HEADER TRANSCRIPTION 01-NOV-21 7Q4N TITLE TRANSCRIPTION FACTOR CDX2 BOUND TO HYDROXYMETHYLATED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (18-MER); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (18-MER); COMPND 7 CHAIN: D, E; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: HOMEOBOX PROTEIN CDX-2; COMPND 11 CHAIN: K, C; COMPND 12 SYNONYM: CDX-3,CAUDAL-TYPE HOMEOBOX PROTEIN 2; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: CDX2, CDX3; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PET20A KEYWDS TRANSCRIPTION FACTOR, HOMEOBOX, COMPLEX, HYDROXYMETHYLATED DNA, KEYWDS 2 TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR E.MORGUNOVA,Y.YIN,A.POPOV,J.TAIPALE REVDAT 2 31-JAN-24 7Q4N 1 REMARK REVDAT 1 16-NOV-22 7Q4N 0 JRNL AUTH E.MORGUNOVA,Y.YIN,A.POPOV,J.TAIPALE JRNL TITL TRANSCRIPTION FACTOR CDX2 BOUND TO HYDROXYMETHYLATED DNA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 6054 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) : 0.240 REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 341 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) : 3.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 423 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.03 REMARK 3 BIN R VALUE (WORKING SET) : 0.2710 REMARK 3 BIN FREE R VALUE SET COUNT : 34 REMARK 3 BIN FREE R VALUE : 0.3150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1138 REMARK 3 NUCLEIC ACID ATOMS : 1482 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 14 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 70.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.88000 REMARK 3 B22 (A**2) : -6.20000 REMARK 3 B33 (A**2) : 2.71000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.71000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.605 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.599 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 82.225 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.933 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.886 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2816 ; 0.009 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 1987 ; 0.002 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4096 ; 2.264 ; 1.711 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4613 ; 1.062 ; 1.568 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 127 ; 5.738 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 84 ;28.499 ;19.286 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 249 ;29.339 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;16.855 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 429 ; 0.138 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2123 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 561 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 2 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 1 39 B 1 39 3612 0.070 0.050 REMARK 3 2 K 189 250 C 189 250 1850 0.220 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 18 REMARK 3 RESIDUE RANGE : D 22 D 39 REMARK 3 ORIGIN FOR THE GROUP (A): -19.0163 -7.1777 -20.0309 REMARK 3 T TENSOR REMARK 3 T11: 0.4059 T22: 0.2291 REMARK 3 T33: 0.5732 T12: 0.2469 REMARK 3 T13: 0.2908 T23: 0.0663 REMARK 3 L TENSOR REMARK 3 L11: 6.6561 L22: 4.0848 REMARK 3 L33: 2.8314 L12: -0.8538 REMARK 3 L13: 0.9254 L23: 0.7967 REMARK 3 S TENSOR REMARK 3 S11: 0.4237 S12: 0.7153 S13: -0.4312 REMARK 3 S21: -0.5450 S22: -0.6999 S23: 0.2673 REMARK 3 S31: 0.1660 S32: 0.1957 S33: 0.2762 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 : K 187 K 252 REMARK 3 ORIGIN FOR THE GROUP (A): -20.2711 -1.8675 -9.1209 REMARK 3 T TENSOR REMARK 3 T11: 0.1366 T22: 0.0949 REMARK 3 T33: 0.5115 T12: 0.0446 REMARK 3 T13: 0.2080 T23: 0.1212 REMARK 3 L TENSOR REMARK 3 L11: 6.4396 L22: 5.3091 REMARK 3 L33: 4.8694 L12: 2.3837 REMARK 3 L13: 0.9924 L23: 0.8510 REMARK 3 S TENSOR REMARK 3 S11: 0.3633 S12: -0.4622 S13: -0.0601 REMARK 3 S21: -0.0988 S22: -0.4806 S23: -0.1985 REMARK 3 S31: -0.0810 S32: 0.0300 S33: 0.1174 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 18 REMARK 3 RESIDUE RANGE : E 22 E 39 REMARK 3 ORIGIN FOR THE GROUP (A): -17.6084 -5.0038 19.0437 REMARK 3 T TENSOR REMARK 3 T11: 0.3210 T22: 0.1890 REMARK 3 T33: 0.5540 T12: -0.1896 REMARK 3 T13: -0.0222 T23: 0.0381 REMARK 3 L TENSOR REMARK 3 L11: 7.4767 L22: 6.2722 REMARK 3 L33: 3.0998 L12: 3.3932 REMARK 3 L13: -1.1521 L23: 1.0016 REMARK 3 S TENSOR REMARK 3 S11: 0.1666 S12: -0.5316 S13: 0.4935 REMARK 3 S21: 0.1505 S22: -0.3961 S23: 0.0250 REMARK 3 S31: -0.1692 S32: 0.4640 S33: 0.2296 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 189 C 251 REMARK 3 ORIGIN FOR THE GROUP (A): -19.8465 -10.4829 7.5757 REMARK 3 T TENSOR REMARK 3 T11: 0.1523 T22: 0.1264 REMARK 3 T33: 0.5782 T12: -0.0796 REMARK 3 T13: 0.0608 T23: 0.0693 REMARK 3 L TENSOR REMARK 3 L11: 5.9408 L22: 4.4111 REMARK 3 L33: 4.5747 L12: -2.9750 REMARK 3 L13: 0.7090 L23: -1.0023 REMARK 3 S TENSOR REMARK 3 S11: 0.2029 S12: 0.4884 S13: 0.1623 REMARK 3 S21: -0.1957 S22: -0.3288 S23: -0.2220 REMARK 3 S31: 0.0587 S32: 0.0093 S33: 0.1258 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 7Q4N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1292118983. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-OCT-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97242 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7406 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.030 REMARK 200 RESOLUTION RANGE LOW (A) : 43.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.27200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 1.40900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 5LTY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 1500, POTASSIUM CHLORIDE, REMARK 280 MAGNESIUM CHLORIDE, PEG 200, BIS-TRIS PROPANE, 8.0, PH 8.0, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-Z+1/2 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 26.33550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.31700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 59.40283 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 26.33550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.31700 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 59.40283 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, K REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, E, 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 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 GLN K 253 REMARK 465 ASP C 187 REMARK 465 LYS C 188 REMARK 465 GLN C 252 REMARK 465 GLN C 253 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 N4 DC B 18 O6 DG E 22 1.87 REMARK 500 OE1 GLU C 241 O HOH C 301 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OP1 DG D 23 O3' DC B 18 2465 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 DT A 1 P DT A 1 OP3 -0.087 REMARK 500 DT B 1 P DT B 1 OP3 -0.082 REMARK 500 DC B 18 P DC B 18 O5' 0.066 REMARK 500 DG E 22 P DG E 22 OP1 0.116 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 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT A 4 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT A 9 O3' - P - OP2 ANGL. DEV. = 7.1 DEGREES REMARK 500 DA A 10 O4' - C4' - C3' ANGL. DEV. = -2.8 DEGREES REMARK 500 DA A 10 C1' - O4' - C4' ANGL. DEV. = -7.4 DEGREES REMARK 500 DT A 16 C3' - O3' - P ANGL. DEV. = -10.1 DEGREES REMARK 500 DC A 18 C1' - O4' - C4' ANGL. DEV. = -6.5 DEGREES REMARK 500 DC A 18 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 DG D 22 C3' - O3' - P ANGL. DEV. = 13.2 DEGREES REMARK 500 DG D 23 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 DG D 23 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 DA D 24 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC D 25 O3' - P - O5' ANGL. DEV. = -11.5 DEGREES REMARK 500 DC D 25 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG D 26 C3' - O3' - P ANGL. DEV. = -7.8 DEGREES REMARK 500 DT D 30 O3' - P - OP1 ANGL. DEV. = 7.0 DEGREES REMARK 500 DA D 32 C3' - C2' - C1' ANGL. DEV. = -5.1 DEGREES REMARK 500 DA D 32 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 DA D 32 C3' - O3' - P ANGL. DEV. = -11.7 DEGREES REMARK 500 DA D 38 C3' - O3' - P ANGL. DEV. = -8.9 DEGREES REMARK 500 DT B 4 C3' - C2' - C1' ANGL. DEV. = -5.6 DEGREES REMARK 500 DA B 10 C1' - O4' - C4' ANGL. DEV. = -6.8 DEGREES REMARK 500 DT B 16 C3' - O3' - P ANGL. DEV. = -10.0 DEGREES REMARK 500 DC B 18 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC B 18 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG E 22 C3' - O3' - P ANGL. DEV. = 9.8 DEGREES REMARK 500 DG E 23 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 DA E 24 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC E 25 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 DC E 25 C1' - O4' - C4' ANGL. DEV. = -7.3 DEGREES REMARK 500 DC E 25 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA E 32 C3' - C2' - C1' ANGL. DEV. = -5.7 DEGREES REMARK 500 DA E 32 C3' - O3' - P ANGL. DEV. = -10.5 DEGREES REMARK 500 DA E 38 C3' - O3' - P ANGL. DEV. = -7.5 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 ARG K 209 0.53 -64.93 REMARK 500 GLN K 251 -43.41 68.99 REMARK 500 TYR C 193 114.60 55.57 REMARK 500 LYS C 248 55.05 -63.91 REMARK 500 GLN C 250 145.39 -36.67 REMARK 500 REMARK 500 REMARK: NULL DBREF 7Q4N A 1 18 PDB 7Q4N 7Q4N 1 18 DBREF 7Q4N D 22 39 PDB 7Q4N 7Q4N 22 39 DBREF 7Q4N K 187 253 UNP Q99626 CDX2_HUMAN 187 253 DBREF 7Q4N B 1 18 PDB 7Q4N 7Q4N 1 18 DBREF 7Q4N E 22 39 PDB 7Q4N 7Q4N 22 39 DBREF 7Q4N C 187 253 UNP Q99626 CDX2_HUMAN 187 253 SEQRES 1 A 18 DT DT DG DT DG DT DT DT DT DA DT DG DA SEQRES 2 A 18 DC DG DT DC DC SEQRES 1 D 18 DG DG DA DC DG DT 5HC DA DT DA DA DA DA SEQRES 2 D 18 DC DA DC DA DA SEQRES 1 K 67 ASP LYS TYR ARG VAL VAL TYR THR ASP HIS GLN ARG LEU SEQRES 2 K 67 GLU LEU GLU LYS GLU PHE HIS TYR SER ARG TYR ILE THR SEQRES 3 K 67 ILE ARG ARG LYS ALA GLU LEU ALA ALA THR LEU GLY LEU SEQRES 4 K 67 SER GLU ARG GLN VAL LYS ILE TRP PHE GLN ASN ARG ARG SEQRES 5 K 67 ALA LYS GLU ARG LYS ILE ASN LYS LYS LYS LEU GLN GLN SEQRES 6 K 67 GLN GLN SEQRES 1 B 18 DT DT DG DT DG DT DT DT DT DA DT DG DA SEQRES 2 B 18 DC DG DT DC DC SEQRES 1 E 18 DG DG DA DC DG DT 5HC DA DT DA DA DA DA SEQRES 2 E 18 DC DA DC DA DA SEQRES 1 C 67 ASP LYS TYR ARG VAL VAL TYR THR ASP HIS GLN ARG LEU SEQRES 2 C 67 GLU LEU GLU LYS GLU PHE HIS TYR SER ARG TYR ILE THR SEQRES 3 C 67 ILE ARG ARG LYS ALA GLU LEU ALA ALA THR LEU GLY LEU SEQRES 4 C 67 SER GLU ARG GLN VAL LYS ILE TRP PHE GLN ASN ARG ARG SEQRES 5 C 67 ALA LYS GLU ARG LYS ILE ASN LYS LYS LYS LEU GLN GLN SEQRES 6 C 67 GLN GLN HET 5HC D 28 21 HET 5HC E 28 21 HETNAM 5HC 2'-DEOXY-5-(HYDROXYMETHYL)CYTIDINE 5'-(DIHYDROGEN HETNAM 2 5HC PHOSPHATE) FORMUL 2 5HC 2(C10 H16 N3 O8 P) FORMUL 7 HOH *14(H2 O) HELIX 1 AA1 THR K 194 SER K 208 1 15 HELIX 2 AA2 THR K 212 LEU K 223 1 12 HELIX 3 AA3 SER K 226 LYS K 248 1 23 HELIX 4 AA4 THR C 194 SER C 208 1 15 HELIX 5 AA5 THR C 212 LEU C 223 1 12 HELIX 6 AA6 SER C 226 LYS C 248 1 23 LINK O3' DT D 27 P 5HC D 28 1555 1555 1.61 LINK O3' 5HC D 28 P DA D 29 1555 1555 1.62 LINK O3' DT E 27 P 5HC E 28 1555 1555 1.60 LINK O3' 5HC E 28 P DA E 29 1555 1555 1.61 CRYST1 69.897 46.634 120.048 90.00 98.25 90.00 I 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 0.014307 0.000000 0.002074 0.00000 SCALE2 0.000000 0.021444 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008417 0.00000