HEADER STRUCTURAL PROTEIN 01-NOV-16 5M9N TITLE CRYSTAL STRUCTURE OF HUMAN TDRD1 EXTENDED TUDOR DOMAIN IN COMPLEX WITH TITLE 2 A SYMMETRICALLY DIMETHYLATED E2F PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUDOR DOMAIN-CONTAINING PROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CANCER/TESTIS ANTIGEN 41.1,CT41.1; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: E2F PEPTIDE; COMPND 8 CHAIN: C; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: 2MR: DIMETHYLATED ARGININE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TDRD1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS RNA-MEDIATED GENE SILENCING, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS KEYWDS 2 CONSORTIUM, SGC, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.TALLANT,P.SAVITSKY,J.MOEHLENBRINK,C.CHAN,G.NUNEZ-ALONSO,J.A.NEWMAN, AUTHOR 2 F.VON DELFT,C.H.ARROWSMITH,A.M.EDWARDS,C.BOUNTRA,O.FEDOROV,N.B.LA AUTHOR 3 THANGUE,S.KNAPP,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 2 17-JAN-24 5M9N 1 REMARK REVDAT 1 16-NOV-16 5M9N 0 JRNL AUTH C.TALLANT,P.SAVITSKY,J.MOEHLENBRINK,C.CHAN,G.NUNEZ-ALONSO, JRNL AUTH 2 J.A.NEWMAN,F.VON DELFT,C.H.ARROWSMITH,A.M.EDWARDS,C.BOUNTRA, JRNL AUTH 3 O.FEDOROV,N.B.LA THANGUE,S.KNAPP JRNL TITL CRYSTAL STRUCTURE OF HUMAN TDRD1 EXTENDED TUDOR DOMAIN IN JRNL TITL 2 COMPLEX WITH A SYMMETRICALLY DIMETHYLATED E2F PEPTIDE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0107 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 29186 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) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1600 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2004 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.29 REMARK 3 BIN R VALUE (WORKING SET) : 0.2930 REMARK 3 BIN FREE R VALUE SET COUNT : 113 REMARK 3 BIN FREE R VALUE : 0.3400 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3132 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 79 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.71 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.57000 REMARK 3 B22 (A**2) : -3.11000 REMARK 3 B33 (A**2) : 3.97000 REMARK 3 B12 (A**2) : 1.66000 REMARK 3 B13 (A**2) : 0.06000 REMARK 3 B23 (A**2) : 0.17000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.190 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.174 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.181 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.633 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3226 ; 0.016 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3199 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4366 ; 1.849 ; 1.998 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7402 ; 0.969 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 404 ; 7.763 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 125 ;36.716 ;25.920 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 574 ;14.718 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;12.824 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 514 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3546 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 643 ; 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): 1619 ; 1.427 ; 2.274 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1618 ; 1.424 ; 2.271 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2016 ; 2.406 ; 3.384 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2017 ; 2.407 ; 3.388 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1607 ; 1.409 ; 2.419 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1607 ; 1.409 ; 2.419 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2349 ; 2.325 ; 3.551 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3431 ; 6.133 ;17.865 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3412 ; 6.127 ;17.761 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 : 2 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 474 A 675 REMARK 3 ORIGIN FOR THE GROUP (A): 38.0802 41.8534 5.5552 REMARK 3 T TENSOR REMARK 3 T11: 0.2042 T22: 0.3303 REMARK 3 T33: 0.0628 T12: -0.0651 REMARK 3 T13: -0.0556 T23: 0.0200 REMARK 3 L TENSOR REMARK 3 L11: 1.0689 L22: 1.1965 REMARK 3 L33: 0.7740 L12: 0.4761 REMARK 3 L13: 0.6276 L23: -0.3491 REMARK 3 S TENSOR REMARK 3 S11: 0.0448 S12: 0.0268 S13: 0.1010 REMARK 3 S21: -0.0275 S22: -0.0420 S23: 0.1113 REMARK 3 S31: 0.0799 S32: 0.0544 S33: -0.0028 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 473 B 672 REMARK 3 ORIGIN FOR THE GROUP (A): 46.4791 26.8437 27.3675 REMARK 3 T TENSOR REMARK 3 T11: 0.2308 T22: 0.3871 REMARK 3 T33: 0.0481 T12: -0.0859 REMARK 3 T13: -0.0873 T23: 0.0900 REMARK 3 L TENSOR REMARK 3 L11: 0.0503 L22: 1.5141 REMARK 3 L33: 1.6444 L12: 0.2312 REMARK 3 L13: -0.0078 L23: -0.0648 REMARK 3 S TENSOR REMARK 3 S11: 0.0474 S12: -0.0642 S13: -0.0362 REMARK 3 S21: 0.0338 S22: 0.0110 S23: -0.0817 REMARK 3 S31: -0.0717 S32: -0.1439 S33: -0.0584 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5M9N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1200002130. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5-8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0282 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30788 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 29.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.03400 REMARK 200 R SYM (I) : 0.02500 REMARK 200 FOR THE DATA SET : 16.7000 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) : 1.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.41100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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: 4B9X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG4000, 0.2M MGCL2, 0.1 M TRIS PH REMARK 280 8.5, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 ASP A 459 REMARK 465 GLN A 460 REMARK 465 SER A 461 REMARK 465 ASP A 462 REMARK 465 PRO A 463 REMARK 465 GLU A 464 REMARK 465 ASP A 465 REMARK 465 VAL A 466 REMARK 465 GLY A 467 REMARK 465 LYS A 468 REMARK 465 MET A 469 REMARK 465 THR A 470 REMARK 465 THR A 471 REMARK 465 GLU A 472 REMARK 465 ASN A 473 REMARK 465 GLN A 676 REMARK 465 SER A 677 REMARK 465 MET A 678 REMARK 465 ASP B 459 REMARK 465 GLN B 460 REMARK 465 SER B 461 REMARK 465 ASP B 462 REMARK 465 PRO B 463 REMARK 465 GLU B 464 REMARK 465 ASP B 465 REMARK 465 VAL B 466 REMARK 465 GLY B 467 REMARK 465 LYS B 468 REMARK 465 MET B 469 REMARK 465 THR B 470 REMARK 465 THR B 471 REMARK 465 GLU B 472 REMARK 465 THR B 657 REMARK 465 PRO B 658 REMARK 465 VAL B 673 REMARK 465 GLY B 674 REMARK 465 GLU B 675 REMARK 465 GLN B 676 REMARK 465 SER B 677 REMARK 465 MET B 678 REMARK 465 SER C 1 REMARK 465 SER C 2 REMARK 465 GLY C 3 REMARK 465 PRO C 4 REMARK 465 ALA C 5 REMARK 465 ARG C 6 REMARK 465 HIS C 11 REMARK 465 PRO C 12 REMARK 465 GLY C 13 REMARK 465 LYS C 14 REMARK 465 GLY C 15 REMARK 465 VAL C 16 REMARK 465 LYS C 17 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 CYS A 590 CA CYS A 590 CB 0.147 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 588 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 588 NE - CZ - NH2 ANGL. DEV. = -5.6 DEGREES REMARK 500 CYS A 590 CA - CB - SG ANGL. DEV. = 18.9 DEGREES REMARK 500 CYS B 590 CA - CB - SG ANGL. DEV. = 10.0 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 LEU A 482 47.87 -107.03 REMARK 500 SER A 537 167.48 72.21 REMARK 500 ALA A 564 149.84 -178.56 REMARK 500 TYR A 578 -38.97 -133.76 REMARK 500 ASN A 632 38.70 39.50 REMARK 500 ASP B 507 90.51 -161.21 REMARK 500 TYR B 578 -54.53 -131.21 REMARK 500 ASN B 645 -0.06 71.45 REMARK 500 2MR C 8 -168.27 50.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 536 SER A 537 137.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 2MR B 701 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 2MR B 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide GLY C 7 and 2MR C 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide 2MR C 8 and GLY C 9 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide GLY C 9 and 2MR C 10 DBREF 5M9N A 459 678 UNP Q9BXT4 TDRD1_HUMAN 460 679 DBREF 5M9N B 459 678 UNP Q9BXT4 TDRD1_HUMAN 460 679 DBREF 5M9N C 1 17 PDB 5M9N 5M9N 1 17 SEQRES 1 A 220 ASP GLN SER ASP PRO GLU ASP VAL GLY LYS MET THR THR SEQRES 2 A 220 GLU ASN ASN ILE VAL VAL ASP LYS SER ASP LEU ILE PRO SEQRES 3 A 220 LYS VAL LEU THR LEU ASN VAL GLY ASP GLU PHE CYS GLY SEQRES 4 A 220 VAL VAL ALA HIS ILE GLN THR PRO GLU ASP PHE PHE CYS SEQRES 5 A 220 GLN GLN LEU GLN SER GLY ARG LYS LEU ALA GLU LEU GLN SEQRES 6 A 220 ALA SER LEU SER LYS TYR CYS ASP GLN LEU PRO PRO ARG SEQRES 7 A 220 SER ASP PHE TYR PRO ALA ILE GLY ASP ILE CYS CYS ALA SEQRES 8 A 220 GLN PHE SER GLU ASP ASP GLN TRP TYR ARG ALA SER VAL SEQRES 9 A 220 LEU ALA TYR ALA SER GLU GLU SER VAL LEU VAL GLY TYR SEQRES 10 A 220 VAL ASP TYR GLY ASN PHE GLU ILE LEU SER LEU MET ARG SEQRES 11 A 220 LEU CYS PRO ILE ILE PRO LYS LEU LEU GLU LEU PRO MET SEQRES 12 A 220 GLN ALA ILE LYS CYS VAL LEU ALA GLY VAL LYS PRO SER SEQRES 13 A 220 LEU GLY ILE TRP THR PRO GLU ALA ILE CYS LEU MET LYS SEQRES 14 A 220 LYS LEU VAL GLN ASN LYS ILE ILE THR VAL LYS VAL VAL SEQRES 15 A 220 ASP LYS LEU GLU ASN SER SER LEU VAL GLU LEU ILE ASP SEQRES 16 A 220 LYS SER GLU THR PRO HIS VAL SER VAL SER LYS VAL LEU SEQRES 17 A 220 LEU ASP ALA GLY PHE ALA VAL GLY GLU GLN SER MET SEQRES 1 B 220 ASP GLN SER ASP PRO GLU ASP VAL GLY LYS MET THR THR SEQRES 2 B 220 GLU ASN ASN ILE VAL VAL ASP LYS SER ASP LEU ILE PRO SEQRES 3 B 220 LYS VAL LEU THR LEU ASN VAL GLY ASP GLU PHE CYS GLY SEQRES 4 B 220 VAL VAL ALA HIS ILE GLN THR PRO GLU ASP PHE PHE CYS SEQRES 5 B 220 GLN GLN LEU GLN SER GLY ARG LYS LEU ALA GLU LEU GLN SEQRES 6 B 220 ALA SER LEU SER LYS TYR CYS ASP GLN LEU PRO PRO ARG SEQRES 7 B 220 SER ASP PHE TYR PRO ALA ILE GLY ASP ILE CYS CYS ALA SEQRES 8 B 220 GLN PHE SER GLU ASP ASP GLN TRP TYR ARG ALA SER VAL SEQRES 9 B 220 LEU ALA TYR ALA SER GLU GLU SER VAL LEU VAL GLY TYR SEQRES 10 B 220 VAL ASP TYR GLY ASN PHE GLU ILE LEU SER LEU MET ARG SEQRES 11 B 220 LEU CYS PRO ILE ILE PRO LYS LEU LEU GLU LEU PRO MET SEQRES 12 B 220 GLN ALA ILE LYS CYS VAL LEU ALA GLY VAL LYS PRO SER SEQRES 13 B 220 LEU GLY ILE TRP THR PRO GLU ALA ILE CYS LEU MET LYS SEQRES 14 B 220 LYS LEU VAL GLN ASN LYS ILE ILE THR VAL LYS VAL VAL SEQRES 15 B 220 ASP LYS LEU GLU ASN SER SER LEU VAL GLU LEU ILE ASP SEQRES 16 B 220 LYS SER GLU THR PRO HIS VAL SER VAL SER LYS VAL LEU SEQRES 17 B 220 LEU ASP ALA GLY PHE ALA VAL GLY GLU GLN SER MET SEQRES 1 C 17 SER SER GLY PRO ALA ARG GLY 2MR GLY 2MR HIS PRO GLY SEQRES 2 C 17 LYS GLY VAL LYS HET 2MR C 8 13 HET 2MR C 10 13 HET EDO A 701 4 HET EDO A 702 4 HET 2MR B 701 13 HET EDO B 702 4 HETNAM 2MR N3, N4-DIMETHYLARGININE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 2MR 3(C8 H18 N4 O2) FORMUL 4 EDO 3(C2 H6 O2) FORMUL 8 HOH *79(H2 O) HELIX 1 AA1 ASP A 478 LEU A 482 5 5 HELIX 2 AA2 SER A 515 GLN A 532 1 18 HELIX 3 AA3 ILE A 593 GLU A 598 5 6 HELIX 4 AA4 THR A 619 GLN A 631 1 13 HELIX 5 AA5 VAL A 662 ALA A 669 1 8 HELIX 6 AA6 ASP B 478 LEU B 482 5 5 HELIX 7 AA7 GLN B 514 LEU B 533 1 20 HELIX 8 AA8 ILE B 593 GLU B 598 5 6 HELIX 9 AA9 THR B 619 GLN B 631 1 13 HELIX 10 AB1 VAL B 662 ALA B 669 1 8 SHEET 1 AA1 7 VAL A 660 SER A 661 0 SHEET 2 AA1 7 SER A 647 ASP A 653 -1 N ASP A 653 O VAL A 660 SHEET 3 AA1 7 ILE A 635 LYS A 642 -1 N THR A 636 O ILE A 652 SHEET 4 AA1 7 GLU A 494 THR A 504 -1 N GLY A 497 O ILE A 635 SHEET 5 AA1 7 ASP A 507 GLN A 512 -1 O ASP A 507 N GLN A 503 SHEET 6 AA1 7 ILE A 604 LEU A 608 -1 O ILE A 604 N CYS A 510 SHEET 7 AA1 7 SER A 647 ASP A 653 1 O SER A 647 N LYS A 605 SHEET 1 AA2 5 PHE A 581 SER A 585 0 SHEET 2 AA2 5 SER A 570 TYR A 575 -1 N VAL A 573 O GLU A 582 SHEET 3 AA2 5 TRP A 557 SER A 567 -1 N ALA A 564 O LEU A 572 SHEET 4 AA2 5 ILE A 546 GLN A 550 -1 N CYS A 547 O ALA A 560 SHEET 5 AA2 5 LEU A 589 CYS A 590 -1 O CYS A 590 N CYS A 548 SHEET 1 AA3 2 VAL A 611 PRO A 613 0 SHEET 2 AA3 2 ALA A 672 GLY A 674 -1 O VAL A 673 N LYS A 612 SHEET 1 AA4 7 VAL B 660 SER B 661 0 SHEET 2 AA4 7 SER B 647 ASP B 653 -1 N ASP B 653 O VAL B 660 SHEET 3 AA4 7 ILE B 635 LYS B 642 -1 N THR B 636 O ILE B 652 SHEET 4 AA4 7 GLU B 494 THR B 504 -1 N PHE B 495 O VAL B 637 SHEET 5 AA4 7 ASP B 507 GLN B 512 -1 O PHE B 509 N ALA B 500 SHEET 6 AA4 7 ILE B 604 LEU B 608 -1 O ILE B 604 N CYS B 510 SHEET 7 AA4 7 SER B 647 ASP B 653 1 O VAL B 649 N VAL B 607 SHEET 1 AA5 5 PHE B 581 SER B 585 0 SHEET 2 AA5 5 SER B 570 TYR B 575 -1 N VAL B 571 O LEU B 584 SHEET 3 AA5 5 TRP B 557 SER B 567 -1 N LEU B 563 O LEU B 572 SHEET 4 AA5 5 ILE B 546 GLN B 550 -1 N CYS B 547 O ALA B 560 SHEET 5 AA5 5 LEU B 589 CYS B 590 -1 O CYS B 590 N CYS B 548 SSBOND 1 CYS A 530 CYS A 590 1555 1555 2.23 SSBOND 2 CYS B 530 CYS B 590 1555 1555 2.18 LINK C GLY C 7 N 2MR C 8 1555 1555 1.34 LINK C 2MR C 8 N GLY C 9 1555 1555 1.34 LINK C GLY C 9 N 2MR C 10 1555 1555 1.34 CISPEP 1 ILE B 483 PRO B 484 0 -2.42 SITE 1 AC1 5 SER A 537 ASP A 538 PHE A 539 LEU A 586 SITE 2 AC1 5 MET A 587 SITE 1 AC2 1 TYR A 575 SITE 1 AC3 6 HIS B 501 PHE B 551 TYR B 558 TYR B 575 SITE 2 AC3 6 TYR B 578 ASN B 580 SITE 1 AC4 2 GLY B 574 TYR B 575 SITE 1 AC5 7 HIS A 501 PHE A 551 TYR A 558 TYR A 575 SITE 2 AC5 7 TYR A 578 ASN A 580 GLY C 9 SITE 1 AC6 9 HIS A 501 PHE A 551 ASP A 554 TYR A 558 SITE 2 AC6 9 TYR A 575 TYR A 578 ASN A 580 GLY C 7 SITE 3 AC6 9 2MR C 10 SITE 1 AC7 5 GLU A 553 ASP A 554 GLN A 556 TYR A 558 SITE 2 AC7 5 2MR C 8 CRYST1 42.910 52.962 59.619 64.94 88.85 67.67 P 1 2 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 0.023305 -0.009573 0.004298 0.00000 SCALE2 0.000000 0.020412 -0.010278 0.00000 SCALE3 0.000000 0.000000 0.018783 0.00000