HEADER TRANSCRIPTION ACTIVATOR/DNA 07-JUN-06 2H8R TITLE HEPATOCYTE NUCLEAR FACTOR 1B BOUND TO DNA: MODY5 GENE PRODUCT COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*TP*TP*GP*GP*TP*TP*AP*AP*TP*AP*AP*TP*TP*CP*AP*CP*CP COMPND 3 *AP*G)-3'; COMPND 4 CHAIN: E; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*GP*CP*TP*GP*GP*TP*GP*AP*AP*TP*TP*AP*TP*TP*AP*AP*CP*CP COMPND 8 *AP*A)-3'; COMPND 9 CHAIN: F; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: HEPATOCYTE NUCLEAR FACTOR 1-BETA; COMPND 13 CHAIN: A, B; COMPND 14 FRAGMENT: DNA BINDING DOMAIN (RESIDUES 91-310); COMPND 15 SYNONYM: HNF-1BETA, HNF-1B, VARIANT HEPATIC NUCLEAR FACTOR 1, VHNF1, COMPND 16 HOMEOPROTEIN LFB3, TRANSCRIPTION FACTOR 2, TCF-2; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 11 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PET41A KEYWDS TRASNCRIPTION FACTOR, POU, HOMEO, PROTEIN-DNA, HUMAN DISEASE, KEYWDS 2 TRANSCRIPTION ACTIVATOR-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.LU,G.B.RHA,Y.I.CHI REVDAT 4 30-AUG-23 2H8R 1 SEQADV REVDAT 3 24-FEB-09 2H8R 1 VERSN REVDAT 2 12-FEB-08 2H8R 1 JRNL REVDAT 1 19-JUN-07 2H8R 0 JRNL AUTH P.LU,G.B.RHA,Y.I.CHI JRNL TITL STRUCTURAL BASIS OF DISEASE-CAUSING MUTATIONS IN HEPATOCYTE JRNL TITL 2 NUCLEAR FACTOR 1BETA. JRNL REF BIOCHEMISTRY V. 46 12071 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17924661 JRNL DOI 10.1021/BI7010527 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.LU,Y.LI,A.GORMAN,Y.I.CHI REMARK 1 TITL CRYSTALLIZATION OF HEPATOCYTE NUCLEAR FACTOR 1BETA IN REMARK 1 TITL 2 COMPLEX WITH DNA. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 62 525 2006 REMARK 1 REFN ESSN 1744-3091 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 11992 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) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.290 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 637 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) : 3.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 528 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 53.30 REMARK 3 BIN R VALUE (WORKING SET) : 0.2300 REMARK 3 BIN FREE R VALUE SET COUNT : 24 REMARK 3 BIN FREE R VALUE : 0.4150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2915 REMARK 3 NUCLEIC ACID ATOMS : 814 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 7 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 57.24 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.43000 REMARK 3 B22 (A**2) : 5.43000 REMARK 3 B33 (A**2) : -8.15000 REMARK 3 B12 (A**2) : 2.72000 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): 0.538 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.374 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 21.564 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.903 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.829 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3866 ; 0.079 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5362 ; 5.450 ; 2.206 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 348 ;12.042 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 530 ; 0.258 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2697 ; 0.020 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2269 ; 0.374 ; 0.200 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): 248 ; 0.294 ; 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): 12 ; 0.236 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.470 ; 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): 1756 ; 2.542 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2814 ; 4.678 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2110 ; 5.745 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2548 ; 8.674 ; 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): 3866 ; 3.686 ; 2.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 7 ;20.239 ; 2.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3717 ; 5.174 ; 2.000 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 : BABINET MODEL WITH 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 2H8R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUN-06. REMARK 100 THE DEPOSITION ID IS D_1000038071. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-DEC-05 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 : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97923 REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK MONOCHROMATOR REMARK 200 HIGH-RESOLUTION DOUBLE-CRYSTAL REMARK 200 SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12582 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 27.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : 0.08300 REMARK 200 FOR THE DATA SET : 28.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 63.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.31300 REMARK 200 R SYM FOR SHELL (I) : 0.27300 REMARK 200 FOR SHELL : 3.350 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: PDB ENTRY 1IC8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6%(V/V) PEG300, 5%(V/V) PEG8000, REMARK 280 8%(V/V) GLYCEROL, 100MM TRIS, PH 8.0, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 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+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,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 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 87.34450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 50.42837 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 24.14467 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 87.34450 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 50.42837 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 24.14467 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 87.34450 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 50.42837 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 24.14467 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 100.85674 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 48.28933 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 100.85674 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 48.28933 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 100.85674 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 48.28933 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 300 REMARK: DIMER WHEN BINDING TO DNA 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 APPLY THE FOLLOWING TO CHAINS: E, F, A, B 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 GLN A 188 REMARK 465 SER A 189 REMARK 465 SER A 190 REMARK 465 GLY A 191 REMARK 465 ASN A 192 REMARK 465 MET A 193 REMARK 465 THR A 194 REMARK 465 ASP A 195 REMARK 465 LYS A 196 REMARK 465 SER A 197 REMARK 465 SER A 198 REMARK 465 GLN A 199 REMARK 465 ASP A 200 REMARK 465 GLN A 201 REMARK 465 LEU A 202 REMARK 465 LEU A 203 REMARK 465 PHE A 204 REMARK 465 LEU A 205 REMARK 465 PHE A 206 REMARK 465 PRO A 207 REMARK 465 GLU A 208 REMARK 465 PHE A 209 REMARK 465 SER A 210 REMARK 465 GLN A 211 REMARK 465 GLN A 212 REMARK 465 SER A 213 REMARK 465 HIS A 214 REMARK 465 GLY A 215 REMARK 465 PRO A 216 REMARK 465 GLY A 217 REMARK 465 GLN A 218 REMARK 465 SER A 219 REMARK 465 ASP A 220 REMARK 465 ASP A 221 REMARK 465 ALA A 222 REMARK 465 CYS A 223 REMARK 465 SER A 224 REMARK 465 GLU A 225 REMARK 465 PRO A 226 REMARK 465 THR A 227 REMARK 465 ASN A 228 REMARK 465 LYS A 229 REMARK 465 LYS A 230 REMARK 465 PHE A 309 REMARK 465 ARG A 310 REMARK 465 THR B 186 REMARK 465 VAL B 187 REMARK 465 GLN B 188 REMARK 465 SER B 189 REMARK 465 SER B 190 REMARK 465 GLY B 191 REMARK 465 ASN B 192 REMARK 465 MET B 193 REMARK 465 THR B 194 REMARK 465 ASP B 195 REMARK 465 LYS B 196 REMARK 465 SER B 197 REMARK 465 SER B 198 REMARK 465 GLN B 199 REMARK 465 ASP B 200 REMARK 465 GLN B 201 REMARK 465 LEU B 202 REMARK 465 LEU B 203 REMARK 465 PHE B 204 REMARK 465 LEU B 205 REMARK 465 PHE B 206 REMARK 465 PRO B 207 REMARK 465 GLU B 208 REMARK 465 PHE B 209 REMARK 465 SER B 210 REMARK 465 GLN B 211 REMARK 465 GLN B 212 REMARK 465 SER B 213 REMARK 465 HIS B 214 REMARK 465 GLY B 215 REMARK 465 PRO B 216 REMARK 465 GLY B 217 REMARK 465 GLN B 218 REMARK 465 SER B 219 REMARK 465 ASP B 220 REMARK 465 ASP B 221 REMARK 465 ALA B 222 REMARK 465 CYS B 223 REMARK 465 SER B 224 REMARK 465 GLU B 225 REMARK 465 PRO B 226 REMARK 465 THR B 227 REMARK 465 ASN B 228 REMARK 465 LYS B 229 REMARK 465 LYS B 230 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 O SER B 257 N GLU B 259 1.90 REMARK 500 O GLN B 106 N ALA B 108 2.08 REMARK 500 OG SER A 279 OG SER A 281 2.14 REMARK 500 O CYS A 268 N ALA A 271 2.15 REMARK 500 O ARG A 304 N GLU A 306 2.17 REMARK 500 O SER A 279 O SER A 281 2.19 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 DC E 1 O5' DC E 1 C5' 0.193 REMARK 500 DC E 1 C5' DC E 1 C4' 0.111 REMARK 500 DC E 1 C4' DC E 1 C3' 0.075 REMARK 500 DC E 1 O4' DC E 1 C4' 0.080 REMARK 500 DC E 1 O3' DC E 1 C3' 0.105 REMARK 500 DC E 1 C1' DC E 1 N1 0.106 REMARK 500 DC E 1 C2 DC E 1 O2 0.129 REMARK 500 DC E 1 N1 DC E 1 C2 0.119 REMARK 500 DC E 1 N1 DC E 1 C6 0.065 REMARK 500 DC E 1 C2 DC E 1 N3 0.137 REMARK 500 DC E 1 N3 DC E 1 C4 0.083 REMARK 500 DC E 1 C5 DC E 1 C6 0.050 REMARK 500 DC E 1 O3' DT E 2 P 0.146 REMARK 500 DT E 2 P DT E 2 OP1 0.174 REMARK 500 DT E 2 P DT E 2 O5' 0.196 REMARK 500 DT E 2 O5' DT E 2 C5' 0.108 REMARK 500 DT E 2 C5' DT E 2 C4' 0.043 REMARK 500 DT E 2 O3' DT E 2 C3' 0.093 REMARK 500 DT E 2 C1' DT E 2 N1 0.099 REMARK 500 DT E 2 N1 DT E 2 C2 0.131 REMARK 500 DT E 2 C2 DT E 2 N3 0.134 REMARK 500 DT E 2 N3 DT E 2 C4 0.062 REMARK 500 DT E 2 C4 DT E 2 C5 0.060 REMARK 500 DT E 2 C5 DT E 2 C6 0.083 REMARK 500 DT E 2 C6 DT E 2 N1 0.093 REMARK 500 DT E 2 C2 DT E 2 O2 0.150 REMARK 500 DT E 2 O3' DT E 3 P 0.207 REMARK 500 DT E 3 P DT E 3 OP2 0.151 REMARK 500 DT E 3 P DT E 3 O5' 0.102 REMARK 500 DT E 3 C5' DT E 3 C4' 0.043 REMARK 500 DT E 3 C2 DT E 3 N3 0.086 REMARK 500 DT E 3 N3 DT E 3 C4 0.087 REMARK 500 DT E 3 C4 DT E 3 C5 0.090 REMARK 500 DT E 3 C5 DT E 3 C6 0.055 REMARK 500 DT E 3 C2 DT E 3 O2 0.069 REMARK 500 DT E 3 C4 DT E 3 O4 0.094 REMARK 500 DG E 4 P DG E 4 OP1 0.108 REMARK 500 DG E 4 P DG E 4 OP2 0.118 REMARK 500 DG E 4 P DG E 4 O5' 0.159 REMARK 500 DG E 4 O5' DG E 4 C5' 0.217 REMARK 500 DG E 4 C5' DG E 4 C4' 0.076 REMARK 500 DG E 4 O3' DG E 4 C3' -0.038 REMARK 500 DG E 4 C4 DG E 4 C5 0.056 REMARK 500 DG E 4 C6 DG E 4 N1 -0.057 REMARK 500 DG E 5 O3' DG E 5 C3' -0.097 REMARK 500 DG E 5 C6 DG E 5 N1 -0.044 REMARK 500 DG E 5 C5 DG E 5 N7 -0.053 REMARK 500 DG E 5 C8 DG E 5 N9 -0.045 REMARK 500 DT E 6 C5' DT E 6 C4' 0.043 REMARK 500 DT E 7 P DT E 7 OP2 0.153 REMARK 500 REMARK 500 THIS ENTRY HAS 596 BOND DEVIATIONS. 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 E 1 O4' - C4' - C3' ANGL. DEV. = -4.9 DEGREES REMARK 500 DC E 1 C5' - C4' - C3' ANGL. DEV. = 15.2 DEGREES REMARK 500 DC E 1 C5' - C4' - O4' ANGL. DEV. = 7.0 DEGREES REMARK 500 DC E 1 C4' - C3' - C2' ANGL. DEV. = 6.8 DEGREES REMARK 500 DC E 1 N1 - C1' - C2' ANGL. DEV. = 12.3 DEGREES REMARK 500 DC E 1 O4' - C1' - N1 ANGL. DEV. = -7.0 DEGREES REMARK 500 DC E 1 N1 - C2 - N3 ANGL. DEV. = -7.3 DEGREES REMARK 500 DC E 1 C2 - N3 - C4 ANGL. DEV. = 6.8 DEGREES REMARK 500 DC E 1 N3 - C4 - C5 ANGL. DEV. = -3.5 DEGREES REMARK 500 DC E 1 C5 - C6 - N1 ANGL. DEV. = 5.6 DEGREES REMARK 500 DC E 1 N1 - C2 - O2 ANGL. DEV. = 6.1 DEGREES REMARK 500 DT E 2 O3' - P - OP2 ANGL. DEV. = -16.5 DEGREES REMARK 500 DT E 2 O3' - P - OP1 ANGL. DEV. = 12.6 DEGREES REMARK 500 DT E 2 OP1 - P - OP2 ANGL. DEV. = -9.3 DEGREES REMARK 500 DT E 2 P - O5' - C5' ANGL. DEV. = 11.9 DEGREES REMARK 500 DT E 2 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT E 2 N3 - C4 - C5 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT E 3 O3' - P - OP2 ANGL. DEV. = 7.4 DEGREES REMARK 500 DT E 3 O5' - P - OP1 ANGL. DEV. = -10.2 DEGREES REMARK 500 DT E 3 N1 - C1' - C2' ANGL. DEV. = 11.1 DEGREES REMARK 500 DT E 3 O4' - C1' - N1 ANGL. DEV. = -10.2 DEGREES REMARK 500 DT E 3 N3 - C4 - C5 ANGL. DEV. = -6.5 DEGREES REMARK 500 DT E 3 N1 - C2 - O2 ANGL. DEV. = -8.6 DEGREES REMARK 500 DT E 3 N3 - C2 - O2 ANGL. DEV. = 9.0 DEGREES REMARK 500 DT E 3 N3 - C4 - O4 ANGL. DEV. = 4.6 DEGREES REMARK 500 DT E 3 C6 - N1 - C1' ANGL. DEV. = 12.5 DEGREES REMARK 500 DT E 3 C2 - N1 - C1' ANGL. DEV. = -15.7 DEGREES REMARK 500 DG E 4 OP1 - P - OP2 ANGL. DEV. = 11.0 DEGREES REMARK 500 DG E 4 O5' - P - OP1 ANGL. DEV. = -12.8 DEGREES REMARK 500 DG E 4 C5' - C4' - O4' ANGL. DEV. = 7.7 DEGREES REMARK 500 DG E 4 N1 - C2 - N3 ANGL. DEV. = 11.6 DEGREES REMARK 500 DG E 4 C2 - N3 - C4 ANGL. DEV. = -12.7 DEGREES REMARK 500 DG E 4 C5 - C6 - N1 ANGL. DEV. = -6.5 DEGREES REMARK 500 DG E 4 N1 - C2 - N2 ANGL. DEV. = -14.8 DEGREES REMARK 500 DG E 4 C5 - C6 - O6 ANGL. DEV. = 8.6 DEGREES REMARK 500 DG E 4 C3' - O3' - P ANGL. DEV. = -9.7 DEGREES REMARK 500 DG E 5 OP1 - P - OP2 ANGL. DEV. = 15.7 DEGREES REMARK 500 DG E 5 O5' - P - OP1 ANGL. DEV. = -12.5 DEGREES REMARK 500 DG E 5 C1' - O4' - C4' ANGL. DEV. = -6.8 DEGREES REMARK 500 DG E 5 C4' - C3' - C2' ANGL. DEV. = -6.6 DEGREES REMARK 500 DG E 5 O4' - C1' - N9 ANGL. DEV. = 11.1 DEGREES REMARK 500 DG E 5 N1 - C2 - N3 ANGL. DEV. = 5.8 DEGREES REMARK 500 DG E 5 C2 - N3 - C4 ANGL. DEV. = -5.8 DEGREES REMARK 500 DG E 5 N3 - C4 - C5 ANGL. DEV. = -4.1 DEGREES REMARK 500 DG E 5 C4 - C5 - C6 ANGL. DEV. = 9.9 DEGREES REMARK 500 DG E 5 C5 - C6 - N1 ANGL. DEV. = -6.3 DEGREES REMARK 500 DG E 5 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 DG E 5 C8 - N9 - C4 ANGL. DEV. = -5.2 DEGREES REMARK 500 DG E 5 N9 - C4 - C5 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG E 5 C6 - C5 - N7 ANGL. DEV. = -9.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 579 ANGLE DEVIATIONS. 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 A 99 74.25 -119.04 REMARK 500 MET A 113 -27.83 -36.91 REMARK 500 PRO A 118 -38.66 -39.29 REMARK 500 ASP A 141 -93.16 -58.57 REMARK 500 VAL A 142 -62.07 -17.68 REMARK 500 ASN A 155 -73.79 -88.96 REMARK 500 VAL A 173 -76.92 -20.96 REMARK 500 GLU A 178 -75.37 -26.87 REMARK 500 THR A 186 -169.58 -78.22 REMARK 500 ASN A 234 170.04 -41.43 REMARK 500 ALA A 241 -74.54 -32.99 REMARK 500 ALA A 249 -10.86 -48.43 REMARK 500 LYS A 258 -51.96 -19.14 REMARK 500 GLU A 260 -72.28 -44.50 REMARK 500 ARG A 261 -77.16 -39.71 REMARK 500 GLU A 262 -36.62 -15.80 REMARK 500 ASN A 269 -29.04 -32.30 REMARK 500 GLU A 272 -38.29 -29.92 REMARK 500 PRO A 280 -12.39 -43.74 REMARK 500 ARG A 303 -15.48 -157.90 REMARK 500 ARG A 304 -68.70 -103.34 REMARK 500 LYS A 305 28.59 -51.35 REMARK 500 GLU A 306 34.57 -147.69 REMARK 500 ILE B 91 -28.40 -38.53 REMARK 500 GLN B 96 0.22 -54.94 REMARK 500 THR B 100 171.13 -42.09 REMARK 500 ALA B 103 -57.63 -26.91 REMARK 500 GLU B 105 -62.87 -20.13 REMARK 500 ARG B 107 -11.10 -43.74 REMARK 500 MET B 113 -32.01 -38.83 REMARK 500 ASP B 117 107.77 -46.95 REMARK 500 LYS B 123 -71.80 -53.97 REMARK 500 MET B 124 -55.59 -20.22 REMARK 500 ASN B 133 89.03 53.64 REMARK 500 GLU B 138 -3.40 -45.43 REMARK 500 SER B 151 -39.86 -30.29 REMARK 500 THR B 162 -66.57 -23.64 REMARK 500 GLU B 178 -37.67 -33.87 REMARK 500 PHE B 183 -82.04 -118.86 REMARK 500 ARG B 232 134.65 5.39 REMARK 500 ASN B 234 129.11 -22.13 REMARK 500 TYR B 250 -6.64 -141.04 REMARK 500 ASP B 251 105.75 -54.43 REMARK 500 ASN B 255 89.21 40.54 REMARK 500 LYS B 258 -3.97 -34.83 REMARK 500 GLU B 262 -29.77 -37.88 REMARK 500 PRO B 280 1.57 -52.50 REMARK 500 GLU B 293 -79.20 -50.71 REMARK 500 VAL B 294 -39.52 -38.95 REMARK 500 GLU B 306 -93.21 -34.13 REMARK 500 REMARK 500 THIS ENTRY HAS 52 RAMACHANDRAN OUTLIERS. 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 PHE A 183 ASN A 184 -143.30 REMARK 500 LEU A 286 GLY A 287 148.91 REMARK 500 REMARK 500 REMARK: NULL DBREF 2H8R A 91 310 UNP P35680 HNF1B_HUMAN 91 310 DBREF 2H8R B 91 310 UNP P35680 HNF1B_HUMAN 91 310 DBREF 2H8R E 1 20 PDB 2H8R 2H8R 1 20 DBREF 2H8R F 2 21 PDB 2H8R 2H8R 2 21 SEQADV 2H8R SER A 90 UNP P35680 CLONING ARTIFACT SEQADV 2H8R SER B 90 UNP P35680 CLONING ARTIFACT SEQRES 1 E 20 DC DT DT DG DG DT DT DA DA DT DA DA DT SEQRES 2 E 20 DT DC DA DC DC DA DG SEQRES 1 F 20 DG DC DT DG DG DT DG DA DA DT DT DA DT SEQRES 2 F 20 DT DA DA DC DC DA DA SEQRES 1 A 221 SER ILE LEU LYS GLU LEU GLN ALA LEU ASN THR GLU GLU SEQRES 2 A 221 ALA ALA GLU GLN ARG ALA GLU VAL ASP ARG MET LEU SER SEQRES 3 A 221 GLU ASP PRO TRP ARG ALA ALA LYS MET ILE LYS GLY TYR SEQRES 4 A 221 MET GLN GLN HIS ASN ILE PRO GLN ARG GLU VAL VAL ASP SEQRES 5 A 221 VAL THR GLY LEU ASN GLN SER HIS LEU SER GLN HIS LEU SEQRES 6 A 221 ASN LYS GLY THR PRO MET LYS THR GLN LYS ARG ALA ALA SEQRES 7 A 221 LEU TYR THR TRP TYR VAL ARG LYS GLN ARG GLU ILE LEU SEQRES 8 A 221 ARG GLN PHE ASN GLN THR VAL GLN SER SER GLY ASN MET SEQRES 9 A 221 THR ASP LYS SER SER GLN ASP GLN LEU LEU PHE LEU PHE SEQRES 10 A 221 PRO GLU PHE SER GLN GLN SER HIS GLY PRO GLY GLN SER SEQRES 11 A 221 ASP ASP ALA CYS SER GLU PRO THR ASN LYS LYS MET ARG SEQRES 12 A 221 ARG ASN ARG PHE LYS TRP GLY PRO ALA SER GLN GLN ILE SEQRES 13 A 221 LEU TYR GLN ALA TYR ASP ARG GLN LYS ASN PRO SER LYS SEQRES 14 A 221 GLU GLU ARG GLU ALA LEU VAL GLU GLU CYS ASN ARG ALA SEQRES 15 A 221 GLU CYS LEU GLN ARG GLY VAL SER PRO SER LYS ALA HIS SEQRES 16 A 221 GLY LEU GLY SER ASN LEU VAL THR GLU VAL ARG VAL TYR SEQRES 17 A 221 ASN TRP PHE ALA ASN ARG ARG LYS GLU GLU ALA PHE ARG SEQRES 1 B 221 SER ILE LEU LYS GLU LEU GLN ALA LEU ASN THR GLU GLU SEQRES 2 B 221 ALA ALA GLU GLN ARG ALA GLU VAL ASP ARG MET LEU SER SEQRES 3 B 221 GLU ASP PRO TRP ARG ALA ALA LYS MET ILE LYS GLY TYR SEQRES 4 B 221 MET GLN GLN HIS ASN ILE PRO GLN ARG GLU VAL VAL ASP SEQRES 5 B 221 VAL THR GLY LEU ASN GLN SER HIS LEU SER GLN HIS LEU SEQRES 6 B 221 ASN LYS GLY THR PRO MET LYS THR GLN LYS ARG ALA ALA SEQRES 7 B 221 LEU TYR THR TRP TYR VAL ARG LYS GLN ARG GLU ILE LEU SEQRES 8 B 221 ARG GLN PHE ASN GLN THR VAL GLN SER SER GLY ASN MET SEQRES 9 B 221 THR ASP LYS SER SER GLN ASP GLN LEU LEU PHE LEU PHE SEQRES 10 B 221 PRO GLU PHE SER GLN GLN SER HIS GLY PRO GLY GLN SER SEQRES 11 B 221 ASP ASP ALA CYS SER GLU PRO THR ASN LYS LYS MET ARG SEQRES 12 B 221 ARG ASN ARG PHE LYS TRP GLY PRO ALA SER GLN GLN ILE SEQRES 13 B 221 LEU TYR GLN ALA TYR ASP ARG GLN LYS ASN PRO SER LYS SEQRES 14 B 221 GLU GLU ARG GLU ALA LEU VAL GLU GLU CYS ASN ARG ALA SEQRES 15 B 221 GLU CYS LEU GLN ARG GLY VAL SER PRO SER LYS ALA HIS SEQRES 16 B 221 GLY LEU GLY SER ASN LEU VAL THR GLU VAL ARG VAL TYR SEQRES 17 B 221 ASN TRP PHE ALA ASN ARG ARG LYS GLU GLU ALA PHE ARG FORMUL 5 HOH *7(H2 O) HELIX 1 1 SER A 90 ASN A 99 1 10 HELIX 2 2 THR A 100 LEU A 114 1 15 HELIX 3 3 ASP A 117 ASN A 133 1 17 HELIX 4 4 PRO A 135 GLY A 144 1 10 HELIX 5 5 ASN A 146 ASN A 155 1 10 HELIX 6 6 LYS A 161 GLN A 182 1 22 HELIX 7 7 GLY A 239 GLN A 253 1 15 HELIX 8 8 SER A 257 ARG A 276 1 20 HELIX 9 9 LYS A 282 GLY A 287 5 6 HELIX 10 10 THR A 292 LYS A 305 1 14 HELIX 11 11 SER B 90 ASN B 99 1 10 HELIX 12 12 THR B 100 MET B 113 1 14 HELIX 13 13 ASP B 117 ASN B 133 1 17 HELIX 14 14 GLN B 136 GLY B 144 1 9 HELIX 15 15 ASN B 146 LYS B 156 1 11 HELIX 16 16 LYS B 161 GLN B 182 1 22 HELIX 17 17 GLY B 239 ALA B 249 1 11 HELIX 18 18 SER B 257 GLY B 277 1 21 HELIX 19 19 SER B 279 ALA B 283 5 5 HELIX 20 20 LEU B 286 LEU B 290 5 5 HELIX 21 21 THR B 292 GLU B 307 1 16 CRYST1 174.689 174.689 72.434 90.00 90.00 120.00 H 3 18 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 0.005724 0.003305 0.000000 0.00000 SCALE2 0.000000 0.006610 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013806 0.00000