HEADER RNA BINDING PROTEIN 30-JUN-11 3SOO TITLE CRYSTAL STRUCTURE OF A LINE-1 TYPE TRANSPOSASE DOMAIN-CONTAINING TITLE 2 PROTEIN 1 (L1TD1) FROM HOMO SAPIENS AT 2.73 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: LINE-1 TYPE TRANSPOSASE DOMAIN-CONTAINING PROTEIN 1; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: RESIDUES 235-321; COMPND 5 SYNONYM: ES CELL-ASSOCIATED PROTEIN 11; 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: BC111559, ECAT11, L1TD1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS ALPHA/BETA PROTEIN, STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL KEYWDS 2 GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-BIOLOGY, RNA KEYWDS 3 BINDING PROTEIN, PARTNERSHIP FOR STEM CELL BIOLOGY, STEMCELL EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG),PARTNERSHIP FOR STEM CELL AUTHOR 2 BIOLOGY (STEMCELL) REVDAT 5 01-FEB-23 3SOO 1 SEQADV REVDAT 4 21-DEC-22 3SOO 1 REMARK SEQADV LINK REVDAT 3 08-NOV-17 3SOO 1 REMARK REVDAT 2 21-OCT-15 3SOO 1 AUTHOR REVDAT 1 20-JUL-11 3SOO 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG), JRNL AUTH 2 PARTNERSHIP FOR STEM CELL BIOLOGY (STEMCELL) JRNL TITL CRYSTAL STRUCTURE OF A LINE-1 TYPE TRANSPOSASE JRNL TITL 2 DOMAIN-CONTAINING PROTEIN 1 (L1TD1) FROM HOMO SAPIENS AT JRNL TITL 3 2.73 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER-TNT 2.8.0 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) : 2.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 11828 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) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860 REMARK 3 FREE R VALUE TEST SET COUNT : 575 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 : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.73 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.99 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2728 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2646 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2595 REMARK 3 BIN R VALUE (WORKING SET) : 0.2625 REMARK 3 BIN FREE R VALUE : 0.3090 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.88 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 133 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 : 1977 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 118.5 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -11.89370 REMARK 3 B22 (A**2) : -11.89370 REMARK 3 B33 (A**2) : 23.78730 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL 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 : 0.931 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2036 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 2754 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 956 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 55 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 284 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2036 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 270 ; 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 : 2143 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.16 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.80 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 3.01 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|0 - 320 } REMARK 3 ORIGIN FOR THE GROUP (A): -31.8879 21.1779 29.3758 REMARK 3 T TENSOR REMARK 3 T11: 0.1375 T22: 0.2831 REMARK 3 T33: -0.2860 T12: -0.0857 REMARK 3 T13: 0.0156 T23: -0.1105 REMARK 3 L TENSOR REMARK 3 L11: 1.1307 L22: 2.6231 REMARK 3 L33: 11.1892 L12: -0.4178 REMARK 3 L13: 0.3999 L23: -0.2080 REMARK 3 S TENSOR REMARK 3 S11: 0.2021 S12: -0.3050 S13: 0.0592 REMARK 3 S21: 0.0740 S22: 0.0959 S23: -0.0059 REMARK 3 S31: -0.3800 S32: 0.5456 S33: -0.2979 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|0 - 320 } REMARK 3 ORIGIN FOR THE GROUP (A): -30.8505 41.6886 20.5772 REMARK 3 T TENSOR REMARK 3 T11: 0.4208 T22: 0.0323 REMARK 3 T33: -0.4103 T12: -0.0242 REMARK 3 T13: 0.1791 T23: -0.0954 REMARK 3 L TENSOR REMARK 3 L11: 2.0925 L22: 3.6694 REMARK 3 L33: 3.1893 L12: 1.0502 REMARK 3 L13: -2.4669 L23: -0.6270 REMARK 3 S TENSOR REMARK 3 S11: 0.5477 S12: -0.3140 S13: 0.7102 REMARK 3 S21: 0.4334 S22: -0.0991 S23: 0.9469 REMARK 3 S31: -0.8674 S32: -0.2324 S33: -0.4486 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { C|235 - 320 } REMARK 3 ORIGIN FOR THE GROUP (A): -20.8968 39.7370 17.6340 REMARK 3 T TENSOR REMARK 3 T11: 0.3422 T22: 0.2760 REMARK 3 T33: -0.3496 T12: -0.0329 REMARK 3 T13: 0.0239 T23: -0.0560 REMARK 3 L TENSOR REMARK 3 L11: 3.7543 L22: 3.2076 REMARK 3 L33: 2.7265 L12: 1.3050 REMARK 3 L13: -1.1046 L23: -0.2003 REMARK 3 S TENSOR REMARK 3 S11: 0.5497 S12: -0.3955 S13: 0.3164 REMARK 3 S21: -0.0374 S22: -0.3127 S23: 0.4038 REMARK 3 S31: -0.5589 S32: -0.0611 S33: -0.2370 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1. A MET-INHIBITION PROTOCOL WAS USED REMARK 3 FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. REMARK 3 THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO REMARK 3 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET REMARK 3 INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B REMARK 3 FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U REMARK 3 FACTORS. 3. SULFATE, CHLORIDE MODELED ARE PRESENT IN PROTEIN/ REMARK 3 CRYSTALLIZATION/ CRYO CONDITIONS. 4. NCS RESTRAINTS WERE APPLIED REMARK 3 USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5. THE REMARK 3 PROTEIN WAS SUBJECTED TO REDUCTIVE METHYLATION PRIOR TO REMARK 3 CRYSTALLIZATION AND LYSINES HAVE BEEN MODELED AS N-DIMETHYL- REMARK 3 LYSINE (MLY). HOWEVER, METHYL GROUPS ON LYSINES WERE NOT MODELED REMARK 3 DUE TO POOR SIDE-CHAIN DENSITY. REMARK 4 REMARK 4 3SOO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUL-11. REMARK 100 THE DEPOSITION ID IS D_1000066461. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-11 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 : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91162,0.97932,0.97907 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11913 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.730 REMARK 200 RESOLUTION RANGE LOW (A) : 48.712 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06300 REMARK 200 FOR THE DATA SET : 15.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.59800 REMARK 200 R SYM FOR SHELL (I) : 0.59800 REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX, SHARP, SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: WHILE DATA WERE SCALED WITH XSCALE, THE FINAL STATISTICS REMARK 200 REPORTED IN THE REMARK 200 SECTION HAVE BEEN CALCULATED WITH REMARK 200 SCALA WITH FIXED SCALES AND NO SD CORRECTION. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M POTASSIUM SODIUM TARTRATE, 2.0M REMARK 280 AMMONIUM SULFATE, 0.1M SODIUM CITRATE PH 5.6, NANODROP', VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 194.84667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 97.42333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 146.13500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 48.71167 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 243.55833 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 194.84667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 97.42333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 48.71167 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 146.13500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 243.55833 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -127.0 KCAL/MOL 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 BIOMT1 2 0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 48.71167 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -95.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 S SO4 A 866 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 GLU A 321 REMARK 465 GLU B 321 REMARK 465 GLY C 0 REMARK 465 GLU C 321 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 MLY A 258 CH1 CH2 REMARK 470 MLY A 275 CH1 CH2 REMARK 470 MLY A 281 CH1 CH2 REMARK 470 MLY A 285 CG CD CE NZ CH1 CH2 REMARK 470 MLY A 291 CH1 CH2 REMARK 470 MLY A 301 CH1 CH2 REMARK 470 MLY A 306 CH1 CH2 REMARK 470 MLY A 310 CH1 CH2 REMARK 470 MLY A 314 CH1 CH2 REMARK 470 GLN A 319 CG CD OE1 NE2 REMARK 470 MLY A 320 CG CD CE NZ CH1 CH2 REMARK 470 MLY B 258 CG CD CE NZ CH1 CH2 REMARK 470 MLY B 275 CG CD CE NZ CH1 CH2 REMARK 470 MLY B 281 CG CD CE NZ CH1 CH2 REMARK 470 MLY B 285 CG CD CE NZ CH1 CH2 REMARK 470 MLY B 291 CH1 CH2 REMARK 470 MLY B 301 CH1 CH2 REMARK 470 MLY B 306 CH1 CH2 REMARK 470 MLY B 310 CG CD CE NZ CH1 CH2 REMARK 470 MLY B 314 CG CD CE NZ CH1 CH2 REMARK 470 GLN B 319 CG CD OE1 NE2 REMARK 470 MLY B 320 CG CD CE NZ CH1 CH2 REMARK 470 ASP C 238 CG OD1 OD2 REMARK 470 GLU C 239 CG CD OE1 OE2 REMARK 470 MLY C 258 CH1 CH2 REMARK 470 MLY C 275 CH1 CH2 REMARK 470 MLY C 281 CH1 CH2 REMARK 470 MLY C 285 CH1 CH2 REMARK 470 MLY C 291 CH1 CH2 REMARK 470 MLY C 301 CG CD CE NZ CH1 CH2 REMARK 470 MLY C 306 CH1 CH2 REMARK 470 MLY C 310 CG CD CE NZ CH1 CH2 REMARK 470 MLY C 314 CG CD CE NZ CH1 CH2 REMARK 470 GLN C 319 CG CD OE1 NE2 REMARK 470 MLY C 320 CG CD CE NZ CH1 CH2 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 CYS A 286 -102.60 -95.83 REMARK 500 MSE A 309 -36.56 -140.81 REMARK 500 CYS B 286 -101.99 -97.69 REMARK 500 ASP C 238 84.48 -66.03 REMARK 500 CYS C 286 -102.21 -101.00 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 SO4 A 866 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 867 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 868 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 869 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 870 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 871 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 872 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 873 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL C 874 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 421449 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 1. THE CONSTRUCT (RESIDUES 235-321) WAS EXPRESSED WITH A N-TERMINAL REMARK 999 PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV REMARK 999 PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET REMARK 999 SEQUENCE. 2. THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO REMARK 999 CRYSTALLIZATION. DBREF 3SOO A 235 321 UNP Q5T7N2 LITD1_HUMAN 235 321 DBREF 3SOO B 235 321 UNP Q5T7N2 LITD1_HUMAN 235 321 DBREF 3SOO C 235 321 UNP Q5T7N2 LITD1_HUMAN 235 321 SEQADV 3SOO GLY A 0 UNP Q5T7N2 EXPRESSION TAG SEQADV 3SOO ALA A 246 UNP Q5T7N2 VAL 246 VARIANT SEQADV 3SOO MSE A 309 UNP Q5T7N2 VAL 309 VARIANT SEQADV 3SOO GLY B 0 UNP Q5T7N2 EXPRESSION TAG SEQADV 3SOO ALA B 246 UNP Q5T7N2 VAL 246 VARIANT SEQADV 3SOO MSE B 309 UNP Q5T7N2 VAL 309 VARIANT SEQADV 3SOO GLY C 0 UNP Q5T7N2 EXPRESSION TAG SEQADV 3SOO ALA C 246 UNP Q5T7N2 VAL 246 VARIANT SEQADV 3SOO MSE C 309 UNP Q5T7N2 VAL 309 VARIANT SEQRES 1 A 88 GLY VAL LEU MSE ASP GLU GLY ALA VAL LEU THR LEU ALA SEQRES 2 A 88 ALA ASP LEU SER SER ALA THR LEU ASP ILE SER MLY GLN SEQRES 3 A 88 TRP SER ASN VAL PHE ASN ILE LEU ARG GLU ASN ASP PHE SEQRES 4 A 88 GLU PRO MLY PHE LEU CYS GLU VAL MLY LEU ALA PHE MLY SEQRES 5 A 88 CYS ASP GLY GLU ILE MLY THR PHE SER ASP LEU GLN SER SEQRES 6 A 88 LEU ARG MLY PHE ALA SER GLN MLY SER SER MSE MLY GLU SEQRES 7 A 88 LEU LEU MLY ASP VAL LEU PRO GLN MLY GLU SEQRES 1 B 88 GLY VAL LEU MSE ASP GLU GLY ALA VAL LEU THR LEU ALA SEQRES 2 B 88 ALA ASP LEU SER SER ALA THR LEU ASP ILE SER MLY GLN SEQRES 3 B 88 TRP SER ASN VAL PHE ASN ILE LEU ARG GLU ASN ASP PHE SEQRES 4 B 88 GLU PRO MLY PHE LEU CYS GLU VAL MLY LEU ALA PHE MLY SEQRES 5 B 88 CYS ASP GLY GLU ILE MLY THR PHE SER ASP LEU GLN SER SEQRES 6 B 88 LEU ARG MLY PHE ALA SER GLN MLY SER SER MSE MLY GLU SEQRES 7 B 88 LEU LEU MLY ASP VAL LEU PRO GLN MLY GLU SEQRES 1 C 88 GLY VAL LEU MSE ASP GLU GLY ALA VAL LEU THR LEU ALA SEQRES 2 C 88 ALA ASP LEU SER SER ALA THR LEU ASP ILE SER MLY GLN SEQRES 3 C 88 TRP SER ASN VAL PHE ASN ILE LEU ARG GLU ASN ASP PHE SEQRES 4 C 88 GLU PRO MLY PHE LEU CYS GLU VAL MLY LEU ALA PHE MLY SEQRES 5 C 88 CYS ASP GLY GLU ILE MLY THR PHE SER ASP LEU GLN SER SEQRES 6 C 88 LEU ARG MLY PHE ALA SER GLN MLY SER SER MSE MLY GLU SEQRES 7 C 88 LEU LEU MLY ASP VAL LEU PRO GLN MLY GLU MODRES 3SOO MSE A 237 MET SELENOMETHIONINE MODRES 3SOO MLY A 258 LYS N-DIMETHYL-LYSINE MODRES 3SOO MLY A 275 LYS N-DIMETHYL-LYSINE MODRES 3SOO MLY A 281 LYS N-DIMETHYL-LYSINE MODRES 3SOO MLY A 285 LYS N-DIMETHYL-LYSINE MODRES 3SOO MLY A 291 LYS N-DIMETHYL-LYSINE MODRES 3SOO MLY A 301 LYS N-DIMETHYL-LYSINE MODRES 3SOO MLY A 306 LYS N-DIMETHYL-LYSINE MODRES 3SOO MSE A 309 MET SELENOMETHIONINE MODRES 3SOO MLY A 310 LYS N-DIMETHYL-LYSINE MODRES 3SOO MLY A 314 LYS N-DIMETHYL-LYSINE MODRES 3SOO MLY A 320 LYS N-DIMETHYL-LYSINE MODRES 3SOO MSE B 237 MET SELENOMETHIONINE MODRES 3SOO MLY B 258 LYS N-DIMETHYL-LYSINE MODRES 3SOO MLY B 275 LYS N-DIMETHYL-LYSINE MODRES 3SOO MLY B 281 LYS N-DIMETHYL-LYSINE MODRES 3SOO MLY B 285 LYS N-DIMETHYL-LYSINE MODRES 3SOO MLY B 291 LYS N-DIMETHYL-LYSINE MODRES 3SOO MLY B 301 LYS N-DIMETHYL-LYSINE MODRES 3SOO MLY B 306 LYS N-DIMETHYL-LYSINE MODRES 3SOO MSE B 309 MET SELENOMETHIONINE MODRES 3SOO MLY B 310 LYS N-DIMETHYL-LYSINE MODRES 3SOO MLY B 314 LYS N-DIMETHYL-LYSINE MODRES 3SOO MLY B 320 LYS N-DIMETHYL-LYSINE MODRES 3SOO MSE C 237 MET SELENOMETHIONINE MODRES 3SOO MLY C 258 LYS N-DIMETHYL-LYSINE MODRES 3SOO MLY C 275 LYS N-DIMETHYL-LYSINE MODRES 3SOO MLY C 281 LYS N-DIMETHYL-LYSINE MODRES 3SOO MLY C 285 LYS N-DIMETHYL-LYSINE MODRES 3SOO MLY C 291 LYS N-DIMETHYL-LYSINE MODRES 3SOO MLY C 301 LYS N-DIMETHYL-LYSINE MODRES 3SOO MLY C 306 LYS N-DIMETHYL-LYSINE MODRES 3SOO MSE C 309 MET SELENOMETHIONINE MODRES 3SOO MLY C 310 LYS N-DIMETHYL-LYSINE MODRES 3SOO MLY C 314 LYS N-DIMETHYL-LYSINE MODRES 3SOO MLY C 320 LYS N-DIMETHYL-LYSINE HET MSE A 237 8 HET MLY A 258 9 HET MLY A 275 9 HET MLY A 281 9 HET MLY A 285 5 HET MLY A 291 9 HET MLY A 301 9 HET MLY A 306 9 HET MSE A 309 8 HET MLY A 310 9 HET MLY A 314 9 HET MLY A 320 5 HET MSE B 237 8 HET MLY B 258 5 HET MLY B 275 5 HET MLY B 281 5 HET MLY B 285 5 HET MLY B 291 9 HET MLY B 301 9 HET MLY B 306 9 HET MSE B 309 8 HET MLY B 310 5 HET MLY B 314 5 HET MLY B 320 5 HET MSE C 237 8 HET MLY C 258 9 HET MLY C 275 9 HET MLY C 281 9 HET MLY C 285 9 HET MLY C 291 9 HET MLY C 301 5 HET MLY C 306 9 HET MSE C 309 8 HET MLY C 310 5 HET MLY C 314 5 HET MLY C 320 5 HET SO4 A 866 5 HET SO4 A 867 5 HET SO4 A 868 5 HET SO4 A 869 5 HET SO4 A 870 5 HET SO4 B 872 5 HET SO4 B 873 5 HET SO4 C 871 5 HET CL C 874 1 HETNAM MSE SELENOMETHIONINE HETNAM MLY N-DIMETHYL-LYSINE HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 1 MLY 30(C8 H18 N2 O2) FORMUL 4 SO4 8(O4 S 2-) FORMUL 12 CL CL 1- HELIX 1 1 SER A 257 ASN A 270 1 14 HELIX 2 2 ASP A 295 GLN A 305 1 11 HELIX 3 3 MLY A 306 GLU A 311 1 6 HELIX 4 4 SER B 257 ASN B 270 1 14 HELIX 5 5 ASP B 295 GLN B 305 1 11 HELIX 6 6 MLY B 306 GLU B 311 1 6 HELIX 7 7 SER C 257 ASN C 270 1 14 HELIX 8 8 ASP C 295 SER C 304 1 10 HELIX 9 9 MLY C 306 GLU C 311 1 6 SHEET 1 A 2 LEU A 282 MLY A 285 0 SHEET 2 A 2 ILE A 290 PHE A 293 -1 O PHE A 293 N LEU A 282 SHEET 1 B 4 ALA B 241 VAL B 242 0 SHEET 2 B 4 MLY C 275 MLY C 285 -1 O CYS C 278 N ALA B 241 SHEET 3 B 4 MLY B 275 MLY B 285 -1 N ALA B 283 O MLY C 275 SHEET 4 B 4 ILE B 290 PHE B 293 -1 O PHE B 293 N LEU B 282 SHEET 1 C 3 ALA B 241 VAL B 242 0 SHEET 2 C 3 MLY C 275 MLY C 285 -1 O CYS C 278 N ALA B 241 SHEET 3 C 3 ILE C 290 PHE C 293 -1 O PHE C 293 N LEU C 282 SHEET 1 D 2 SER B 251 ASP B 255 0 SHEET 2 D 2 SER C 251 ASP C 255 -1 O LEU C 254 N ALA B 252 LINK C LEU A 236 N MSE A 237 1555 1555 1.32 LINK C MSE A 237 N ASP A 238 1555 1555 1.34 LINK C SER A 257 N MLY A 258 1555 1555 1.35 LINK C MLY A 258 N GLN A 259 1555 1555 1.35 LINK C PRO A 274 N MLY A 275 1555 1555 1.33 LINK C MLY A 275 N PHE A 276 1555 1555 1.33 LINK C VAL A 280 N MLY A 281 1555 1555 1.34 LINK C MLY A 281 N LEU A 282 1555 1555 1.34 LINK C PHE A 284 N MLY A 285 1555 1555 1.34 LINK C MLY A 285 N CYS A 286 1555 1555 1.34 LINK C ILE A 290 N MLY A 291 1555 1555 1.33 LINK C MLY A 291 N THR A 292 1555 1555 1.35 LINK C ARG A 300 N MLY A 301 1555 1555 1.35 LINK C MLY A 301 N PHE A 302 1555 1555 1.34 LINK C GLN A 305 N MLY A 306 1555 1555 1.36 LINK C MLY A 306 N SER A 307 1555 1555 1.36 LINK C SER A 308 N MSE A 309 1555 1555 1.35 LINK C MSE A 309 N MLY A 310 1555 1555 1.35 LINK C MLY A 310 N GLU A 311 1555 1555 1.34 LINK C LEU A 313 N MLY A 314 1555 1555 1.34 LINK C MLY A 314 N ASP A 315 1555 1555 1.35 LINK C GLN A 319 N MLY A 320 1555 1555 1.36 LINK C LEU B 236 N MSE B 237 1555 1555 1.34 LINK C MSE B 237 N ASP B 238 1555 1555 1.33 LINK C SER B 257 N MLY B 258 1555 1555 1.35 LINK C MLY B 258 N GLN B 259 1555 1555 1.34 LINK C PRO B 274 N MLY B 275 1555 1555 1.36 LINK C MLY B 275 N PHE B 276 1555 1555 1.35 LINK C VAL B 280 N MLY B 281 1555 1555 1.35 LINK C MLY B 281 N LEU B 282 1555 1555 1.33 LINK C PHE B 284 N MLY B 285 1555 1555 1.35 LINK C MLY B 285 N CYS B 286 1555 1555 1.34 LINK C ILE B 290 N MLY B 291 1555 1555 1.32 LINK C MLY B 291 N THR B 292 1555 1555 1.34 LINK C ARG B 300 N MLY B 301 1555 1555 1.35 LINK C MLY B 301 N PHE B 302 1555 1555 1.35 LINK C GLN B 305 N MLY B 306 1555 1555 1.36 LINK C MLY B 306 N SER B 307 1555 1555 1.35 LINK C SER B 308 N MSE B 309 1555 1555 1.36 LINK C MSE B 309 N MLY B 310 1555 1555 1.35 LINK C MLY B 310 N GLU B 311 1555 1555 1.35 LINK C LEU B 313 N MLY B 314 1555 1555 1.35 LINK C MLY B 314 N ASP B 315 1555 1555 1.35 LINK C GLN B 319 N MLY B 320 1555 1555 1.36 LINK C LEU C 236 N MSE C 237 1555 1555 1.34 LINK C MSE C 237 N ASP C 238 1555 1555 1.35 LINK C SER C 257 N MLY C 258 1555 1555 1.34 LINK C MLY C 258 N GLN C 259 1555 1555 1.36 LINK C PRO C 274 N MLY C 275 1555 1555 1.33 LINK C MLY C 275 N PHE C 276 1555 1555 1.33 LINK C VAL C 280 N MLY C 281 1555 1555 1.35 LINK C MLY C 281 N LEU C 282 1555 1555 1.34 LINK C PHE C 284 N MLY C 285 1555 1555 1.35 LINK C MLY C 285 N CYS C 286 1555 1555 1.33 LINK C ILE C 290 N MLY C 291 1555 1555 1.32 LINK C MLY C 291 N THR C 292 1555 1555 1.35 LINK C ARG C 300 N MLY C 301 1555 1555 1.35 LINK C MLY C 301 N PHE C 302 1555 1555 1.34 LINK C GLN C 305 N MLY C 306 1555 1555 1.33 LINK C MLY C 306 N SER C 307 1555 1555 1.34 LINK C SER C 308 N MSE C 309 1555 1555 1.33 LINK C MSE C 309 N MLY C 310 1555 1555 1.35 LINK C MLY C 310 N GLU C 311 1555 1555 1.35 LINK C LEU C 313 N MLY C 314 1555 1555 1.37 LINK C MLY C 314 N ASP C 315 1555 1555 1.34 LINK C GLN C 319 N MLY C 320 1555 1555 1.36 SITE 1 AC1 3 GLN A 305 MLY A 306 SER A 307 SITE 1 AC2 5 TRP A 260 SER A 294 ASP A 295 LEU A 296 SITE 2 AC2 5 GLY B 0 SITE 1 AC3 2 ARG A 300 MLY A 301 SITE 1 AC4 4 MSE A 237 ASP A 238 SER B 257 MLY B 258 SITE 1 AC5 4 SER A 257 MLY A 258 MSE B 237 ASP B 238 SITE 1 AC6 5 GLY A 0 TRP B 260 SER C 294 ASP C 295 SITE 2 AC6 5 LEU C 296 SITE 1 AC7 4 CYS A 278 VAL A 280 GLY B 0 LEU B 236 SITE 1 AC8 3 ASP B 295 LEU B 296 TRP C 260 SITE 1 AC9 2 MLY C 291 THR C 292 CRYST1 69.140 69.140 292.270 90.00 90.00 120.00 P 65 2 2 36 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 0.014463 0.008350 0.000000 0.00000 SCALE2 0.000000 0.016701 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003421 0.00000