HEADER TRANSCRIPTION 12-SEP-16 5LUX TITLE HOMEOBOX TRANSCRIPTION FACTOR CDX1 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*C)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HOMEOBOX PROTEIN CDX-1; COMPND 8 CHAIN: K, L; COMPND 9 SYNONYM: CAUDAL-TYPE HOMEOBOX PROTEIN 1; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM) COMPND 13 P*GP*AP*CP*CP*TP*CP*C)-3'); COMPND 14 CHAIN: B; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DNA (5'-D(P*GP*AP*GP*GP*TP*(5CM) COMPND 18 P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3'); COMPND 19 CHAIN: F; COMPND 20 ENGINEERED: YES; COMPND 21 MOL_ID: 5; COMPND 22 MOLECULE: DNA (5'-D(P*GP*GP*AP*GP*GP*TP*(5CM) COMPND 23 P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3'); COMPND 24 CHAIN: E; COMPND 25 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 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 GENE: CDX1; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 12 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); 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_TAXID: 9606; SOURCE 20 MOL_ID: 4; SOURCE 21 SYNTHETIC: YES; SOURCE 22 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 23 ORGANISM_TAXID: 9606; SOURCE 24 MOL_ID: 5; SOURCE 25 SYNTHETIC: YES; SOURCE 26 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 27 ORGANISM_TAXID: 9606 KEYWDS TRANSCRIPTION, TRANSCRIPTION FACTOR, METHYLATED DNA EXPDTA X-RAY DIFFRACTION AUTHOR E.MORGUNOVA,A.POPOV,J.TAIPALE REVDAT 2 17-JAN-24 5LUX 1 REMARK REVDAT 1 17-MAY-17 5LUX 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. 3.23 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 58.12 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 4909 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) : 0.247 REMARK 3 R VALUE (WORKING SET) : 0.241 REMARK 3 FREE R VALUE : 0.300 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.500 REMARK 3 FREE R VALUE TEST SET COUNT : 515 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) : 3.23 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.32 REMARK 3 REFLECTION IN BIN (WORKING SET) : 262 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.35 REMARK 3 BIN R VALUE (WORKING SET) : 0.3380 REMARK 3 BIN FREE R VALUE SET COUNT : 27 REMARK 3 BIN FREE R VALUE : 0.2900 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1103 REMARK 3 NUCLEIC ACID ATOMS : 1439 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 10 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 57.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 90.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.69000 REMARK 3 B22 (A**2) : -2.68000 REMARK 3 B33 (A**2) : -2.04000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.38000 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): 0.729 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.697 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 100.709 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.917 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.864 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2731 ; 0.013 ; 0.015 REMARK 3 BOND LENGTHS OTHERS (A): 1929 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3970 ; 1.852 ; 1.521 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4473 ; 1.689 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 123 ; 8.182 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 64 ;37.059 ;21.562 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 238 ;21.348 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;15.538 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 365 ; 0.124 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2042 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 615 ; 0.003 ; 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): 498 ; 3.548 ; 4.388 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 497 ; 3.529 ; 4.371 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 619 ; 6.051 ; 6.540 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 16 B 1 16 5198 0.010 0.050 REMARK 3 2 K 153 213 L 153 213 15516 0.080 0.050 REMARK 3 3 F 20 35 E 20 35 5388 0.010 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 17 REMARK 3 RESIDUE RANGE : F 20 F 36 REMARK 3 ORIGIN FOR THE GROUP (A): -16.9594 -28.0758 -18.8237 REMARK 3 T TENSOR REMARK 3 T11: 0.0627 T22: 0.0728 REMARK 3 T33: 1.2139 T12: -0.0169 REMARK 3 T13: -0.1382 T23: 0.0922 REMARK 3 L TENSOR REMARK 3 L11: 3.7738 L22: 8.5789 REMARK 3 L33: 1.0503 L12: -5.3455 REMARK 3 L13: 1.1137 L23: -0.7686 REMARK 3 S TENSOR REMARK 3 S11: 0.0883 S12: 0.0943 S13: -0.0935 REMARK 3 S21: -0.2177 S22: -0.1055 S23: 0.3280 REMARK 3 S31: -0.0066 S32: -0.0123 S33: 0.0172 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 153 K 215 REMARK 3 ORIGIN FOR THE GROUP (A): -16.3559 -19.2056 -8.3546 REMARK 3 T TENSOR REMARK 3 T11: 0.0884 T22: 0.0683 REMARK 3 T33: 1.0710 T12: 0.0463 REMARK 3 T13: -0.1102 T23: 0.0197 REMARK 3 L TENSOR REMARK 3 L11: 3.0003 L22: 4.9472 REMARK 3 L33: 8.2518 L12: -0.4198 REMARK 3 L13: -0.7761 L23: -0.8368 REMARK 3 S TENSOR REMARK 3 S11: -0.0088 S12: -0.1938 S13: 0.4035 REMARK 3 S21: 0.1509 S22: 0.3714 S23: 0.1172 REMARK 3 S31: -0.1827 S32: -0.3809 S33: -0.3626 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 19 E 36 REMARK 3 ORIGIN FOR THE GROUP (A): -17.2022 -26.1199 19.0727 REMARK 3 T TENSOR REMARK 3 T11: 0.1097 T22: 0.0468 REMARK 3 T33: 1.4353 T12: -0.0271 REMARK 3 T13: -0.1752 T23: -0.0149 REMARK 3 L TENSOR REMARK 3 L11: 2.4681 L22: 7.2239 REMARK 3 L33: 0.5077 L12: 4.1588 REMARK 3 L13: -0.0137 L23: 0.2636 REMARK 3 S TENSOR REMARK 3 S11: -0.0367 S12: -0.0832 S13: 0.4386 REMARK 3 S21: -0.0412 S22: -0.0567 S23: 0.6200 REMARK 3 S31: 0.0848 S32: 0.0868 S33: 0.0934 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 : L 153 L 214 REMARK 3 ORIGIN FOR THE GROUP (A): -15.8970 -34.0289 8.4250 REMARK 3 T TENSOR REMARK 3 T11: 0.1140 T22: 0.1439 REMARK 3 T33: 1.1686 T12: -0.1174 REMARK 3 T13: -0.1012 T23: 0.0210 REMARK 3 L TENSOR REMARK 3 L11: 3.8612 L22: 2.9736 REMARK 3 L33: 7.9813 L12: 2.7022 REMARK 3 L13: -0.8118 L23: -0.6212 REMARK 3 S TENSOR REMARK 3 S11: -0.3573 S12: 0.6044 S13: -0.1185 REMARK 3 S21: 0.0009 S22: 0.2294 S23: -0.1786 REMARK 3 S31: 0.4174 S32: -0.4584 S33: 0.1279 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 5LUX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1200001406. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.25 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5425 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.230 REMARK 200 RESOLUTION RANGE LOW (A) : 58.120 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.17400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.53300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.910 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 5LTX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG MME (5000),KCL, MGCL2, 2-METHYL REMARK 280 PROPANOL, TRIS BUFFER, PH 8.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 28.47472 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.77750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 58.12211 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 28.47472 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.77750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 58.12211 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: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, L, 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 LYS L 215 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 OP2 DA A 10 OH TYR K 161 2.13 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 8 O3' DT A 9 P -0.087 REMARK 500 DA F 30 O3' DA F 31 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 ASP K 155 N - CA - C ANGL. DEV. = 16.7 DEGREES REMARK 500 ARG K 158 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ASP L 155 N - CA - C ANGL. DEV. = 16.3 DEGREES REMARK 500 DG E 22 O5' - P - OP1 ANGL. DEV. = -9.0 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 156 84.92 170.13 REMARK 500 LYS L 156 85.19 169.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS K 156 TYR K 157 -31.06 REMARK 500 LYS L 156 TYR L 157 -33.01 REMARK 500 REMARK 500 REMARK: NULL DBREF 5LUX A 1 17 PDB 5LUX 5LUX 1 17 DBREF 5LUX K 153 215 UNP P47902 CDX1_HUMAN 153 215 DBREF 5LUX B 1 18 PDB 5LUX 5LUX 1 18 DBREF 5LUX L 153 215 UNP P47902 CDX1_HUMAN 153 215 DBREF 5LUX F 20 36 PDB 5LUX 5LUX 20 36 DBREF 5LUX E 19 36 PDB 5LUX 5LUX 19 36 SEQRES 1 A 17 DT DT DG DT DG DT DT DT DT DA 5CM DG DA SEQRES 2 A 17 DC DC DT DC SEQRES 1 K 63 THR LYS ASP LYS TYR ARG VAL VAL TYR THR ASP HIS GLN SEQRES 2 K 63 ARG LEU GLU LEU GLU LYS GLU PHE HIS TYR SER ARG TYR SEQRES 3 K 63 ILE THR ILE ARG ARG LYS SER GLU LEU ALA ALA ASN LEU SEQRES 4 K 63 GLY LEU THR GLU ARG GLN VAL LYS ILE TRP PHE GLN ASN SEQRES 5 K 63 ARG ARG ALA LYS GLU ARG LYS VAL ASN LYS LYS 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 L 63 THR LYS ASP LYS TYR ARG VAL VAL TYR THR ASP HIS GLN SEQRES 2 L 63 ARG LEU GLU LEU GLU LYS GLU PHE HIS TYR SER ARG TYR SEQRES 3 L 63 ILE THR ILE ARG ARG LYS SER GLU LEU ALA ALA ASN LEU SEQRES 4 L 63 GLY LEU THR GLU ARG GLN VAL LYS ILE TRP PHE GLN ASN SEQRES 5 L 63 ARG ARG ALA LYS GLU ARG LYS VAL ASN LYS LYS SEQRES 1 F 17 DG DA DG DG DT 5CM DG DT DA DA DA DA DC SEQRES 2 F 17 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 *10(H2 O) HELIX 1 AA1 THR K 162 SER K 176 1 15 HELIX 2 AA2 THR K 180 GLY K 192 1 13 HELIX 3 AA3 THR K 194 LYS K 215 1 22 HELIX 4 AA4 THR L 162 SER L 176 1 15 HELIX 5 AA5 THR L 180 GLY L 192 1 13 HELIX 6 AA6 THR L 194 LYS L 214 1 21 LINK O3' DA A 10 P 5CM A 11 1555 1555 1.59 LINK O3' 5CM A 11 P DG A 12 1555 1555 1.61 LINK O3' DA B 10 P 5CM B 11 1555 1555 1.55 LINK O3' 5CM B 11 P DG B 12 1555 1555 1.59 LINK O3' DT F 24 P 5CM F 25 1555 1555 1.65 LINK O3' 5CM F 25 P DG F 26 1555 1555 1.58 LINK O3' DT E 24 P 5CM E 25 1555 1555 1.61 LINK O3' 5CM E 25 P DG E 26 1555 1555 1.58 CRYST1 64.650 45.555 116.499 90.00 93.79 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 0.015468 0.000000 0.001024 0.00000 SCALE2 0.000000 0.021951 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008603 0.00000