HEADER TRANSCRIPTION 07-DEC-22 8BX2 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: POU DOMAIN, CLASS 5, TRANSCRIPTION FACTOR 1; COMPND 7 CHAIN: A; COMPND 8 SYNONYM: NF-A3,OCTAMER-BINDING PROTEIN 3,OCT-3,OCTAMER-BINDING COMPND 9 PROTEIN 4,OCT-4,OCTAMER-BINDING TRANSCRIPTION FACTOR 3,OTF-3; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: UTF1_R; COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: UTF1_F; COMPND 17 CHAIN: D; 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: 1446512; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 10 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 11 ORGANISM_TAXID: 10090; SOURCE 12 GENE: POU5F1, OCT-3, OCT-4, OTF-3, OTF3; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 17 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 18 ORGANISM_TAXID: 10090; SOURCE 19 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 21 MOL_ID: 4; SOURCE 22 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 23 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 24 ORGANISM_TAXID: 10090; SOURCE 25 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 26 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OCT4, SOX2, UTF1, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR G.CHOJNOWSKI,M.WILMANNS,E.ROUND REVDAT 1 20-DEC-23 8BX2 0 JRNL AUTH G.CHOJNOWSKI,M.WILMANNS,E.ROUND JRNL TITL CRYSTAL STRUCTURE OF OCT4-SOC2-UTF1 COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.14 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) : 3.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 81.72 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 77.5 REMARK 3 NUMBER OF REFLECTIONS : 8135 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.300 REMARK 3 FREE R VALUE TEST SET COUNT : 368 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) : 3.14 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.22 REMARK 3 REFLECTION IN BIN (WORKING SET) : 74 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 10.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.2950 REMARK 3 BIN FREE R VALUE SET COUNT : 10 REMARK 3 BIN FREE R VALUE : 0.4030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1396 REMARK 3 NUCLEIC ACID ATOMS : 902 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 144.7 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.50000 REMARK 3 B22 (A**2) : 1.50000 REMARK 3 B33 (A**2) : -4.86000 REMARK 3 B12 (A**2) : 0.75000 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): 0.465 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.337 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 20.584 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2428 ; 0.009 ; 0.011 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3459 ; 2.508 ; 1.716 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 174 ; 5.676 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 83 ;30.133 ;20.482 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 267 ;19.764 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;19.878 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 357 ; 0.219 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1512 ; 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): 700 ;13.128 ;12.807 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 870 ;19.059 ;19.231 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1728 ;15.027 ;15.678 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): 10019 ;28.635 ; 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 : NULL 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 8BX2 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_1292121465. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 20200417 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.27, STARANISO 2.3.28 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8506 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.137 REMARK 200 RESOLUTION RANGE LOW (A) : 81.585 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 77.4 REMARK 200 DATA REDUNDANCY : 19.50 REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.14 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 22.7 REMARK 200 DATA REDUNDANCY IN SHELL : 18.40 REMARK 200 R MERGE FOR SHELL (I) : 2.13500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 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 (%): 66.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, 70% (V/V) MPD, PH 7.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,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 -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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 19.89600 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 19.89600 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 19.89600 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: 6730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, A, C, 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 E -2 REMARK 465 ALA E -1 REMARK 465 MET E 0 REMARK 465 ASP E 1 REMARK 465 THR E 78 REMARK 465 LYS E 79 REMARK 465 THR E 80 REMARK 465 GLY A -2 REMARK 465 ALA A -1 REMARK 465 ILE A 100 REMARK 465 GLU A 101 REMARK 465 ASN A 102 REMARK 465 ARG A 103 REMARK 465 VAL A 104 REMARK 465 ARG A 105 REMARK 465 TRP A 106 REMARK 465 SER A 107 REMARK 465 LEU A 108 REMARK 465 GLU A 109 REMARK 465 THR A 110 REMARK 465 MET A 111 REMARK 465 PHE A 112 REMARK 465 LEU A 113 REMARK 465 LYS A 114 REMARK 465 SER A 115 REMARK 465 PRO A 116 REMARK 465 LYS A 117 REMARK 465 PRO A 118 REMARK 465 SER A 119 REMARK 465 LEU A 120 REMARK 465 GLN A 121 REMARK 465 GLN A 122 REMARK 465 ILE A 123 REMARK 465 THR A 124 REMARK 465 HIS A 125 REMARK 465 ILE A 126 REMARK 465 ALA A 127 REMARK 465 ASN A 128 REMARK 465 GLN A 129 REMARK 465 LEU A 130 REMARK 465 GLY A 131 REMARK 465 LEU A 132 REMARK 465 GLU A 133 REMARK 465 LYS A 134 REMARK 465 ASP A 135 REMARK 465 VAL A 136 REMARK 465 VAL A 137 REMARK 465 ARG A 138 REMARK 465 VAL A 139 REMARK 465 TRP A 140 REMARK 465 PHE A 141 REMARK 465 SER A 142 REMARK 465 ASN A 143 REMARK 465 ARG A 144 REMARK 465 ARG A 145 REMARK 465 GLN A 146 REMARK 465 LYS A 147 REMARK 465 GLY A 148 REMARK 465 LYS A 149 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 LYS E 4 CG CD CE NZ REMARK 470 LYS E 27 CG CD CE NZ REMARK 470 GLU E 32 CG CD OE1 OE2 REMARK 470 LYS E 65 CG CD CE NZ REMARK 470 MET A 0 CG SD CE REMARK 470 LYS A 3 CG CD CE NZ REMARK 470 LYS A 7 CG CD CE NZ REMARK 470 GLU A 8 CG CD OE1 OE2 REMARK 470 GLU A 10 O REMARK 470 LYS A 40 CG CD CE NZ REMARK 470 LEU A 53 O REMARK 470 LYS A 58 CE NZ REMARK 470 LYS A 62 CD CE NZ REMARK 470 LYS A 69 CE NZ REMARK 470 LYS A 85 CG CD CE NZ REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 ARG A 95 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 96 CD CE NZ REMARK 470 ARG A 97 CG CD NE CZ NH1 NH2 REMARK 470 SER A 99 OG 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 ARG E 75 CG - CD - NE ANGL. DEV. = 15.6 DEGREES REMARK 500 LYS E 77 CB - CA - C ANGL. DEV. = 13.0 DEGREES REMARK 500 DA C 1 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 DC C 2 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC C 14 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT C 15 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DA C 16 C3' - O3' - P ANGL. DEV. = 9.8 DEGREES REMARK 500 DA C 20 C3' - O3' - P ANGL. DEV. = 11.3 DEGREES REMARK 500 DA C 21 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT D 1 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC D 2 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DT D 4 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA D 6 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DT D 8 C3' - O3' - P ANGL. DEV. = -12.3 DEGREES REMARK 500 DA D 12 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT D 13 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DC D 16 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA D 17 C3' - O3' - P ANGL. DEV. = -8.9 DEGREES REMARK 500 DG D 20 O5' - P - OP2 ANGL. DEV. = -6.5 DEGREES REMARK 500 DG D 20 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA D 21 O4' - C1' - N9 ANGL. DEV. = 2.8 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 E 27 17.83 57.27 REMARK 500 HIS E 67 79.17 -114.98 REMARK 500 GLN A 91 -72.05 -48.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: SASDP65 RELATED DB: SASBDB DBREF 8BX2 E 1 80 UNP P48432 SOX2_MOUSE 41 120 DBREF 8BX2 A 1 152 UNP P20263 PO5F1_MOUSE 131 282 DBREF 8BX2 C 1 22 PDB 8BX2 8BX2 1 22 DBREF 8BX2 D 1 22 PDB 8BX2 8BX2 1 22 SEQADV 8BX2 GLY E -2 UNP P48432 EXPRESSION TAG SEQADV 8BX2 ALA E -1 UNP P48432 EXPRESSION TAG SEQADV 8BX2 MET E 0 UNP P48432 EXPRESSION TAG SEQADV 8BX2 GLY A -2 UNP P20263 EXPRESSION TAG SEQADV 8BX2 ALA A -1 UNP P20263 EXPRESSION TAG SEQADV 8BX2 MET A 0 UNP P20263 EXPRESSION TAG SEQADV 8BX2 SER A 48 UNP P20263 CYS 178 CONFLICT SEQADV 8BX2 SER A 61 UNP P20263 CYS 191 CONFLICT SEQADV 8BX2 SER A 84 UNP P20263 CYS 214 CONFLICT SEQADV 8BX2 SER A 115 UNP P20263 CYS 245 CONFLICT SEQADV 8BX2 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 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 SEQRES 1 C 22 DA DC DT DC DA DT DT DG DT DT DA DT DG SEQRES 2 C 22 DC DT DA DG DT DG DA DA DG SEQRES 1 D 22 DT DC DT DT DC DA DC DT DA DG DC DA DT SEQRES 2 D 22 DA DA DC DA DA DT DG DA DG HELIX 1 AA1 ASN E 8 ASN E 25 1 18 HELIX 2 AA2 HIS E 29 LEU E 43 1 15 HELIX 3 AA3 SER E 45 HIS E 67 1 23 HELIX 4 AA4 ASP A 1 GLY A 24 1 24 HELIX 5 AA5 THR A 26 GLY A 39 1 14 HELIX 6 AA6 SER A 43 ALA A 52 1 10 HELIX 7 AA7 SER A 56 SER A 99 1 44 CRYST1 163.169 163.169 39.792 90.00 90.00 120.00 P 63 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 0.006129 0.003538 0.000000 0.00000 SCALE2 0.000000 0.007077 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025131 0.00000