HEADER TRANSCRIPTION 07-DEC-22 8BX1 TITLE OCT4/SOX2 PROTEIN:DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION FACTOR SOX-2; COMPND 3 CHAIN: E; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HOXB1_R; COMPND 7 CHAIN: D; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: HOXB1_F; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: POU DOMAIN, CLASS 5, TRANSCRIPTION FACTOR 1; COMPND 15 CHAIN: A; COMPND 16 SYNONYM: NF-A3,OCTAMER-BINDING PROTEIN 3,OCT-3,OCTAMER-BINDING COMPND 17 PROTEIN 4,OCT-4,OCTAMER-BINDING TRANSCRIPTION FACTOR 3,OTF-3; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: SOX2, SOX-2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 10 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 11 ORGANISM_TAXID: 10090; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 14 MOL_ID: 3; SOURCE 15 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 16 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 17 ORGANISM_TAXID: 10090; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 20 MOL_ID: 4; SOURCE 21 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 22 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 23 ORGANISM_TAXID: 10090; SOURCE 24 GENE: POU5F1, OCT-3, OCT-4, OTF-3, OTF3; SOURCE 25 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 26 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OCT4, SOX2, HOXB1, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR G.CHOJNOWSKI,M.WILMANNS,E.ROUND REVDAT 1 20-DEC-23 8BX1 0 JRNL AUTH G.CHOJNOWSKI,M.WILMANNS,E.ROUND JRNL TITL CRYSTAL STRUCTURE OF OCT4-SOC2-HOXB1 COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.50 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 58.48 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 14681 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) : 0.254 REMARK 3 R VALUE (WORKING SET) : 0.253 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 747 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1065 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.56 REMARK 3 BIN R VALUE (WORKING SET) : 0.4030 REMARK 3 BIN FREE R VALUE SET COUNT : 61 REMARK 3 BIN FREE R VALUE : 0.3260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1671 REMARK 3 NUCLEIC ACID ATOMS : 861 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 4 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 75.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.16000 REMARK 3 B22 (A**2) : -2.88000 REMARK 3 B33 (A**2) : 3.04000 REMARK 3 B12 (A**2) : 0.00000 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): 0.482 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.290 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.255 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 26.716 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.927 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2665 ; 0.012 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3757 ; 2.375 ; 1.707 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 201 ; 6.069 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 99 ;30.944 ;20.303 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 345 ;18.966 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;17.754 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 375 ; 0.158 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1682 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 811 ; 4.413 ; 5.660 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1007 ; 6.906 ; 8.466 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1854 ; 5.683 ; 5.915 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): 10792 ;13.137 ; 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 : 4 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 : E 1 E 77 REMARK 3 ORIGIN FOR THE GROUP (A): -0.7674 -16.0785 -11.9833 REMARK 3 T TENSOR REMARK 3 T11: 0.1030 T22: 0.0564 REMARK 3 T33: 0.0650 T12: -0.0188 REMARK 3 T13: -0.0075 T23: -0.0179 REMARK 3 L TENSOR REMARK 3 L11: 0.9038 L22: 2.6675 REMARK 3 L33: 0.6761 L12: -0.4560 REMARK 3 L13: -0.1197 L23: 0.1043 REMARK 3 S TENSOR REMARK 3 S11: 0.0921 S12: 0.0902 S13: -0.1126 REMARK 3 S21: 0.1204 S22: -0.1315 S23: 0.1599 REMARK 3 S31: 0.0751 S32: -0.0029 S33: 0.0394 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 2 D 22 REMARK 3 ORIGIN FOR THE GROUP (A): 12.4983 0.2394 -17.4779 REMARK 3 T TENSOR REMARK 3 T11: 0.1392 T22: 0.0907 REMARK 3 T33: 0.1288 T12: 0.0411 REMARK 3 T13: 0.0375 T23: 0.0360 REMARK 3 L TENSOR REMARK 3 L11: 0.1840 L22: 4.7917 REMARK 3 L33: 0.5790 L12: -0.2791 REMARK 3 L13: 0.0196 L23: -1.3213 REMARK 3 S TENSOR REMARK 3 S11: 0.1512 S12: 0.0387 S13: 0.0780 REMARK 3 S21: -0.0888 S22: -0.1796 S23: -0.3607 REMARK 3 S31: 0.0152 S32: 0.1410 S33: 0.0284 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 : C 2 C 22 REMARK 3 ORIGIN FOR THE GROUP (A): 12.2269 1.4926 -18.3770 REMARK 3 T TENSOR REMARK 3 T11: 0.1351 T22: 0.1669 REMARK 3 T33: 0.1997 T12: 0.0639 REMARK 3 T13: 0.0203 T23: 0.1376 REMARK 3 L TENSOR REMARK 3 L11: 0.8486 L22: 2.6520 REMARK 3 L33: 1.0247 L12: 1.4210 REMARK 3 L13: -0.8717 L23: -1.3521 REMARK 3 S TENSOR REMARK 3 S11: 0.1738 S12: -0.0227 S13: 0.0401 REMARK 3 S21: 0.1684 S22: -0.2021 S23: 0.0156 REMARK 3 S31: -0.1698 S32: 0.0070 S33: 0.0284 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 : A -2 A 149 REMARK 3 ORIGIN FOR THE GROUP (A): 8.8463 11.3465 -22.1965 REMARK 3 T TENSOR REMARK 3 T11: 0.2338 T22: 0.3015 REMARK 3 T33: 0.1538 T12: 0.1277 REMARK 3 T13: 0.0758 T23: 0.1305 REMARK 3 L TENSOR REMARK 3 L11: 0.6209 L22: 0.6269 REMARK 3 L33: 0.9388 L12: 0.3122 REMARK 3 L13: -0.3042 L23: 0.0329 REMARK 3 S TENSOR REMARK 3 S11: 0.3096 S12: 0.3412 S13: 0.2394 REMARK 3 S21: 0.3194 S22: -0.0298 S23: 0.0585 REMARK 3 S31: 0.0329 S32: -0.0995 S33: -0.2797 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: NULL REMARK 4 REMARK 4 8BX1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1292121462. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUN-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97624 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15480 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 126.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.28000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP 11.7.03 REMARK 200 STARTING MODEL: 6HT5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE, 12% (V/V) PEG REMARK 280 4000, PH 4.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 25.59950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.46000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.94600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.46000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.59950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.94600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, D, C, A 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 E -2 REMARK 465 ALA E -1 REMARK 465 MET E 0 REMARK 465 THR E 78 REMARK 465 LYS E 79 REMARK 465 THR E 80 REMARK 465 DT D 1 REMARK 465 DA C 1 REMARK 465 ASN A 77 REMARK 465 GLU A 78 REMARK 465 ASN A 79 REMARK 465 LEU A 80 REMARK 465 GLN A 81 REMARK 465 GLU A 82 REMARK 465 ILE A 83 REMARK 465 SER A 84 REMARK 465 LYS A 85 REMARK 465 SER A 86 REMARK 465 GLU A 87 REMARK 465 THR A 88 REMARK 465 LEU A 89 REMARK 465 VAL A 90 REMARK 465 GLN A 91 REMARK 465 ALA A 92 REMARK 465 ARG A 93 REMARK 465 LYS A 94 REMARK 465 ARG A 95 REMARK 465 LYS A 96 REMARK 465 ARG A 97 REMARK 465 THR A 98 REMARK 465 SER A 99 REMARK 465 ILE A 100 REMARK 465 GLU A 101 REMARK 465 ARG A 150 REMARK 465 SER A 151 REMARK 465 SER A 152 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 10 O REMARK 470 LEU A 53 O REMARK 470 LYS A 114 CG CD CE NZ REMARK 470 LYS A 117 CG CD CE NZ REMARK 470 GLN A 121 CG CD OE1 NE2 REMARK 470 LYS A 134 CG CD CE NZ REMARK 470 ARG A 144 CG CD NE CZ NH1 NH2 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 MET E 64 CB - CG - SD ANGL. DEV. = -18.7 DEGREES REMARK 500 DT D 4 C3' - O3' - P ANGL. DEV. = -10.4 DEGREES REMARK 500 DG D 10 O5' - P - OP1 ANGL. DEV. = -8.3 DEGREES REMARK 500 DG C 2 O5' - P - OP1 ANGL. DEV. = 7.8 DEGREES REMARK 500 DT C 5 O5' - C5' - C4' ANGL. DEV. = -5.5 DEGREES REMARK 500 DT C 6 O5' - P - OP2 ANGL. DEV. = -8.6 DEGREES REMARK 500 DT C 21 C3' - O3' - P ANGL. DEV. = -9.5 DEGREES REMARK 500 ARG A 20 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 49 NE - CZ - NH2 ANGL. DEV. = -3.1 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 A 103 -62.77 68.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: SASDP75 RELATED DB: SASBDB DBREF 8BX1 E 1 80 UNP P48432 SOX2_MOUSE 41 120 DBREF 8BX1 D 1 22 PDB 8BX1 8BX1 1 22 DBREF 8BX1 C 1 22 PDB 8BX1 8BX1 1 22 DBREF 8BX1 A 1 152 UNP P20263 PO5F1_MOUSE 131 282 SEQADV 8BX1 GLY E -2 UNP P48432 EXPRESSION TAG SEQADV 8BX1 ALA E -1 UNP P48432 EXPRESSION TAG SEQADV 8BX1 MET E 0 UNP P48432 EXPRESSION TAG SEQADV 8BX1 GLY A -2 UNP P20263 EXPRESSION TAG SEQADV 8BX1 ALA A -1 UNP P20263 EXPRESSION TAG SEQADV 8BX1 MET A 0 UNP P20263 EXPRESSION TAG SEQADV 8BX1 SER A 48 UNP P20263 CYS 178 CONFLICT SEQADV 8BX1 SER A 61 UNP P20263 CYS 191 CONFLICT SEQADV 8BX1 SER A 84 UNP P20263 CYS 214 CONFLICT SEQADV 8BX1 SER A 115 UNP P20263 CYS 245 CONFLICT SEQADV 8BX1 SER A 142 UNP P20263 CYS 272 CONFLICT SEQRES 1 E 83 GLY ALA MET ASP ARG VAL LYS ARG PRO MET ASN ALA PHE SEQRES 2 E 83 MET VAL TRP SER ARG GLY GLN ARG ARG LYS MET ALA GLN SEQRES 3 E 83 GLU ASN PRO LYS MET HIS ASN SER GLU ILE SER LYS ARG SEQRES 4 E 83 LEU GLY ALA GLU TRP LYS LEU LEU SER GLU THR GLU LYS SEQRES 5 E 83 ARG PRO PHE ILE ASP GLU ALA LYS ARG LEU ARG ALA LEU SEQRES 6 E 83 HIS MET LYS GLU HIS PRO ASP TYR LYS TYR ARG PRO ARG SEQRES 7 E 83 ARG LYS THR LYS THR SEQRES 1 D 22 DT DA DA DT DC DA DT DT DA DG DC DA DT SEQRES 2 D 22 DG DA DC DA DA DA DG DA DC SEQRES 1 C 22 DA DG DT DC DT DT DT DG DT DC DA DT DG SEQRES 2 C 22 DC DT DA DA DT DG DA DT DT SEQRES 1 A 155 GLY ALA MET ASP MET LYS ALA LEU GLN LYS GLU LEU GLU SEQRES 2 A 155 GLN PHE ALA LYS LEU LEU LYS GLN LYS ARG ILE THR LEU SEQRES 3 A 155 GLY TYR THR GLN ALA ASP VAL GLY LEU THR LEU GLY VAL SEQRES 4 A 155 LEU PHE GLY LYS VAL PHE SER GLN THR THR ILE SER ARG SEQRES 5 A 155 PHE GLU ALA LEU GLN LEU SER LEU LYS ASN MET SER LYS SEQRES 6 A 155 LEU ARG PRO LEU LEU GLU LYS TRP VAL GLU GLU ALA ASP SEQRES 7 A 155 ASN ASN GLU ASN LEU GLN GLU ILE SER LYS SER GLU THR SEQRES 8 A 155 LEU VAL GLN ALA ARG LYS ARG LYS ARG THR SER ILE GLU SEQRES 9 A 155 ASN ARG VAL ARG TRP SER LEU GLU THR MET PHE LEU LYS SEQRES 10 A 155 SER PRO LYS PRO SER LEU GLN GLN ILE THR HIS ILE ALA SEQRES 11 A 155 ASN GLN LEU GLY LEU GLU LYS ASP VAL VAL ARG VAL TRP SEQRES 12 A 155 PHE SER ASN ARG ARG GLN LYS GLY LYS ARG SER SER FORMUL 5 HOH *4(H2 O) HELIX 1 AA1 ASN E 8 ASN E 25 1 18 HELIX 2 AA2 HIS E 29 LEU E 44 1 16 HELIX 3 AA3 SER E 45 HIS E 67 1 23 HELIX 4 AA4 ALA A -1 LEU A 23 1 25 HELIX 5 AA5 THR A 26 GLY A 39 1 14 HELIX 6 AA6 SER A 43 LEU A 53 1 11 HELIX 7 AA7 SER A 56 ASP A 75 1 20 HELIX 8 AA8 ARG A 103 SER A 115 1 13 HELIX 9 AA9 SER A 119 GLY A 131 1 13 HELIX 10 AB1 GLU A 133 GLY A 148 1 16 CRYST1 51.199 65.892 126.920 90.00 90.00 90.00 P 21 21 21 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 0.019532 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015176 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007879 0.00000