PDB Short entry for 1H89 HEADER TRANSCRIPTION/DNA 30-JAN-01 1H89 TITLE CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAAT/ENHANCER BINDING PROTEIN BETA; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 273-336; COMPND 5 SYNONYM: C/EBP BETA, NFIL-6; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: BZIP DOMAIN; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: MYB PROTO-ONCOGENE PROTEIN; COMPND 10 CHAIN: C; COMPND 11 FRAGMENT: RESIDUES 35-193; COMPND 12 SYNONYM: C-MYB; COMPND 13 ENGINEERED: YES; COMPND 14 MUTATION: YES; COMPND 15 OTHER_DETAILS: DNA BINDING DOMAIN; COMPND 16 MOL_ID: 3; COMPND 17 MOLECULE: DNA(5'-(*GP*AP*TP*GP*TP*GP*GP*CP*GP*CP*AP* COMPND 18 AP*TP*CP*CP*TP*TP*AP*AP*CP*GP*GP*AP*CP*TP*G)-3'); COMPND 19 CHAIN: D; COMPND 20 FRAGMENT: FRAGMENT FROM TOM-1A PROMOTER; COMPND 21 ENGINEERED: YES; COMPND 22 MOL_ID: 4; COMPND 23 MOLECULE: DNA(5'-(*CP*CP*AP*GP*TP*CP*CP*GP*TP*TP*AP* COMPND 24 AP*GP*GP*AP*TP*TP*GP*CP*GP*CP*CP*AP*CP*AP*T)-3'); COMPND 25 CHAIN: E; COMPND 26 FRAGMENT: FRAGMENT FROM TOM-1A PROMOTER; COMPND 27 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PAR2156; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 12 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 13 ORGANISM_TAXID: 10090; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; 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: PAR2156; SOURCE 19 MOL_ID: 3; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 22 ORGANISM_TAXID: 9606; SOURCE 23 MOL_ID: 4; SOURCE 24 SYNTHETIC: YES; SOURCE 25 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 26 ORGANISM_TAXID: 9606 KEYWDS TRANSCRIPTION/DNA, PROTEIN-DNA COMPLEX, TRANSCRIPTION REGULATION, KEYWDS 2 BZIP, PROTO-ONCOGENE, MYB, C-MYB, C/EBP, TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.H.TAHIROV,K.OGATA REVDAT 4 13-DEC-23 1H89 1 LINK REVDAT 3 08-MAY-19 1H89 1 SOURCE REMARK REVDAT 2 24-FEB-09 1H89 1 VERSN REVDAT 1 28-JAN-02 1H89 0 JRNL AUTH T.H.TAHIROV,K.SATO,E.ICHIKAWA-IWATA,M.SASAKI,T.INOUE-BUNGO, JRNL AUTH 2 M.SHIINA,K.KIMURA,S.TAKATA,A.FUJIKAWA,H.MORII,T.KUMASAKA, JRNL AUTH 3 M.YAMAMOTO,S.ISHII,K.OGATA JRNL TITL MECHANISM OF C-MYB-C/EBPBETA COOPERATION FROM SEPARATED JRNL TITL 2 SITES ON A PROMOTER JRNL REF CELL(CAMBRIDGE,MASS.) V. 108 57 2002 JRNL REFN ISSN 0092-8674 JRNL PMID 11792321 JRNL DOI 10.1016/S0092-8674(01)00636-5 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.H.TAHIROV,T.INOUE,M.SASAKI,M.SHIINA,K.KIMURA,K.SATO, REMARK 1 AUTH 2 T.KUMASAKA,M.YAMAMOTO,N.KAMIYA,K.OGATA REMARK 1 TITL CRYSTALS OF TERNARY PROTEIN-DNA COMPLEXES COMPOSED OF REMARK 1 TITL 2 DNA-BINDING DOMAINS C-MYB OR V-MYB, C/EBPALPHA OR C/EBPBETA REMARK 1 TITL 3 AND TOM-1A PROMOTER FRAGMENT REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 57 1655 2001 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 11679735 REMARK 1 DOI 10.1107/S0907444901011982 REMARK 1 REFERENCE 2 REMARK 1 AUTH T.H.TAHIROV,H.MORII,H.UEDAIRA,M.SASAKI,A.SARAI,S.ADACHI, REMARK 1 AUTH 2 S.Y.PARK,N.KAMIYA,K.OGATA REMARK 1 TITL CRYSTAL STRUCTURES OF C-MYB DNA-BINDING DOMAIN IN FREE REMARK 1 TITL 2 STATE: AN EVIDENCE FOR BINDING OF NA+ AND COMPARISON WITH REMARK 1 TITL 3 SOLUTION STRUCTURE RUNT DOMAIN, CBFBETA AND THE C/EBPBETA REMARK 1 TITL 4 BZIP REGION REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 1 REFERENCE 3 REMARK 1 AUTH T.H.TAHIROV,T.INOUE-BUNGO,H.MORII,A.FUJIKAWA,M.SASAKI, REMARK 1 AUTH 2 K.KIMURA,M.SHIINA,K.SATO,T.KUMASAKA,M.YAMAMOTO,S.ISHII, REMARK 1 AUTH 3 K.OGATA REMARK 1 TITL STRUCTURAL ANALYSES OF DNA RECOGNITION BY THE AML1/ RUNX-1 REMARK 1 TITL 2 RUNT DOMAIN AND ITS ALLOSTERIC CONTROL BY CBFBETA REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 104 755 2001 REMARK 1 REFN ISSN 0092-8674 REMARK 1 PMID 11257229 REMARK 1 DOI 10.1016/S0092-8674(01)00271-9 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 979672.690 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 27319 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) : 0.229 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1339 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.60 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3725 REMARK 3 BIN R VALUE (WORKING SET) : 0.4220 REMARK 3 BIN FREE R VALUE : 0.3930 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 213 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.027 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2080 REMARK 3 NUCLEIC ACID ATOMS : 1060 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 123 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 67.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 65.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 12.16000 REMARK 3 B22 (A**2) : 6.54000 REMARK 3 B33 (A**2) : -18.70000 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) : 0.38 REMARK 3 ESD FROM SIGMAA (A) : 0.60 REMARK 3 LOW RESOLUTION CUTOFF (A) : 20.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.45 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.71 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.140 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) : 6.930 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 9.810 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 12.380; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 14.780; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.29 REMARK 3 BSOL : 38.09 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: BULK SOLVENT MODEL USED. ATOMS C, O, N, REMARK 3 CA AND CB ARE HARMONICALLY RESTRAINED DURING REFINEMENT WITH REMARK 3 HARMONIC RESTRAINT CONSTANT OF 100 REMARK 4 REMARK 4 1H89 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-JAN-01. REMARK 100 THE DEPOSITION ID IS D_1290005846. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-NOV-98 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL45XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.04 REMARK 200 MONOCHROMATOR : DIAMOND REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27451 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 7.496 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 27.5043 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.39700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.162 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.851 REMARK 200 STARTING MODEL: 1H88 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M KCL, 0.05 MGSO4, 4% V/V MPD, 6% REMARK 280 V/V GLYCEROL, 0.05 M NA HEPES PH 7.0 AT 24 DEGREES C, PH 7.00, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 297K 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 31.34200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 80.84950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.69150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 80.84950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.34200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.69150 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 300 REMARK: OF C/EBP BETA AND MONOMER OF MYB PROTO- REMARK 300 ONCOGENE PROTEINBOUND TO A DUPLEX DNA FRAGMENTFOR REMARK 300 THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350 THE 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: PENTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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 400 REMARK 400 COMPOUND REMARK 400 CHAIN C ENGINEERED MUTATION LYS35MET, ARG36GLY REMARK 400 C/EBP BETA IS IMPORTANT TRANSCRIPTIONAL ACTIVATOR IN THE REGULATION REMARK 400 OF GENES INVOLVED IN IMMUNE AND INFLAMMATORY RESPONSES. SPECIFICALL 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 MET C 35 REMARK 465 GLY C 36 REMARK 465 HIS C 37 REMARK 465 LEU C 38 REMARK 465 GLY C 39 REMARK 465 LYS C 40 REMARK 465 THR C 41 REMARK 465 ARG C 42 REMARK 465 TRP C 43 REMARK 465 THR C 44 REMARK 465 ARG C 45 REMARK 465 GLU C 46 REMARK 465 GLU C 47 REMARK 465 ASP C 48 REMARK 465 GLU C 49 REMARK 465 LYS C 50 REMARK 465 LEU C 51 REMARK 465 LYS C 52 REMARK 465 LYS C 53 REMARK 465 LEU C 54 REMARK 465 VAL C 55 REMARK 465 GLU C 56 REMARK 465 GLN C 57 REMARK 465 ASN C 58 REMARK 465 GLY C 59 REMARK 465 THR C 60 REMARK 465 ASP C 61 REMARK 465 ASP C 62 REMARK 465 TRP C 63 REMARK 465 LYS C 64 REMARK 465 VAL C 65 REMARK 465 ILE C 66 REMARK 465 ALA C 67 REMARK 465 ASN C 68 REMARK 465 TYR C 69 REMARK 465 LEU C 70 REMARK 465 PRO C 71 REMARK 465 ASN C 72 REMARK 465 ARG C 73 REMARK 465 THR C 74 REMARK 465 ASP C 75 REMARK 465 VAL C 76 REMARK 465 LYS C 192 REMARK 465 VAL C 193 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 DA D 19 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG E 13 N9 - C1' - C2' ANGL. DEV. = 9.0 DEGREES REMARK 500 DG E 13 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG E 20 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC E 24 O4' - C1' - N1 ANGL. DEV. = 2.2 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 274 -63.07 -21.05 REMARK 500 LYS B 332 -0.25 -54.97 REMARK 500 VAL C 85 -79.66 -143.00 REMARK 500 PRO C 88 0.17 -67.57 REMARK 500 ARG C 165 67.26 -101.35 REMARK 500 PRO C 174 -74.22 -27.75 REMARK 500 SER C 187 -105.75 -127.46 REMARK 500 THR C 188 -59.80 -24.51 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 DG D 1 0.06 SIDE CHAIN REMARK 500 DC D 8 0.06 SIDE CHAIN REMARK 500 DC E 19 0.07 SIDE CHAIN REMARK 500 DG E 20 0.05 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K C1192 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 336 OE1 REMARK 620 2 ALA C 119 O 133.8 REMARK 620 3 LEU C 122 O 136.6 73.1 REMARK 620 4 ARG C 125 O 70.7 86.3 80.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K C1193 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA C 170 O REMARK 620 2 LEU C 173 O 66.5 REMARK 620 3 PRO C 174 O 123.9 62.8 REMARK 620 4 ARG C 176 O 81.3 87.0 117.2 REMARK 620 5 HOH C2018 O 167.3 126.1 68.1 96.7 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K C1192 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K C1193 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1H88 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX1 REMARK 900 RELATED ID: 1HJB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RUNX-1/AML1/CBFALPHA RUNT DOMAIN AND C/EBPBETA REMARK 900 BZIP DIMERIC BOUND TO A DNA FRAGMENT FROM THE CSF-1R PROMOTER REMARK 900 RELATED ID: 1IO4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RUNX-1/AML1/CBFALPHA RUNT DOMAIN-CBFBETA CORE REMARK 900 DOMAIN DIMERIC AND C/EBPBETA BZIP DIMERIC BOUND TO A DNA FRAGMENT REMARK 900 FROM THE CSF-1R PROMOTER REMARK 999 REMARK 999 SEQUENCE REMARK 999 LYS 35 WAS REPLACED BY MET AND ARG 36 REMARK 999 WAS REPLACED BY GLY BECAUSE OF EXPRESSION REMARK 999 IN ESCHERICHIA COLI. DBREF 1H89 A 273 336 UNP P17676 CEBB_HUMAN 273 336 DBREF 1H89 B 273 336 UNP P17676 CEBB_HUMAN 273 336 DBREF 1H89 C 35 193 GENP CAA26552 CAA26552 35 193 DBREF 1H89 D 1 26 PDB 1H89 1H89 1 26 DBREF 1H89 E 1 26 PDB 1H89 1H89 1 26 SEQADV 1H89 MET C 35 GENP CAA26552 LYS 35 ENGINEERED MUTATION SEQADV 1H89 GLY C 36 GENP CAA26552 ARG 36 ENGINEERED MUTATION SEQRES 1 A 64 GLU TYR LYS ILE ARG ARG GLU ARG ASN ASN ILE ALA VAL SEQRES 2 A 64 ARG LYS SER ARG ASP LYS ALA LYS MET ARG ASN LEU GLU SEQRES 3 A 64 THR GLN HIS LYS VAL LEU GLU LEU THR ALA GLU ASN GLU SEQRES 4 A 64 ARG LEU GLN LYS LYS VAL GLU GLN LEU SER ARG GLU LEU SEQRES 5 A 64 SER THR LEU ARG ASN LEU PHE LYS GLN LEU PRO GLU SEQRES 1 B 64 GLU TYR LYS ILE ARG ARG GLU ARG ASN ASN ILE ALA VAL SEQRES 2 B 64 ARG LYS SER ARG ASP LYS ALA LYS MET ARG ASN LEU GLU SEQRES 3 B 64 THR GLN HIS LYS VAL LEU GLU LEU THR ALA GLU ASN GLU SEQRES 4 B 64 ARG LEU GLN LYS LYS VAL GLU GLN LEU SER ARG GLU LEU SEQRES 5 B 64 SER THR LEU ARG ASN LEU PHE LYS GLN LEU PRO GLU SEQRES 1 C 159 MET GLY HIS LEU GLY LYS THR ARG TRP THR ARG GLU GLU SEQRES 2 C 159 ASP GLU LYS LEU LYS LYS LEU VAL GLU GLN ASN GLY THR SEQRES 3 C 159 ASP ASP TRP LYS VAL ILE ALA ASN TYR LEU PRO ASN ARG SEQRES 4 C 159 THR ASP VAL GLN CYS GLN HIS ARG TRP GLN LYS VAL LEU SEQRES 5 C 159 ASN PRO GLU LEU ILE LYS GLY PRO TRP THR LYS GLU GLU SEQRES 6 C 159 ASP GLN ARG VAL ILE LYS LEU VAL GLN LYS TYR GLY PRO SEQRES 7 C 159 LYS ARG TRP SER VAL ILE ALA LYS HIS LEU LYS GLY ARG SEQRES 8 C 159 ILE GLY LYS GLN CYS ARG GLU ARG TRP HIS ASN HIS LEU SEQRES 9 C 159 ASN PRO GLU VAL LYS LYS THR SER TRP THR GLU GLU GLU SEQRES 10 C 159 ASP ARG ILE ILE TYR GLN ALA HIS LYS ARG LEU GLY ASN SEQRES 11 C 159 ARG TRP ALA GLU ILE ALA LYS LEU LEU PRO GLY ARG THR SEQRES 12 C 159 ASP ASN ALA ILE LYS ASN HIS TRP ASN SER THR MET ARG SEQRES 13 C 159 ARG LYS VAL SEQRES 1 D 26 DG DA DT DG DT DG DG DC DG DC DA DA DT SEQRES 2 D 26 DC DC DT DT DA DA DC DG DG DA DC DT DG SEQRES 1 E 26 DC DC DA DG DT DC DC DG DT DT DA DA DG SEQRES 2 E 26 DG DA DT DT DG DC DG DC DC DA DC DA DT HET K C1192 1 HET K C1193 1 HETNAM K POTASSIUM ION FORMUL 6 K 2(K 1+) FORMUL 8 HOH *123(H2 O) HELIX 1 1 GLU A 273 GLN A 333 1 61 HELIX 2 2 GLU B 273 LYS B 332 1 60 HELIX 3 3 GLN C 77 LYS C 84 1 8 HELIX 4 4 THR C 96 GLY C 111 1 16 HELIX 5 5 ARG C 114 HIS C 121 1 8 HELIX 6 6 ILE C 126 HIS C 137 1 12 HELIX 7 7 THR C 148 GLY C 163 1 16 HELIX 8 8 ARG C 165 LYS C 171 1 7 HELIX 9 9 THR C 177 SER C 187 1 11 LINK OE1 GLU B 336 K K C1192 2765 1555 2.51 LINK O ALA C 119 K K C1192 1555 1555 2.61 LINK O LEU C 122 K K C1192 1555 1555 2.53 LINK O ARG C 125 K K C1192 1555 1555 2.83 LINK O ALA C 170 K K C1193 1555 1555 2.99 LINK O LEU C 173 K K C1193 1555 1555 2.71 LINK O PRO C 174 K K C1193 1555 1555 3.19 LINK O ARG C 176 K K C1193 1555 1555 2.98 LINK K K C1193 O HOH C2018 1555 1555 3.45 SITE 1 AC1 4 GLU B 336 ALA C 119 LEU C 122 ARG C 125 SITE 1 AC2 4 ALA C 170 LEU C 173 PRO C 174 ARG C 176 CRYST1 62.684 73.383 161.699 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 0.015953 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013627 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006184 0.00000