HEADER TRANSCRIPTION 28-OCT-21 7Q3O TITLE STRUCTURE OF CDX1 BOUND TO HYDROXYMETHYLATED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYDROXYMETHYLATED DNA (18-MER); COMPND 3 CHAIN: A, B, D, F; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HYDROXYMETHYLATED DNA (18-MER); COMPND 7 CHAIN: H, I, J, L; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: HOMEOBOX PROTEIN CDX-1; COMPND 11 CHAIN: K, C, E, G; COMPND 12 SYNONYM: CAUDAL-TYPE HOMEOBOX PROTEIN 1; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: CDX1; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PETG20A KEYWDS TRANSCRIPTION FACTOR, DNA-BINDING PROTEIN, HYDROXYMETHYLATED DNA, KEYWDS 2 TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR E.MORGUNOVA,Y.YIN,A.POPOV,J.TAIPALE REVDAT 2 31-JAN-24 7Q3O 1 REMARK REVDAT 1 16-NOV-22 7Q3O 0 JRNL AUTH E.MORGUNOVA,Y.YIN,A.POPOV,J.TAIPALE JRNL TITL STRUCTURE OF CDX1 BOUND TO HYDROXYMETHYLATED DNA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.78 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0257 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) : 2.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.18 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 3 NUMBER OF REFLECTIONS : 14157 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) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 709 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.78 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 946 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.68 REMARK 3 BIN R VALUE (WORKING SET) : 0.4550 REMARK 3 BIN FREE R VALUE SET COUNT : 53 REMARK 3 BIN FREE R VALUE : 0.4910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2168 REMARK 3 NUCLEIC ACID ATOMS : 2964 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 70 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 81.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.70000 REMARK 3 B22 (A**2) : 3.36000 REMARK 3 B33 (A**2) : -0.55000 REMARK 3 B12 (A**2) : 3.78000 REMARK 3 B13 (A**2) : -0.02000 REMARK 3 B23 (A**2) : 0.75000 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): 0.507 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.476 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 54.294 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.911 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5672 ; 0.009 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 3790 ; 0.002 ; 0.019 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8063 ; 1.734 ; 1.396 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8835 ; 1.492 ; 2.215 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 992 ;26.660 ; 6.678 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 152 ;24.067 ;18.750 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 428 ;21.786 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;16.440 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 829 ; 0.246 ; 0.243 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4113 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1252 ; 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 : 12 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 1 39 B 1 39 3536 0.040 0.050 REMARK 3 2 A 1 39 D 1 39 3535 0.040 0.050 REMARK 3 3 A 1 39 F 1 39 3565 0.030 0.050 REMARK 3 4 B 1 39 D 1 39 3591 0.030 0.050 REMARK 3 5 B 1 39 F 1 39 3540 0.040 0.050 REMARK 3 6 D 1 39 F 1 39 3535 0.040 0.050 REMARK 3 7 K 183 242 C 183 242 2044 0.100 0.050 REMARK 3 8 K 185 242 E 185 242 1972 0.100 0.050 REMARK 3 9 K 183 243 G 183 243 2069 0.090 0.050 REMARK 3 10 C 185 243 E 185 243 2018 0.090 0.050 REMARK 3 11 C 183 242 G 183 242 2064 0.100 0.050 REMARK 3 12 E 185 242 G 185 242 1974 0.100 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 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 : H 1 H 18 REMARK 3 ORIGIN FOR THE GROUP (A): -7.1568 18.7467 -20.2358 REMARK 3 T TENSOR REMARK 3 T11: 0.0976 T22: 0.3477 REMARK 3 T33: 0.3704 T12: -0.1450 REMARK 3 T13: 0.0596 T23: -0.0624 REMARK 3 L TENSOR REMARK 3 L11: 1.8443 L22: 1.5373 REMARK 3 L33: 0.9395 L12: -0.2814 REMARK 3 L13: 0.0198 L23: -0.1535 REMARK 3 S TENSOR REMARK 3 S11: -0.1473 S12: 0.0849 S13: -0.1377 REMARK 3 S21: -0.1481 S22: -0.0910 S23: 0.0607 REMARK 3 S31: -0.0438 S32: 0.1478 S33: 0.2383 REMARK 3 REMARK 3 TLS GROUP : 2 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 : I 1 I 18 REMARK 3 ORIGIN FOR THE GROUP (A): -6.1592 16.9904 18.2277 REMARK 3 T TENSOR REMARK 3 T11: 0.0670 T22: 0.2894 REMARK 3 T33: 0.2151 T12: 0.0637 REMARK 3 T13: 0.0045 T23: -0.0226 REMARK 3 L TENSOR REMARK 3 L11: 3.4109 L22: 2.6567 REMARK 3 L33: 1.3482 L12: -1.7905 REMARK 3 L13: -1.5252 L23: 0.1439 REMARK 3 S TENSOR REMARK 3 S11: -0.2803 S12: -0.0914 S13: -0.0081 REMARK 3 S21: 0.2753 S22: 0.1223 S23: -0.1340 REMARK 3 S31: -0.0024 S32: 0.0426 S33: 0.1580 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 : D 1 D 18 REMARK 3 RESIDUE RANGE : J 1 J 18 REMARK 3 ORIGIN FOR THE GROUP (A): -10.5408 46.5482 19.0251 REMARK 3 T TENSOR REMARK 3 T11: 0.0645 T22: 0.3678 REMARK 3 T33: 0.1957 T12: 0.1234 REMARK 3 T13: 0.0349 T23: 0.0285 REMARK 3 L TENSOR REMARK 3 L11: 3.4705 L22: 2.7442 REMARK 3 L33: 0.8740 L12: -2.1676 REMARK 3 L13: -0.0529 L23: -0.1946 REMARK 3 S TENSOR REMARK 3 S11: -0.3798 S12: -0.4127 S13: -0.1337 REMARK 3 S21: 0.2358 S22: 0.3008 S23: 0.1862 REMARK 3 S31: -0.0046 S32: 0.0771 S33: 0.0790 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : F 1 F 18 REMARK 3 RESIDUE RANGE : L 1 L 18 REMARK 3 ORIGIN FOR THE GROUP (A): -9.3754 47.0668 -19.5527 REMARK 3 T TENSOR REMARK 3 T11: 0.0775 T22: 0.2981 REMARK 3 T33: 0.3781 T12: -0.1053 REMARK 3 T13: -0.0012 T23: 0.0380 REMARK 3 L TENSOR REMARK 3 L11: 2.6452 L22: 1.8855 REMARK 3 L33: 0.9648 L12: 0.5942 REMARK 3 L13: -0.3138 L23: 0.1121 REMARK 3 S TENSOR REMARK 3 S11: -0.2172 S12: 0.0087 S13: 0.0033 REMARK 3 S21: -0.1462 S22: -0.0165 S23: -0.1417 REMARK 3 S31: -0.0211 S32: -0.1769 S33: 0.2337 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : K 183 K 243 REMARK 3 ORIGIN FOR THE GROUP (A): 0.9615 17.4148 -10.1170 REMARK 3 T TENSOR REMARK 3 T11: 0.1277 T22: 0.2489 REMARK 3 T33: 0.2996 T12: -0.0465 REMARK 3 T13: 0.0335 T23: -0.0110 REMARK 3 L TENSOR REMARK 3 L11: 0.4213 L22: 2.7988 REMARK 3 L33: 4.8391 L12: 0.8455 REMARK 3 L13: 0.1405 L23: 2.0623 REMARK 3 S TENSOR REMARK 3 S11: 0.0085 S12: 0.0819 S13: -0.0212 REMARK 3 S21: 0.2653 S22: 0.0642 S23: -0.1829 REMARK 3 S31: 0.1248 S32: 0.2316 S33: -0.0726 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 183 C 243 REMARK 3 ORIGIN FOR THE GROUP (A): -13.1383 17.1174 7.9890 REMARK 3 T TENSOR REMARK 3 T11: 0.0938 T22: 0.2919 REMARK 3 T33: 0.2402 T12: 0.0282 REMARK 3 T13: 0.0280 T23: -0.0061 REMARK 3 L TENSOR REMARK 3 L11: 0.9838 L22: 3.5496 REMARK 3 L33: 3.0113 L12: -0.7241 REMARK 3 L13: -1.0818 L23: -1.0531 REMARK 3 S TENSOR REMARK 3 S11: -0.0618 S12: -0.0541 S13: 0.0331 REMARK 3 S21: -0.1972 S22: 0.0446 S23: 0.2465 REMARK 3 S31: 0.1847 S32: -0.2933 S33: 0.0172 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 185 E 243 REMARK 3 ORIGIN FOR THE GROUP (A): -2.8528 46.8296 8.4397 REMARK 3 T TENSOR REMARK 3 T11: 0.0617 T22: 0.2964 REMARK 3 T33: 0.2007 T12: 0.0648 REMARK 3 T13: 0.0202 T23: -0.0039 REMARK 3 L TENSOR REMARK 3 L11: 1.5995 L22: 4.9713 REMARK 3 L33: 2.4766 L12: 0.3226 REMARK 3 L13: 0.6304 L23: -0.0300 REMARK 3 S TENSOR REMARK 3 S11: -0.0864 S12: -0.2603 S13: -0.0315 REMARK 3 S21: -0.1966 S22: 0.2064 S23: -0.2362 REMARK 3 S31: -0.0693 S32: 0.2345 S33: -0.1200 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : G 183 G 243 REMARK 3 ORIGIN FOR THE GROUP (A): -17.4540 47.8539 -9.3116 REMARK 3 T TENSOR REMARK 3 T11: 0.0949 T22: 0.2336 REMARK 3 T33: 0.2614 T12: -0.0065 REMARK 3 T13: 0.0114 T23: 0.0097 REMARK 3 L TENSOR REMARK 3 L11: 0.6520 L22: 2.4290 REMARK 3 L33: 3.9268 L12: 0.3399 REMARK 3 L13: -0.0224 L23: -1.6318 REMARK 3 S TENSOR REMARK 3 S11: -0.0486 S12: 0.2071 S13: -0.0164 REMARK 3 S21: 0.3706 S22: 0.0768 S23: 0.2915 REMARK 3 S31: -0.1704 S32: -0.1610 S33: -0.0282 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 7Q3O 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_1292118874. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-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) : 0.972420 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 0.7.3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14867 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.780 REMARK 200 RESOLUTION RANGE LOW (A) : 42.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 200 DATA REDUNDANCY : 2.100 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.78 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.69300 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: 5LUX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, POTASSIUM CHLORIDE, REMARK 280 MAGNESIUM CHLORIDE, PEG 200, TRIS, PH 8.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 298K 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, 3, 4 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: 3760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, H, 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: 3870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, I, 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: 3 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: 3700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, J, E REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 4 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: 9690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: F, L, G 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 VAL K 244 REMARK 465 ASN K 245 REMARK 465 LYS K 246 REMARK 465 LYS K 247 REMARK 465 LYS C 246 REMARK 465 LYS C 247 REMARK 465 THR E 183 REMARK 465 ARG E 184 REMARK 465 ASN E 245 REMARK 465 LYS E 246 REMARK 465 LYS E 247 REMARK 465 VAL G 244 REMARK 465 ASN G 245 REMARK 465 LYS G 246 REMARK 465 LYS G 247 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 N7 DA L 17 O HOH L 101 2.01 REMARK 500 O HOH G 301 O HOH G 304 2.10 REMARK 500 O HOH C 301 O HOH C 304 2.12 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 O6 DG H 1 OP1 DA I 11 1554 2.14 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 -0.109 REMARK 500 DT B 1 P DT B 1 OP3 -0.128 REMARK 500 DT D 1 P DT D 1 OP3 -0.116 REMARK 500 DT F 1 P DT F 1 OP3 -0.122 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 DC B 14 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC I 4 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC L 4 O4' - C1' - N1 ANGL. DEV. = 2.0 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 LYS K 186 -113.97 -158.29 REMARK 500 LYS C 186 -107.80 -159.50 REMARK 500 TYR E 189 91.83 35.56 REMARK 500 ARG E 190 127.31 46.93 REMARK 500 LYS G 186 -114.03 -152.62 REMARK 500 REMARK 500 REMARK: NULL DBREF 7Q3O A 1 18 PDB 7Q3O 7Q3O 1 18 DBREF 7Q3O H 1 18 PDB 7Q3O 7Q3O 1 18 DBREF 7Q3O B 1 18 PDB 7Q3O 7Q3O 1 18 DBREF 7Q3O I 1 18 PDB 7Q3O 7Q3O 1 18 DBREF 7Q3O D 1 18 PDB 7Q3O 7Q3O 1 18 DBREF 7Q3O J 1 18 PDB 7Q3O 7Q3O 1 18 DBREF 7Q3O F 1 18 PDB 7Q3O 7Q3O 1 18 DBREF 7Q3O L 1 18 PDB 7Q3O 7Q3O 1 18 DBREF 7Q3O K 183 247 UNP P47902 CDX1_HUMAN 151 215 DBREF 7Q3O C 183 247 UNP P47902 CDX1_HUMAN 151 215 DBREF 7Q3O E 183 247 UNP P47902 CDX1_HUMAN 151 215 DBREF 7Q3O G 183 247 UNP P47902 CDX1_HUMAN 151 215 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 H 18 DG DG DA DC DG DT 5HC DA DT DA DA DA DA SEQRES 2 H 18 DC DA DC DA DA 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 I 18 DG DG DA DC DG DT 5HC DA DT DA DA DA DA SEQRES 2 I 18 DC DA DC DA DA SEQRES 1 D 18 DT DT DG DT DG DT DT DT DT DA DT DG DA SEQRES 2 D 18 DC DG DT DC DC SEQRES 1 J 18 DG DG DA DC DG DT 5HC DA DT DA DA DA DA SEQRES 2 J 18 DC DA DC DA DA SEQRES 1 F 18 DT DT DG DT DG DT DT DT DT DA DT DG DA SEQRES 2 F 18 DC DG DT DC DC SEQRES 1 L 18 DG DG DA DC DG DT 5HC DA DT DA DA DA DA SEQRES 2 L 18 DC DA DC DA DA SEQRES 1 K 65 THR ARG THR LYS ASP LYS TYR ARG VAL VAL TYR THR ASP SEQRES 2 K 65 HIS GLN ARG LEU GLU LEU GLU LYS GLU PHE HIS TYR SER SEQRES 3 K 65 ARG TYR ILE THR ILE ARG ARG LYS SER GLU LEU ALA ALA SEQRES 4 K 65 ASN LEU GLY LEU THR GLU ARG GLN VAL LYS ILE TRP PHE SEQRES 5 K 65 GLN ASN ARG ARG ALA LYS GLU ARG LYS VAL ASN LYS LYS SEQRES 1 C 65 THR ARG THR LYS ASP LYS TYR ARG VAL VAL TYR THR ASP SEQRES 2 C 65 HIS GLN ARG LEU GLU LEU GLU LYS GLU PHE HIS TYR SER SEQRES 3 C 65 ARG TYR ILE THR ILE ARG ARG LYS SER GLU LEU ALA ALA SEQRES 4 C 65 ASN LEU GLY LEU THR GLU ARG GLN VAL LYS ILE TRP PHE SEQRES 5 C 65 GLN ASN ARG ARG ALA LYS GLU ARG LYS VAL ASN LYS LYS SEQRES 1 E 65 THR ARG THR LYS ASP LYS TYR ARG VAL VAL TYR THR ASP SEQRES 2 E 65 HIS GLN ARG LEU GLU LEU GLU LYS GLU PHE HIS TYR SER SEQRES 3 E 65 ARG TYR ILE THR ILE ARG ARG LYS SER GLU LEU ALA ALA SEQRES 4 E 65 ASN LEU GLY LEU THR GLU ARG GLN VAL LYS ILE TRP PHE SEQRES 5 E 65 GLN ASN ARG ARG ALA LYS GLU ARG LYS VAL ASN LYS LYS SEQRES 1 G 65 THR ARG THR LYS ASP LYS TYR ARG VAL VAL TYR THR ASP SEQRES 2 G 65 HIS GLN ARG LEU GLU LEU GLU LYS GLU PHE HIS TYR SER SEQRES 3 G 65 ARG TYR ILE THR ILE ARG ARG LYS SER GLU LEU ALA ALA SEQRES 4 G 65 ASN LEU GLY LEU THR GLU ARG GLN VAL LYS ILE TRP PHE SEQRES 5 G 65 GLN ASN ARG ARG ALA LYS GLU ARG LYS VAL ASN LYS LYS HET 5HC H 7 21 HET 5HC I 7 21 HET 5HC J 7 21 HET 5HC L 7 21 HETNAM 5HC 2'-DEOXY-5-(HYDROXYMETHYL)CYTIDINE 5'-(DIHYDROGEN HETNAM 2 5HC PHOSPHATE) FORMUL 2 5HC 4(C10 H16 N3 O8 P) FORMUL 13 HOH *70(H2 O) HELIX 1 AA1 THR K 194 SER K 208 1 15 HELIX 2 AA2 THR K 212 ASN K 222 1 11 HELIX 3 AA3 THR K 226 LYS K 243 1 18 HELIX 4 AA4 THR C 194 SER C 208 1 15 HELIX 5 AA5 THR C 212 ASN C 222 1 11 HELIX 6 AA6 THR C 226 ASN C 245 1 20 HELIX 7 AA7 THR E 194 SER E 208 1 15 HELIX 8 AA8 THR E 212 ASN E 222 1 11 HELIX 9 AA9 THR E 226 VAL E 244 1 19 HELIX 10 AB1 THR G 194 SER G 208 1 15 HELIX 11 AB2 THR G 212 ASN G 222 1 11 HELIX 12 AB3 THR G 226 LYS G 243 1 18 LINK O3' DT H 6 P 5HC H 7 1555 1555 1.59 LINK O3' 5HC H 7 P DA H 8 1555 1555 1.65 LINK O3' DT I 6 P 5HC I 7 1555 1555 1.58 LINK O3' 5HC I 7 P DA I 8 1555 1555 1.63 LINK O3' DT J 6 P 5HC J 7 1555 1555 1.60 LINK O3' 5HC J 7 P DA J 8 1555 1555 1.62 LINK O3' DT L 6 P 5HC L 7 1555 1555 1.58 LINK O3' 5HC L 7 P DA L 8 1555 1555 1.62 CRYST1 45.373 64.669 67.028 112.37 108.11 93.93 P 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 0.022040 0.001514 0.008668 0.00000 SCALE2 0.000000 0.015500 0.007254 0.00000 SCALE3 0.000000 0.000000 0.017331 0.00000