HEADER TRANSCRIPTION/DNA 06-FEB-03 1NWQ TITLE CRYSTAL STRUCTURE OF C/EBPALPHA-DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*TP*TP*CP*CP*TP*AP*TP*TP*GP*CP*GP*CP*AP*AP*TP*CP*CP*AP COMPND 3 *GP*TP*T)-3'; COMPND 4 CHAIN: B; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*AP*AP*AP*CP*TP*GP*GP*AP*TP*TP*GP*CP*GP*CP*AP*AP*TP*AP COMPND 8 *GP*GP*A)-3'; COMPND 9 CHAIN: D; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: CCAAT/ENHANCER BINDING PROTEIN ALPHA; COMPND 13 CHAIN: A, C; COMPND 14 FRAGMENT: BASIC REGION, LEUCINE ZIPPER DOMAIN; COMPND 15 SYNONYM: C/EBP ALPHA, TRANSCRIPTION FACTOR C/EBPALPHA; COMPND 16 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: RATTUS NORVEGICUS; SOURCE 7 ORGANISM_COMMON: NORWAY RAT; SOURCE 8 ORGANISM_TAXID: 10116; SOURCE 9 GENE: CEBPA; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PT5 KEYWDS BASIC LEUCINE ZIPPER, PROTEIN-DNA COMPLEX, TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.MILLER,J.D.SHUMAN,T.SEBASTIAN,Z.DAUTER,P.F.JOHNSON REVDAT 3 16-AUG-23 1NWQ 1 SEQADV REVDAT 2 24-FEB-09 1NWQ 1 VERSN REVDAT 1 13-MAY-03 1NWQ 0 JRNL AUTH M.MILLER,J.D.SHUMAN,T.SEBASTIAN,Z.DAUTER,P.F.JOHNSON JRNL TITL STRUCTURAL BASIS FOR DNA RECOGNITION BY THE BASIC REGION JRNL TITL 2 LEUCINE ZIPPER TRANSCRIPTION FACTOR CCAAT/ENHANCER BINDING JRNL TITL 3 PROTEIN ALPHA JRNL REF J.BIOL.CHEM. V. 278 15178 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12578822 JRNL DOI 10.1074/JBC.M300417200 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.53 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1483361.250 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 12415 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 SET) : 0.221 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 630 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.93 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1331 REMARK 3 BIN R VALUE (WORKING SET) : 0.4160 REMARK 3 BIN FREE R VALUE : 0.4780 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 93 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1020 REMARK 3 NUCLEIC ACID ATOMS : 855 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 34 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 78.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 92.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -21.10000 REMARK 3 B22 (A**2) : 43.07000 REMARK 3 B33 (A**2) : -21.97000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.48 REMARK 3 ESD FROM SIGMAA (A) : 0.77 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.62 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.83 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.019 REMARK 3 BOND ANGLES (DEGREES) : 2.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.250 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 3.750 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.720 ; 4.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 6.840 ; 4.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 10.050; 7.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.25 REMARK 3 BSOL : 37.03 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NWQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAR-03. REMARK 100 THE DEPOSITION ID IS D_1000018291. 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 : 5.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.07 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12416 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 17.80 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.41500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1DH3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NACL, MGCL2, PEG 400, MES, GLYCEROL, REMARK 280 PH 5.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 70.44600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.54450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 70.44600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.54450 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 APPLY THE FOLLOWING TO CHAINS: B, D, A, C 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 A 279 REMARK 465 SER A 280 REMARK 465 GLY C 279 REMARK 465 SER C 280 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 D 5 C3' - C2' - C1' ANGL. DEV. = -8.1 DEGREES REMARK 500 LEU C 315 CA - CB - CG ANGL. DEV. = -24.2 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 TYR A 285 -82.30 -25.72 REMARK 500 ASN A 293 -5.16 -53.43 REMARK 500 THR A 337 -71.80 -73.31 REMARK 500 LEU A 338 -86.93 -35.35 REMARK 500 ARG A 339 -79.40 -42.17 REMARK 500 SER C 282 -70.65 -96.12 REMARK 500 GLN C 305 -81.53 -43.55 REMARK 500 GLU C 309 -57.44 -20.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DC B -7 0.07 SIDE CHAIN REMARK 500 DG D -7 0.05 SIDE CHAIN REMARK 500 TYR C 285 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DH3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A CREB BZIP-CRE COMPLEX REVEALS THE BASIS FOR REMARK 900 CREB FAMILY SELECTIVE DIMERIZATION AND DNA BINDING DBREF 1NWQ A 281 340 UNP P05554 CEBPA_RAT 281 340 DBREF 1NWQ C 281 340 UNP P05554 CEBPA_RAT 281 340 DBREF 1NWQ B -10 11 PDB 1NWQ 1NWQ -10 11 DBREF 1NWQ D -12 9 PDB 1NWQ 1NWQ -12 9 SEQADV 1NWQ GLY A 279 UNP P05554 CLONING ARTIFACT SEQADV 1NWQ SER A 280 UNP P05554 CLONING ARTIFACT SEQADV 1NWQ GLY C 279 UNP P05554 CLONING ARTIFACT SEQADV 1NWQ SER C 280 UNP P05554 CLONING ARTIFACT SEQRES 1 B 21 DT DT DC DC DT DA DT DT DG DC DG DC DA SEQRES 2 B 21 DA DT DC DC DA DG DT DT SEQRES 1 D 21 DA DA DA DC DT DG DG DA DT DT DG DC DG SEQRES 2 D 21 DC DA DA DT DA DG DG DA SEQRES 1 A 62 GLY SER ASN SER ASN GLU TYR ARG VAL ARG ARG GLU ARG SEQRES 2 A 62 ASN ASN ILE ALA VAL ARG LYS SER ARG ASP LYS ALA LYS SEQRES 3 A 62 GLN ARG ASN VAL GLU THR GLN GLN LYS VAL LEU GLU LEU SEQRES 4 A 62 THR SER ASP ASN ASP ARG LEU ARG LYS ARG VAL GLU GLN SEQRES 5 A 62 LEU SER ARG GLU LEU ASP THR LEU ARG GLY SEQRES 1 C 62 GLY SER ASN SER ASN GLU TYR ARG VAL ARG ARG GLU ARG SEQRES 2 C 62 ASN ASN ILE ALA VAL ARG LYS SER ARG ASP LYS ALA LYS SEQRES 3 C 62 GLN ARG ASN VAL GLU THR GLN GLN LYS VAL LEU GLU LEU SEQRES 4 C 62 THR SER ASP ASN ASP ARG LEU ARG LYS ARG VAL GLU GLN SEQRES 5 C 62 LEU SER ARG GLU LEU ASP THR LEU ARG GLY FORMUL 5 HOH *34(H2 O) HELIX 1 1 ASN A 281 ARG A 339 1 59 HELIX 2 2 ASN C 281 THR C 337 1 57 CRYST1 140.892 53.089 67.406 90.00 90.00 90.00 P 21 21 2 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 0.007098 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018836 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014835 0.00000