HEADER TRANSCRIPTION/DNA 29-OCT-08 3F27 TITLE STRUCTURE OF SOX17 BOUND TO DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*DGP*DTP*DCP*DTP*DCP*DTP*DAP*DTP*DTP*DGP*DTP*DCP*DCP*DTP*DGP*DG)- COMPND 4 3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: LAMA1; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'- COMPND 10 D(*DCP*DCP*DAP*DGP*DGP*DAP*DCP*DAP*DAP*DTP*DAP*DGP*DAP*DGP*DAP*DC)- COMPND 11 3'); COMPND 12 CHAIN: B; COMPND 13 ENGINEERED: YES; COMPND 14 OTHER_DETAILS: LAMA1; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: TRANSCRIPTION FACTOR SOX-17; COMPND 17 CHAIN: D; COMPND 18 FRAGMENT: HMG BOX, RESIDUES 66-144; COMPND 19 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: MUS MUSCULUS; SOURCE 11 ORGANISM_COMMON: MOUSE; SOURCE 12 ORGANISM_TAXID: 10090; SOURCE 13 GENE: SOX-17, SOX17; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PETG20A KEYWDS PROTEIN-DNA COMPLEX, HMG DOMAIN, ENDODERMAL, ACTIVATOR, DNA-BINDING, KEYWDS 2 NUCLEUS, TRANSCRIPTION, TRANSCRIPTION REGULATION, TRANSCRIPTION-DNA KEYWDS 3 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.PALASINGAM,R.JAUCH,C.K.L.NG,P.R.KOLATKAR REVDAT 5 08-NOV-23 3F27 1 REMARK REVDAT 4 14-JUN-23 3F27 1 SOURCE REMARK SEQADV REVDAT 3 13-JUL-11 3F27 1 VERSN REVDAT 2 28-APR-09 3F27 1 JRNL REVDAT 1 07-APR-09 3F27 0 JRNL AUTH P.PALASINGAM,R.JAUCH,C.K.L.NG,P.R.KOLATKAR JRNL TITL THE STRUCTURE OF SOX17 BOUND TO DNA REVEALS A CONSERVED JRNL TITL 2 BENDING TOPOLOGY BUT SELECTIVE PROTEIN INTERACTION PLATFORMS JRNL REF J.MOL.BIOL. V. 388 619 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19328208 JRNL DOI 10.1016/J.JMB.2009.03.055 REMARK 2 REMARK 2 RESOLUTION. 2.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 4703 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) : 0.243 REMARK 3 R VALUE (WORKING SET) : 0.242 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 228 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) : 2.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.82 REMARK 3 REFLECTION IN BIN (WORKING SET) : 328 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2530 REMARK 3 BIN FREE R VALUE SET COUNT : 24 REMARK 3 BIN FREE R VALUE : 0.4300 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 633 REMARK 3 NUCLEIC ACID ATOMS : 650 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.25000 REMARK 3 B22 (A**2) : 2.25000 REMARK 3 B33 (A**2) : -3.38000 REMARK 3 B12 (A**2) : 1.13000 REMARK 3 B13 (A**2) : 0.00000 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): 0.388 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.305 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 32.153 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.917 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1376 ; 0.012 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1988 ; 1.861 ; 2.542 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 73 ; 4.808 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 36 ;37.735 ;21.944 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 128 ;21.173 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;27.490 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 211 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 826 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 492 ; 0.246 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 847 ; 0.310 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 38 ; 0.159 ; 0.200 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): 23 ; 0.225 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 1 ; 0.214 ; 0.200 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): 386 ; 0.562 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 599 ; 1.004 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1330 ; 1.262 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1389 ; 1.977 ; 4.500 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 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 16 REMARK 3 RESIDUE RANGE : B 1 B 16 REMARK 3 ORIGIN FOR THE GROUP (A): 25.0085 -11.5796 -1.7137 REMARK 3 T TENSOR REMARK 3 T11: 0.0383 T22: 0.2546 REMARK 3 T33: 0.3792 T12: 0.1902 REMARK 3 T13: 0.1510 T23: 0.1423 REMARK 3 L TENSOR REMARK 3 L11: 2.3504 L22: 5.3848 REMARK 3 L33: 5.4475 L12: 1.6149 REMARK 3 L13: -1.3506 L23: 0.8553 REMARK 3 S TENSOR REMARK 3 S11: 0.0069 S12: 0.2600 S13: -0.8129 REMARK 3 S21: -0.4882 S22: -0.1643 S23: -1.2346 REMARK 3 S31: 0.3837 S32: 0.6207 S33: 0.1574 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 : D 67 D 141 REMARK 3 ORIGIN FOR THE GROUP (A): 13.1432 -4.6958 -0.9446 REMARK 3 T TENSOR REMARK 3 T11: -0.0439 T22: 0.2693 REMARK 3 T33: -0.0721 T12: 0.1113 REMARK 3 T13: 0.0220 T23: 0.0628 REMARK 3 L TENSOR REMARK 3 L11: 4.8203 L22: 5.8270 REMARK 3 L33: 4.1348 L12: 1.9245 REMARK 3 L13: -2.4766 L23: -1.5973 REMARK 3 S TENSOR REMARK 3 S11: -0.0770 S12: 0.5033 S13: -0.1479 REMARK 3 S21: -0.4991 S22: -0.2235 S23: -0.2488 REMARK 3 S31: 0.1549 S32: -0.3818 S33: 0.3005 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 REMARK 4 REMARK 4 3F27 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-OCT-08. REMARK 100 THE DEPOSITION ID IS D_1000050053. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : PLATINUM REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SAINT REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4970 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 REMARK 200 RESOLUTION RANGE LOW (A) : 66.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.860 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.7500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 7.60 REMARK 200 R MERGE FOR SHELL (I) : 0.38700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.750 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1GT0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 3350, 0.2M MGCL2, PH 7.4, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.21933 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 22.10967 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 22.10967 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 44.21933 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: 4020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D 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 GLY D 62 REMARK 465 SER D 63 REMARK 465 PHE D 64 REMARK 465 THR D 65 REMARK 465 SER D 66 REMARK 465 ARG D 67 REMARK 465 ARG D 142 REMARK 465 LYS D 143 REMARK 465 GLN D 144 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 DG A 10 O3' DG A 10 C3' -0.072 REMARK 500 DC A 12 O3' DC A 12 C3' -0.040 REMARK 500 DT B 10 O3' DT B 10 C3' -0.038 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 DT A 2 C1' - O4' - C4' ANGL. DEV. = -7.4 DEGREES REMARK 500 DT A 2 O4' - C1' - N1 ANGL. DEV. = 6.9 DEGREES REMARK 500 DC A 3 O4' - C1' - N1 ANGL. DEV. = 7.4 DEGREES REMARK 500 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DT A 6 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 DA A 7 O4' - C4' - C3' ANGL. DEV. = -3.6 DEGREES REMARK 500 DA A 7 C1' - O4' - C4' ANGL. DEV. = -7.8 DEGREES REMARK 500 DA A 7 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 DT A 9 O5' - C5' - C4' ANGL. DEV. = -5.5 DEGREES REMARK 500 DT A 11 C4 - C5 - C7 ANGL. DEV. = 5.5 DEGREES REMARK 500 DT A 11 C6 - C5 - C7 ANGL. DEV. = -5.8 DEGREES REMARK 500 DC B 1 C3' - O3' - P ANGL. DEV. = 8.0 DEGREES REMARK 500 DC B 2 C3' - C2' - C1' ANGL. DEV. = -6.4 DEGREES REMARK 500 DC B 2 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG B 5 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 DT B 10 O4' - C4' - C3' ANGL. DEV. = -3.2 DEGREES REMARK 500 DT B 10 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG B 14 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DC B 16 O4' - C4' - C3' ANGL. DEV. = -2.5 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 D 70 152.43 -41.13 REMARK 500 GLU D 82 -38.55 -35.73 REMARK 500 REMARK 500 REMARK: NULL DBREF 3F27 A 1 16 PDB 3F27 3F27 1 16 DBREF 3F27 B 1 16 PDB 3F27 3F27 1 16 DBREF 3F27 D 66 144 UNP Q61473 SOX17_MOUSE 66 144 SEQADV 3F27 GLY D 62 UNP Q61473 EXPRESSION TAG SEQADV 3F27 SER D 63 UNP Q61473 EXPRESSION TAG SEQADV 3F27 PHE D 64 UNP Q61473 EXPRESSION TAG SEQADV 3F27 THR D 65 UNP Q61473 EXPRESSION TAG SEQRES 1 A 16 DG DT DC DT DC DT DA DT DT DG DT DC DC SEQRES 2 A 16 DT DG DG SEQRES 1 B 16 DC DC DA DG DG DA DC DA DA DT DA DG DA SEQRES 2 B 16 DG DA DC SEQRES 1 D 83 GLY SER PHE THR SER ARG ILE ARG ARG PRO MET ASN ALA SEQRES 2 D 83 PHE MET VAL TRP ALA LYS ASP GLU ARG LYS ARG LEU ALA SEQRES 3 D 83 GLN GLN ASN PRO ASP LEU HIS ASN ALA GLU LEU SER LYS SEQRES 4 D 83 MET LEU GLY LYS SER TRP LYS ALA LEU THR LEU ALA GLU SEQRES 5 D 83 LYS ARG PRO PHE VAL GLU GLU ALA GLU ARG LEU ARG VAL SEQRES 6 D 83 GLN HIS MET GLN ASP HIS PRO ASN TYR LYS TYR ARG PRO SEQRES 7 D 83 ARG ARG ARG LYS GLN HELIX 1 1 ASN D 73 ASN D 90 1 18 HELIX 2 2 HIS D 94 LEU D 109 1 16 HELIX 3 3 THR D 110 HIS D 132 1 23 CRYST1 68.753 68.753 66.329 90.00 90.00 120.00 P 32 2 1 6 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 0.014545 0.008397 0.000000 0.00000 SCALE2 0.000000 0.016795 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015076 0.00000