PDB Short entry for 5LTY HEADER TRANSCRIPTION 07-SEP-16 5LTY TITLE HOMEOBOX TRANSCRIPTION FACTOR CDX2 BOUND TO METHYLATED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM) COMPND 3 P*GP*AP*CP*CP*TP*CP*C)-3'); COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HOMEOBOX PROTEIN CDX-2; COMPND 8 CHAIN: K, M; COMPND 9 SYNONYM: CDX-3,CAUDAL-TYPE HOMEOBOX PROTEIN 2; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(P*GP*GP*AP*GP*GP*TP*(5CM) COMPND 13 P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3'); COMPND 14 CHAIN: F, E; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 GENE: CDX2, CDX3; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 12 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 13 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 14 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 15 EXPRESSION_SYSTEM_PLASMID: PETG20A; SOURCE 16 MOL_ID: 3; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 19 ORGANISM_COMMON: HUMAN; SOURCE 20 ORGANISM_TAXID: 9606 KEYWDS TRANSCRIPTION, TRANSCRIPTION FACTOR, METHYLATED DNA EXPDTA X-RAY DIFFRACTION AUTHOR E.MORGUNOVA,A.POPOV,J.TAIPALE REVDAT 1 31-MAY-17 5LTY 0 JRNL AUTH Y.YIN,E.MORGUNOVA,A.JOLMA,E.KAASINEN,B.SAHU,S.KHUND-SAYEED, JRNL AUTH 2 P.K.DAS,T.KIVIOJA,K.DAVE,F.ZHONG,K.R.NITTA,M.TAIPALE, JRNL AUTH 3 A.POPOV,P.A.GINNO,S.DOMCKE,J.YAN,D.SCHUBELER,C.VINSON, JRNL AUTH 4 J.TAIPALE JRNL TITL IMPACT OF CYTOSINE METHYLATION ON DNA BINDING SPECIFICITIES JRNL TITL 2 OF HUMAN TRANSCRIPTION FACTORS. JRNL REF SCIENCE V. 356 2017 JRNL REFN ESSN 1095-9203 JRNL PMID 28473536 JRNL DOI 10.1126/SCIENCE.AAJ2239 REMARK 2 REMARK 2 RESOLUTION. 2.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 63.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 10459 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) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 519 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) : 2.66 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.73 REMARK 3 REFLECTION IN BIN (WORKING SET) : 727 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.21 REMARK 3 BIN R VALUE (WORKING SET) : 0.4110 REMARK 3 BIN FREE R VALUE SET COUNT : 38 REMARK 3 BIN FREE R VALUE : 0.3370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1243 REMARK 3 NUCLEIC ACID ATOMS : 1480 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 34 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 73.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 77.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.73000 REMARK 3 B22 (A**2) : -4.67000 REMARK 3 B33 (A**2) : 2.60000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.76000 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): 0.337 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.293 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 31.140 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2989 ; 0.017 ; 0.015 REMARK 3 BOND LENGTHS OTHERS (A): 2104 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4224 ; 2.161 ; 1.533 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4876 ; 1.690 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 544 ;20.305 ; 9.680 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 70 ;37.011 ;22.714 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 262 ;21.368 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;15.037 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 448 ; 0.176 ; 0.240 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2247 ; 0.014 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 671 ; 0.004 ; 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): 562 ; 1.988 ; 3.005 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 561 ; 1.980 ; 2.999 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 699 ; 3.229 ; 4.480 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 : 3 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 1 18 B 1 18 5674 0.040 0.050 REMARK 3 2 K 186 254 M 186 254 17276 0.080 0.050 REMARK 3 3 F 19 36 E 19 36 5716 0.040 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 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 1 A 18 REMARK 3 ORIGIN FOR THE GROUP (A): -19.4945 -7.4969 -21.1436 REMARK 3 T TENSOR REMARK 3 T11: 0.5150 T22: 0.4157 REMARK 3 T33: 0.3717 T12: 0.0573 REMARK 3 T13: 0.0645 T23: -0.0336 REMARK 3 L TENSOR REMARK 3 L11: 2.5321 L22: 3.4671 REMARK 3 L33: 1.5043 L12: -1.6011 REMARK 3 L13: 0.4680 L23: -0.6905 REMARK 3 S TENSOR REMARK 3 S11: 0.2700 S12: 0.2889 S13: -0.3026 REMARK 3 S21: -0.5196 S22: -0.2594 S23: 0.1430 REMARK 3 S31: 0.1032 S32: 0.0939 S33: -0.0106 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 1 B 18 REMARK 3 ORIGIN FOR THE GROUP (A): -17.2056 -5.0669 20.1021 REMARK 3 T TENSOR REMARK 3 T11: 0.4410 T22: 0.4864 REMARK 3 T33: 0.3341 T12: -0.1521 REMARK 3 T13: -0.1168 T23: 0.0209 REMARK 3 L TENSOR REMARK 3 L11: 4.5471 L22: 4.3190 REMARK 3 L33: 1.5422 L12: 2.3783 REMARK 3 L13: -0.9353 L23: 0.4145 REMARK 3 S TENSOR REMARK 3 S11: 0.2038 S12: -0.6700 S13: 0.4740 REMARK 3 S21: 0.2017 S22: -0.1176 S23: 0.0966 REMARK 3 S31: -0.0038 S32: 0.4585 S33: -0.0862 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : K 185 K 255 REMARK 3 ORIGIN FOR THE GROUP (A): -20.3093 -2.2104 -9.3639 REMARK 3 T TENSOR REMARK 3 T11: 0.3886 T22: 0.4920 REMARK 3 T33: 0.2854 T12: 0.0733 REMARK 3 T13: 0.0072 T23: 0.0394 REMARK 3 L TENSOR REMARK 3 L11: 1.9116 L22: 3.5473 REMARK 3 L33: 1.3171 L12: -0.1813 REMARK 3 L13: 0.2552 L23: -0.2456 REMARK 3 S TENSOR REMARK 3 S11: 0.1706 S12: -0.1459 S13: 0.1590 REMARK 3 S21: -0.0200 S22: -0.1600 S23: -0.0285 REMARK 3 S31: -0.0271 S32: 0.0931 S33: -0.0105 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 : M 186 M 255 REMARK 3 ORIGIN FOR THE GROUP (A): -19.5343 -9.8213 7.9789 REMARK 3 T TENSOR REMARK 3 T11: 0.3379 T22: 0.4351 REMARK 3 T33: 0.2701 T12: -0.0760 REMARK 3 T13: -0.0721 T23: 0.0846 REMARK 3 L TENSOR REMARK 3 L11: 3.2252 L22: 1.7868 REMARK 3 L33: 1.0287 L12: -0.4367 REMARK 3 L13: -0.2668 L23: -0.8755 REMARK 3 S TENSOR REMARK 3 S11: 0.0179 S12: -0.0133 S13: -0.1319 REMARK 3 S21: 0.2361 S22: -0.1587 S23: -0.0570 REMARK 3 S31: 0.0356 S32: 0.1738 S33: 0.1408 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 : F 19 F 36 REMARK 3 ORIGIN FOR THE GROUP (A): -18.8468 -6.6472 -19.2811 REMARK 3 T TENSOR REMARK 3 T11: 0.5201 T22: 0.3918 REMARK 3 T33: 0.3573 T12: 0.0498 REMARK 3 T13: 0.0794 T23: 0.0124 REMARK 3 L TENSOR REMARK 3 L11: 2.4813 L22: 3.6577 REMARK 3 L33: 0.8458 L12: -1.9927 REMARK 3 L13: 0.0420 L23: 0.5897 REMARK 3 S TENSOR REMARK 3 S11: 0.0529 S12: 0.2147 S13: -0.0789 REMARK 3 S21: -0.2131 S22: -0.1407 S23: -0.0049 REMARK 3 S31: 0.0505 S32: -0.0125 S33: 0.0877 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 : E 19 E 36 REMARK 3 ORIGIN FOR THE GROUP (A): -16.8206 -5.7746 18.0904 REMARK 3 T TENSOR REMARK 3 T11: 0.3018 T22: 0.2428 REMARK 3 T33: 0.1672 T12: -0.0953 REMARK 3 T13: -0.1217 T23: 0.0354 REMARK 3 L TENSOR REMARK 3 L11: 1.1909 L22: 2.1311 REMARK 3 L33: 2.0439 L12: 0.3419 REMARK 3 L13: -0.7109 L23: 0.4907 REMARK 3 S TENSOR REMARK 3 S11: 0.0665 S12: -0.1849 S13: 0.2418 REMARK 3 S21: 0.3026 S22: -0.1108 S23: 0.1914 REMARK 3 S31: -0.2586 S32: 0.1830 S33: 0.0444 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: U VALUES : WITH TLS ADDED HYDROGENS REMARK 3 HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 4 REMARK 4 5LTY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1200001319. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-16 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) : 0.9724 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.25 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10979 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.660 REMARK 200 RESOLUTION RANGE LOW (A) : 63.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.66 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.63700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.700 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: 5EEA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 5000, POTASSIUM CHLORIDE, REMARK 280 MAGNESIUM CHLORIDE, PEG 400,TRIS BUFFER, PH 8.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K 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 25.58238 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.30650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 59.55880 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 25.58238 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.30650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 59.55880 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: 5110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, K, F 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: 5060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, M, 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 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 THR M 185 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 N1 DA E 35 O HOH E 101 1.85 REMARK 500 OP2 5CM B 11 NH2 ARG M 228 2.00 REMARK 500 N3 DT B 2 O HOH E 101 2.09 REMARK 500 OP2 5CM A 11 NH2 ARG K 228 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 OP2 DC A 17 P DG E 19 2465 2.05 REMARK 500 OP2 DC A 17 O5' DG E 19 2465 2.08 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 GLU M 218 CG GLU M 218 CD 0.117 REMARK 500 DG F 22 O3' DG F 23 P -0.087 REMARK 500 DG F 23 O3' DT F 24 P -0.072 REMARK 500 DG E 22 O3' DG E 23 P -0.072 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 12 O5' - P - OP2 ANGL. DEV. = -7.0 DEGREES REMARK 500 ASP K 195 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP K 195 CB - CG - OD2 ANGL. DEV. = -7.2 DEGREES REMARK 500 ARG K 238 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 LYS M 188 CB - CA - C ANGL. DEV. = 12.0 DEGREES REMARK 500 GLU M 218 OE1 - CD - OE2 ANGL. DEV. = -8.9 DEGREES REMARK 500 DG F 22 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG E 22 O5' - P - OP1 ANGL. DEV. = -6.8 DEGREES REMARK 500 DG E 22 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA E 29 O5' - C5' - C4' ANGL. DEV. = -5.0 DEGREES REMARK 500 DA E 30 O5' - P - OP1 ANGL. DEV. = -6.5 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 LYS K 188 81.84 160.59 REMARK 500 LYS M 188 79.33 161.35 REMARK 500 REMARK 500 REMARK: NULL DBREF 5LTY A 1 18 PDB 5LTY 5LTY 1 18 DBREF 5LTY B 1 18 PDB 5LTY 5LTY 1 18 DBREF 5LTY K 185 255 UNP Q99626 CDX2_HUMAN 185 255 DBREF 5LTY M 185 255 UNP Q99626 CDX2_HUMAN 185 255 DBREF 5LTY F 19 36 PDB 5LTY 5LTY 19 36 DBREF 5LTY E 19 36 PDB 5LTY 5LTY 19 36 SEQRES 1 A 18 DT DT DG DT DG DT DT DT DT DA 5CM DG DA SEQRES 2 A 18 DC DC DT DC DC SEQRES 1 B 18 DT DT DG DT DG DT DT DT DT DA 5CM DG DA SEQRES 2 B 18 DC DC DT DC DC SEQRES 1 K 71 THR LYS ASP LYS TYR ARG VAL VAL TYR THR ASP HIS GLN SEQRES 2 K 71 ARG LEU GLU LEU GLU LYS GLU PHE HIS TYR SER ARG TYR SEQRES 3 K 71 ILE THR ILE ARG ARG LYS ALA GLU LEU ALA ALA THR LEU SEQRES 4 K 71 GLY LEU SER GLU ARG GLN VAL LYS ILE TRP PHE GLN ASN SEQRES 5 K 71 ARG ARG ALA LYS GLU ARG LYS ILE ASN LYS LYS LYS LEU SEQRES 6 K 71 GLN GLN GLN GLN GLN GLN SEQRES 1 M 71 THR LYS ASP LYS TYR ARG VAL VAL TYR THR ASP HIS GLN SEQRES 2 M 71 ARG LEU GLU LEU GLU LYS GLU PHE HIS TYR SER ARG TYR SEQRES 3 M 71 ILE THR ILE ARG ARG LYS ALA GLU LEU ALA ALA THR LEU SEQRES 4 M 71 GLY LEU SER GLU ARG GLN VAL LYS ILE TRP PHE GLN ASN SEQRES 5 M 71 ARG ARG ALA LYS GLU ARG LYS ILE ASN LYS LYS LYS LEU SEQRES 6 M 71 GLN GLN GLN GLN GLN GLN SEQRES 1 F 18 DG DG DA DG DG DT 5CM DG DT DA DA DA DA SEQRES 2 F 18 DC DA DC DA DA SEQRES 1 E 18 DG DG DA DG DG DT 5CM DG DT DA DA DA DA SEQRES 2 E 18 DC DA DC DA DA HET 5CM A 11 20 HET 5CM B 11 20 HET 5CM F 25 20 HET 5CM E 25 20 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE FORMUL 1 5CM 4(C10 H16 N3 O7 P) FORMUL 7 HOH *34(H2 O) HELIX 1 AA1 THR K 194 SER K 208 1 15 HELIX 2 AA2 THR K 212 GLY K 224 1 13 HELIX 3 AA3 SER K 226 GLN K 255 1 30 HELIX 4 AA4 THR M 194 SER M 208 1 15 HELIX 5 AA5 THR M 212 GLY M 224 1 13 HELIX 6 AA6 SER M 226 GLN M 255 1 30 LINK O3' DA A 10 P 5CM A 11 1555 1555 1.60 LINK O3' 5CM A 11 P DG A 12 1555 1555 1.59 LINK O3' DA B 10 P 5CM B 11 1555 1555 1.57 LINK O3' 5CM B 11 P DG B 12 1555 1555 1.61 LINK O3' DT F 24 P 5CM F 25 1555 1555 1.59 LINK O3' 5CM F 25 P DG F 26 1555 1555 1.59 LINK O3' DT E 24 P 5CM E 25 1555 1555 1.56 LINK O3' 5CM E 25 P DG E 26 1555 1555 1.61 CISPEP 1 LYS K 188 TYR K 189 0 -26.92 CISPEP 2 LYS M 188 TYR M 189 0 -22.15 CRYST1 68.882 46.613 120.428 90.00 98.46 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 0.014518 0.000000 0.002159 0.00000 SCALE2 0.000000 0.021453 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008395 0.00000