 90.00 84.26 90.00 P 1 21 1 4 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 0.027254 0.000000 -0.002740 0.00000 SCALE2 0.000000 0.018588 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009300 0.00000