HEADER DNA BINDING PROTEIN/DNA,TRANSCRIPTION 29-OCT-19 6L6Y TITLE CRYSTAL STRUCTURE OF PLURIPOTENCY REPROGRAMMING FACTOR SOX17 MUTANT TITLE 2 (SOX17EK) HMG DOMAIN BOUND TO DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(P*GP*GP*TP*CP*TP*CP*TP*AP*TP*TP*GP*TP*CP*CP*TP*G)-3'); COMPND 4 CHAIN: A, C; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*CP*CP*AP*GP*GP*AP*CP*AP*AP*TP*AP*GP*AP*GP*AP*C)- COMPND 8 3'); COMPND 9 CHAIN: B, E; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: TRANSCRIPTION FACTOR SOX-17; COMPND 13 CHAIN: D, F; COMPND 14 ENGINEERED: YES; COMPND 15 MUTATION: 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 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 11 ORGANISM_COMMON: MOUSE; SOURCE 12 ORGANISM_TAXID: 10090; SOURCE 13 GENE: SOX17, SOX-17; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); 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 HMG, STEM CELL TRANSCRIPTION FACTOR, PLURIPOTENCY REPROGRAMMING KEYWDS 2 FACTOR, DNA BINDING PROTEIN-DNA, TRANSCRIPTION COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.BALASUBRAMANIAN,P.R.KOLATKAR REVDAT 2 22-NOV-23 6L6Y 1 REMARK REVDAT 1 04-NOV-20 6L6Y 0 JRNL AUTH M.BALASUBRAMANIAN,P.R.KOLATKAR JRNL TITL CRYSTAL STRUCTURE OF PLURIPOTENCY REPROGRAMMING FACTOR SOX17 JRNL TITL 2 MUTANT (SOX17EK) HMG DOMAIN BOUND TO DNA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.ELBASIR,B.MOOVARKUMUDALVAN,K.KUNJI,P.R.KOLATKAR,R.MALL, REMARK 1 AUTH 2 H.BENSMAIL REMARK 1 TITL DEEPCRYSTAL: A DEEP LEARNING FRAMEWORK FOR SEQUENCE-BASED REMARK 1 TITL 2 PROTEIN CRYSTALLIZATION PREDICTION. REMARK 1 REF BIOINFORMATICS V. 35 2216 2019 REMARK 1 REFN ESSN 1367-4811 REMARK 1 DOI 10.1093/BIOINFORMATICS/BTY953 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17_3644 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 16478 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1632 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 20.9700 - 6.8000 0.99 1221 144 0.1562 0.2202 REMARK 3 2 6.8000 - 5.4300 1.00 1241 133 0.1685 0.2179 REMARK 3 3 5.4200 - 4.7500 1.00 1249 139 0.1771 0.2368 REMARK 3 4 4.7500 - 4.3200 1.00 1230 134 0.1644 0.2059 REMARK 3 5 4.3200 - 4.0100 1.00 1251 132 0.1556 0.2154 REMARK 3 6 4.0100 - 3.7800 1.00 1240 132 0.1747 0.2278 REMARK 3 7 3.7800 - 3.5900 1.00 1232 132 0.1918 0.3091 REMARK 3 8 3.5900 - 3.4300 1.00 1244 129 0.2073 0.2723 REMARK 3 9 3.4300 - 3.3000 1.00 1225 149 0.2134 0.3039 REMARK 3 10 3.3000 - 3.1900 1.00 1213 136 0.2338 0.3008 REMARK 3 11 3.1900 - 3.0900 1.00 1248 145 0.2402 0.2735 REMARK 3 12 3.0900 - 3.0000 1.00 1252 127 0.2982 0.3797 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.385 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.889 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.63 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.012 2854 REMARK 3 ANGLE : 1.256 4110 REMARK 3 CHIRALITY : 0.068 436 REMARK 3 PLANARITY : 0.007 306 REMARK 3 DIHEDRAL : 33.160 810 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 0 THROUGH 15) REMARK 3 ORIGIN FOR THE GROUP (A): 21.8438 20.3971 4.8828 REMARK 3 T TENSOR REMARK 3 T11: 0.2095 T22: 0.3734 REMARK 3 T33: 0.2524 T12: -0.1608 REMARK 3 T13: 0.0590 T23: 0.0655 REMARK 3 L TENSOR REMARK 3 L11: 1.4498 L22: 2.2577 REMARK 3 L33: 2.8309 L12: -0.0150 REMARK 3 L13: -0.6481 L23: -1.5292 REMARK 3 S TENSOR REMARK 3 S11: 0.0528 S12: 0.1463 S13: 0.4893 REMARK 3 S21: -0.2077 S22: -0.0042 S23: -0.4499 REMARK 3 S31: -0.3915 S32: 0.3911 S33: 0.0140 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 1 THROUGH 16) REMARK 3 ORIGIN FOR THE GROUP (A): 19.4235 21.3070 5.5309 REMARK 3 T TENSOR REMARK 3 T11: 0.2451 T22: 0.2874 REMARK 3 T33: 0.0829 T12: 0.0146 REMARK 3 T13: -0.1019 T23: 0.1668 REMARK 3 L TENSOR REMARK 3 L11: 1.7630 L22: 1.7820 REMARK 3 L33: 1.7396 L12: 0.2030 REMARK 3 L13: -0.0828 L23: 0.3752 REMARK 3 S TENSOR REMARK 3 S11: 0.0242 S12: -0.3680 S13: 0.1699 REMARK 3 S21: 0.3347 S22: 0.1036 S23: -0.1598 REMARK 3 S31: -0.2060 S32: -0.1272 S33: 0.3699 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'D' AND RESID 62 THROUGH 141) REMARK 3 ORIGIN FOR THE GROUP (A): 19.8226 7.7738 7.7837 REMARK 3 T TENSOR REMARK 3 T11: 0.1084 T22: 0.1559 REMARK 3 T33: 0.1807 T12: -0.0110 REMARK 3 T13: 0.0538 T23: 0.0848 REMARK 3 L TENSOR REMARK 3 L11: 2.0671 L22: 0.5823 REMARK 3 L33: 0.8358 L12: 0.2833 REMARK 3 L13: -0.5543 L23: -0.3128 REMARK 3 S TENSOR REMARK 3 S11: 0.0401 S12: -0.3583 S13: -0.3502 REMARK 3 S21: -0.0911 S22: -0.0464 S23: -0.1436 REMARK 3 S31: 0.1595 S32: 0.1242 S33: 0.0265 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN 'C' AND RESID 0 THROUGH 15) REMARK 3 ORIGIN FOR THE GROUP (A): 37.3556 -8.4214 -5.1549 REMARK 3 T TENSOR REMARK 3 T11: 0.6422 T22: 0.8601 REMARK 3 T33: 0.2962 T12: 0.3808 REMARK 3 T13: -0.0387 T23: -0.1130 REMARK 3 L TENSOR REMARK 3 L11: 0.7275 L22: 1.4409 REMARK 3 L33: 1.2453 L12: 1.0179 REMARK 3 L13: 0.3397 L23: 0.4200 REMARK 3 S TENSOR REMARK 3 S11: -0.1013 S12: -0.6519 S13: -0.2038 REMARK 3 S21: 0.5457 S22: 0.1713 S23: -0.4374 REMARK 3 S31: 0.6494 S32: 0.7410 S33: 0.0777 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN 'E' AND RESID 1 THROUGH 16) REMARK 3 ORIGIN FOR THE GROUP (A): 36.9650 -10.8735 -5.6298 REMARK 3 T TENSOR REMARK 3 T11: 0.7345 T22: 0.8744 REMARK 3 T33: 0.4292 T12: 0.3958 REMARK 3 T13: -0.0432 T23: 0.0402 REMARK 3 L TENSOR REMARK 3 L11: 1.6961 L22: 1.6007 REMARK 3 L33: 0.4453 L12: 0.8188 REMARK 3 L13: 0.3272 L23: 0.8365 REMARK 3 S TENSOR REMARK 3 S11: 0.1201 S12: -0.5585 S13: -0.6561 REMARK 3 S21: 0.4446 S22: 0.2485 S23: -0.4697 REMARK 3 S31: 0.8699 S32: 0.5517 S33: -0.0352 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN 'F' AND RESID 62 THROUGH 141) REMARK 3 ORIGIN FOR THE GROUP (A): 25.8671 -3.2894 -6.6122 REMARK 3 T TENSOR REMARK 3 T11: 0.3061 T22: 0.3637 REMARK 3 T33: 0.2532 T12: -0.0668 REMARK 3 T13: 0.0301 T23: -0.1300 REMARK 3 L TENSOR REMARK 3 L11: 2.1937 L22: 2.1898 REMARK 3 L33: 2.4521 L12: 0.8456 REMARK 3 L13: 1.2539 L23: 1.0147 REMARK 3 S TENSOR REMARK 3 S11: 0.1667 S12: -0.1768 S13: -0.4255 REMARK 3 S21: 0.3188 S22: -0.1046 S23: -0.2824 REMARK 3 S31: 0.7578 S32: -0.1114 S33: -0.0552 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SF FILE CONTAINS FRIEDEL PAIRS UNDER REMARK 3 I_MINUS AND I_PLUS COLUMNS. REMARK 4 REMARK 4 6L6Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1300014207. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUL-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER D8 QUEST REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CMOS REMARK 200 DETECTOR MANUFACTURER : BRUKER PHOTON 100 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROTEUM REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16478 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.990 REMARK 200 RESOLUTION RANGE LOW (A) : 20.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 9.610 REMARK 200 R MERGE (I) : 0.17000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.3 REMARK 200 DATA REDUNDANCY IN SHELL : 7.04 REMARK 200 R MERGE FOR SHELL (I) : 0.45000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.740 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.17_3644 REMARK 200 STARTING MODEL: 3F27 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 30% PEG 4000, REMARK 280 0.1 M TRIS PH 8.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291K 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 35.52000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.97600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.60250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.97600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.52000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.60250 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 4160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 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: 4070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, E, 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 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 ARG D 142 REMARK 465 LYS D 143 REMARK 465 GLN D 144 REMARK 465 ARG F 142 REMARK 465 LYS F 143 REMARK 465 GLN F 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' -0.057 REMARK 500 DC A 13 O3' DC A 13 C3' -0.047 REMARK 500 DC B 1 O3' DC B 1 C3' 0.114 REMARK 500 DC B 1 C1' DC B 1 N1 0.136 REMARK 500 DC B 2 C5' DC B 2 C4' 0.049 REMARK 500 DG B 5 O3' DG B 5 C3' -0.061 REMARK 500 DA B 6 O3' DA B 6 C3' -0.061 REMARK 500 DG B 12 O3' DG B 12 C3' -0.039 REMARK 500 DA E 8 O3' DA E 8 C3' -0.058 REMARK 500 DC E 16 O5' DC E 16 C5' 0.098 REMARK 500 DC E 16 C5' DC E 16 C4' 0.071 REMARK 500 DC E 16 C1' DC E 16 N1 0.092 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 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA A 7 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC B 1 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 DC B 1 O4' - C1' - N1 ANGL. DEV. = 12.6 DEGREES REMARK 500 DG B 4 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC B 7 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC B 16 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG C 0 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 DA E 15 O4' - C1' - N9 ANGL. DEV. = 3.0 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 ASN D 90 64.56 -152.87 REMARK 500 LYS F 107 22.04 -76.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 D 201 DBREF 6L6Y A 0 15 PDB 6L6Y 6L6Y 0 15 DBREF 6L6Y B 1 16 PDB 6L6Y 6L6Y 1 16 DBREF 6L6Y D 66 144 UNP Q61473 SOX17_MOUSE 66 144 DBREF 6L6Y C 0 15 PDB 6L6Y 6L6Y 0 15 DBREF 6L6Y E 1 16 PDB 6L6Y 6L6Y 1 16 DBREF 6L6Y F 66 144 UNP Q61473 SOX17_MOUSE 66 144 SEQADV 6L6Y GLY D 62 UNP Q61473 EXPRESSION TAG SEQADV 6L6Y SER D 63 UNP Q61473 EXPRESSION TAG SEQADV 6L6Y PHE D 64 UNP Q61473 EXPRESSION TAG SEQADV 6L6Y THR D 65 UNP Q61473 EXPRESSION TAG SEQADV 6L6Y LYS D 122 UNP Q61473 GLU 122 ENGINEERED MUTATION SEQADV 6L6Y GLY F 62 UNP Q61473 EXPRESSION TAG SEQADV 6L6Y SER F 63 UNP Q61473 EXPRESSION TAG SEQADV 6L6Y PHE F 64 UNP Q61473 EXPRESSION TAG SEQADV 6L6Y THR F 65 UNP Q61473 EXPRESSION TAG SEQADV 6L6Y LYS F 122 UNP Q61473 GLU 122 ENGINEERED MUTATION SEQRES 1 A 16 DG DG DT DC DT DC DT DA DT DT DG DT DC SEQRES 2 A 16 DC DT 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 LYS 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 SEQRES 1 C 16 DG DG DT DC DT DC DT DA DT DT DG DT DC SEQRES 2 C 16 DC DT DG SEQRES 1 E 16 DC DC DA DG DG DA DC DA DA DT DA DG DA SEQRES 2 E 16 DG DA DC SEQRES 1 F 83 GLY SER PHE THR SER ARG ILE ARG ARG PRO MET ASN ALA SEQRES 2 F 83 PHE MET VAL TRP ALA LYS ASP GLU ARG LYS ARG LEU ALA SEQRES 3 F 83 GLN GLN ASN PRO ASP LEU HIS ASN ALA GLU LEU SER LYS SEQRES 4 F 83 MET LEU GLY LYS SER TRP LYS ALA LEU THR LEU ALA GLU SEQRES 5 F 83 LYS ARG PRO PHE VAL GLU GLU ALA LYS ARG LEU ARG VAL SEQRES 6 F 83 GLN HIS MET GLN ASP HIS PRO ASN TYR LYS TYR ARG PRO SEQRES 7 F 83 ARG ARG ARG LYS GLN HET SO4 D 201 5 HETNAM SO4 SULFATE ION FORMUL 7 SO4 O4 S 2- FORMUL 8 HOH *13(H2 O) HELIX 1 AA1 ASN D 73 ASN D 90 1 18 HELIX 2 AA2 HIS D 94 ALA D 108 1 15 HELIX 3 AA3 THR D 110 HIS D 132 1 23 HELIX 4 AA4 ASN F 73 ASN F 90 1 18 HELIX 5 AA5 HIS F 94 LYS F 107 1 14 HELIX 6 AA6 LYS F 114 HIS F 132 1 19 SITE 1 AC1 4 DT B 10 ARG D 67 ARG D 69 HOH D 304 CRYST1 71.040 73.205 81.952 90.00 90.00 90.00 P 21 21 21 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 0.014077 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013660 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012202 0.00000