PDB Short entry for 1H9D HEADER TRANSCRIPTION FACTOR 07-MAR-01 1H9D TITLE AML1/CBF-BETA/DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: CORE-BINDING FACTOR ALPHA SUBUNIT1; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: RUNT DOMAIN RESIDUES 50-183; COMPND 5 SYNONYM: CBFA2/PEPBP2AB/RUNX1, AML-1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: CORE-BINDING FACTOR CBF-BETA; COMPND 9 CHAIN: B, D; COMPND 10 FRAGMENT: HETERODIMERISATION DOMAIN RESIDUES 2-135; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-(*GP*TP*TP*GP*CP*GP*GP*TP*TP*G)-3'); COMPND 14 CHAIN: E, G; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DNA (5'-(*CP*AP*AP*CP*CP*GP*CP*AP*AP*C)-3'); COMPND 18 CHAIN: F, H; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: AML1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: C41; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PRSET; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: CBFB; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_VARIANT: C41; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PRSET; SOURCE 21 MOL_ID: 3; SOURCE 22 SYNTHETIC: YES; SOURCE 23 MOL_ID: 4; SOURCE 24 SYNTHETIC: YES KEYWDS TRANSCRIPTION FACTOR EXPDTA X-RAY DIFFRACTION AUTHOR J.BRAVO,A.J.WARREN REVDAT 7 13-DEC-23 1H9D 1 REMARK REVDAT 6 24-JAN-18 1H9D 1 SOURCE REMARK REVDAT 5 24-FEB-09 1H9D 1 VERSN REVDAT 4 05-MAR-03 1H9D 1 REMARK HETATM REVDAT 3 02-JUL-02 1H9D 1 ATOM REVDAT 2 16-AUG-01 1H9D 1 REMARK SHEET MASTER REVDAT 1 31-MAR-01 1H9D 0 JRNL AUTH J.BRAVO,Z.LI,N.A.SPECK,A.J.WARREN JRNL TITL THE LEUKEMIA-ASSOCIATED AML1 (RUNX1)-CBFBETA COMPLEX JRNL TITL 2 FUNCTIONS AS A DNA-INDUCED MOLECULAR CLAMP JRNL REF NAT.STRUCT.BIOL. V. 8 371 2001 JRNL REFN ISSN 1072-8368 JRNL PMID 11276260 JRNL DOI 10.1038/86264 REMARK 2 REMARK 2 RESOLUTION. 2.60 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.02 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1104447.410 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 27926 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) : 0.237 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2272 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4174 REMARK 3 BIN R VALUE (WORKING SET) : 0.3600 REMARK 3 BIN FREE R VALUE : 0.4070 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 367 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.021 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4003 REMARK 3 NUCLEIC ACID ATOMS : 808 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 56 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 60.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.93000 REMARK 3 B22 (A**2) : 8.93000 REMARK 3 B33 (A**2) : -17.85000 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) : 0.36 REMARK 3 ESD FROM SIGMAA (A) : 0.39 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) : 0.44 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.44 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 BOND ANGLES (DEGREES) : 1.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.540 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) : 1.210 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.090 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.820 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.750 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 44.39 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 : NULL REMARK 3 TOPOLOGY FILE 1 : &_1_TOPOLOGY_INFILE_1 REMARK 3 TOPOLOGY FILE 2 : &_1_TOPOLOGY_INFILE_2 REMARK 3 TOPOLOGY FILE 3 : &_1_TOPOLOGY_INFILE_3 REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1H9D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-MAR-01. REMARK 100 THE DEPOSITION ID IS D_1290005776. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-00 REMARK 200 TEMPERATURE (KELVIN) : 110.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9366 REMARK 200 MONOCHROMATOR : DIAMOND (111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27926 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.38000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 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 1E50 REMARK 200 REMARK 200 REMARK: ON HOLD REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -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 -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 66.96250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 57.51650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 57.51650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 100.44375 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 57.51650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 57.51650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 33.48125 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 57.51650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 57.51650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 100.44375 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 57.51650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 57.51650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 33.48125 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 66.96250 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 4800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 4830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.5 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, G, H 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 SER A 50 REMARK 465 MET A 51 REMARK 465 VAL A 52 REMARK 465 GLU A 53 REMARK 465 HIS A 179 REMARK 465 ARG A 180 REMARK 465 GLN A 181 REMARK 465 LYS A 182 REMARK 465 LEU A 183 REMARK 465 ALA B 71 REMARK 465 SER B 72 REMARK 465 TRP B 73 REMARK 465 GLN B 74 REMARK 465 GLY B 75 REMARK 465 GLU B 76 REMARK 465 GLN B 77 REMARK 465 ARG B 78 REMARK 465 GLN B 79 REMARK 465 SER C 50 REMARK 465 MET C 51 REMARK 465 VAL C 52 REMARK 465 GLU C 53 REMARK 465 HIS C 179 REMARK 465 ARG C 180 REMARK 465 GLN C 181 REMARK 465 LYS C 182 REMARK 465 LEU C 183 REMARK 465 GLY D 75 REMARK 465 GLU D 76 REMARK 465 GLN D 77 REMARK 465 ARG D 78 REMARK 465 GLN D 79 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 VAL A 54 CG1 CG2 REMARK 470 LEU A 55 CG CD1 CD2 REMARK 470 ASP A 57 CG OD1 OD2 REMARK 470 ARG A 178 CG CD NE CZ NH1 NH2 REMARK 470 VAL C 54 CG1 CG2 REMARK 470 LEU C 55 CG CD1 CD2 REMARK 470 ASP C 57 CG OD1 OD2 REMARK 470 ARG C 178 CG CD NE CZ NH1 NH2 REMARK 470 TRP D 73 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP D 73 CZ3 CH2 REMARK 470 GLN D 74 CG CD OE1 NE2 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 VAL A 54 REMARK 475 LEU A 55 REMARK 475 ALA A 56 REMARK 475 ARG A 178 REMARK 475 VAL C 54 REMARK 475 LEU C 55 REMARK 475 ARG C 178 REMARK 475 TRP D 73 REMARK 475 GLN D 74 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 N1 DA H 8 O HOH H 2002 2.14 REMARK 500 OH TYR C 113 NH1 ARG D 33 2.14 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 CYS A 81 CB CYS A 81 SG -0.110 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 DT E 2 O5' - P - OP1 ANGL. DEV. = -5.8 DEGREES REMARK 500 DC F 1 O5' - C5' - C4' ANGL. DEV. = -5.2 DEGREES REMARK 500 DA F 3 N9 - C1' - C2' ANGL. DEV. = -11.7 DEGREES REMARK 500 DC F 7 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC G 5 N1 - C1' - C2' ANGL. DEV. = 9.3 DEGREES REMARK 500 DC G 5 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DA H 3 C4' - C3' - O3' ANGL. DEV. = 12.3 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 ALA A 56 114.02 74.27 REMARK 500 ASP A 57 86.13 152.38 REMARK 500 HIS A 58 -21.35 -148.17 REMARK 500 LEU A 94 -72.22 -79.05 REMARK 500 ARG A 142 139.00 -39.79 REMARK 500 PHE B 32 50.36 36.18 REMARK 500 GLU B 89 -79.00 -72.04 REMARK 500 ARG B 90 -54.73 3.15 REMARK 500 ALA C 56 110.32 71.94 REMARK 500 ASP C 57 87.87 156.30 REMARK 500 HIS C 58 -26.19 -149.27 REMARK 500 ASP C 66 0.94 -68.25 REMARK 500 ASN C 109 -176.98 -173.37 REMARK 500 ALA C 120 36.31 -86.70 REMARK 500 SER D 72 108.36 103.08 REMARK 500 GLU D 89 -77.93 -73.84 REMARK 500 ARG D 90 -53.97 4.04 REMARK 500 LEU D 116 -5.08 -59.23 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 F 4 0.09 SIDE CHAIN REMARK 500 DG F 6 0.06 SIDE CHAIN REMARK 500 DC F 10 0.07 SIDE CHAIN REMARK 500 DG G 1 0.05 SIDE CHAIN REMARK 500 DC H 4 0.12 SIDE CHAIN REMARK 500 DA H 8 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CMO RELATED DB: PDB REMARK 900 IMMUNOGLOBULIN MOTIF DEOXYRIBONUCLEIC ACID- RECOGNITION AND REMARK 900 HETERODIMERIZATION FOR THE PEBP2/CBF RUNT-DOMAIN REMARK 900 RELATED ID: 1CO1 RELATED DB: PDB REMARK 900 FOLD OF THE CBFA REMARK 900 RELATED ID: 1E50 RELATED DB: PDB REMARK 900 AML1/CBF-BETA COMPLEX REMARK 900 RELATED ID: 1CL3 RELATED DB: PDB REMARK 900 MOLECULAR INSIGHTS INTO PEBP2/CBF-SMMHC ASSOCIATED ACUTE LEUKEMIA REMARK 900 REVEALED FROM THE THREE-DIMENSIONAL STRUCTURE OF PEBP2/CBF BETA DBREF 1H9D A 50 183 UNP Q01196 AML1_HUMAN 50 183 DBREF 1H9D B 2 135 UNP Q13951 PEBB_HUMAN 2 135 DBREF 1H9D C 50 183 UNP Q01196 AML1_HUMAN 50 183 DBREF 1H9D D 2 135 UNP Q13951 PEBB_HUMAN 2 135 DBREF 1H9D E 1 10 PDB 1H9D 1H9D 1 10 DBREF 1H9D F 1 10 PDB 1H9D 1H9D 1 10 DBREF 1H9D G 1 10 PDB 1H9D 1H9D 1 10 DBREF 1H9D H 1 10 PDB 1H9D 1H9D 1 10 SEQRES 1 A 134 SER MET VAL GLU VAL LEU ALA ASP HIS PRO GLY GLU LEU SEQRES 2 A 134 VAL ARG THR ASP SER PRO ASN PHE LEU CYS SER VAL LEU SEQRES 3 A 134 PRO THR HIS TRP ARG CYS ASN LYS THR LEU PRO ILE ALA SEQRES 4 A 134 PHE LYS VAL VAL ALA LEU GLY ASP VAL PRO ASP GLY THR SEQRES 5 A 134 LEU VAL THR VAL MET ALA GLY ASN ASP GLU ASN TYR SER SEQRES 6 A 134 ALA GLU LEU ARG ASN ALA THR ALA ALA MET LYS ASN GLN SEQRES 7 A 134 VAL ALA ARG PHE ASN ASP LEU ARG PHE VAL GLY ARG SER SEQRES 8 A 134 GLY ARG GLY LYS SER PHE THR LEU THR ILE THR VAL PHE SEQRES 9 A 134 THR ASN PRO PRO GLN VAL ALA THR TYR HIS ARG ALA ILE SEQRES 10 A 134 LYS ILE THR VAL ASP GLY PRO ARG GLU PRO ARG ARG HIS SEQRES 11 A 134 ARG GLN LYS LEU SEQRES 1 B 134 PRO ARG VAL VAL PRO ASP GLN ARG SER LYS PHE GLU ASN SEQRES 2 B 134 GLU GLU PHE PHE ARG LYS LEU SER ARG GLU CYS GLU ILE SEQRES 3 B 134 LYS TYR THR GLY PHE ARG ASP ARG PRO HIS GLU GLU ARG SEQRES 4 B 134 GLN ALA ARG PHE GLN ASN ALA CYS ARG ASP GLY ARG SER SEQRES 5 B 134 GLU ILE ALA PHE VAL ALA THR GLY THR ASN LEU SER LEU SEQRES 6 B 134 GLN PHE PHE PRO ALA SER TRP GLN GLY GLU GLN ARG GLN SEQRES 7 B 134 THR PRO SER ARG GLU TYR VAL ASP LEU GLU ARG GLU ALA SEQRES 8 B 134 GLY LYS VAL TYR LEU LYS ALA PRO MET ILE LEU ASN GLY SEQRES 9 B 134 VAL CYS VAL ILE TRP LYS GLY TRP ILE ASP LEU GLN ARG SEQRES 10 B 134 LEU ASP GLY MET GLY CYS LEU GLU PHE ASP GLU GLU ARG SEQRES 11 B 134 ALA GLN GLN GLU SEQRES 1 C 134 SER MET VAL GLU VAL LEU ALA ASP HIS PRO GLY GLU LEU SEQRES 2 C 134 VAL ARG THR ASP SER PRO ASN PHE LEU CYS SER VAL LEU SEQRES 3 C 134 PRO THR HIS TRP ARG CYS ASN LYS THR LEU PRO ILE ALA SEQRES 4 C 134 PHE LYS VAL VAL ALA LEU GLY ASP VAL PRO ASP GLY THR SEQRES 5 C 134 LEU VAL THR VAL MET ALA GLY ASN ASP GLU ASN TYR SER SEQRES 6 C 134 ALA GLU LEU ARG ASN ALA THR ALA ALA MET LYS ASN GLN SEQRES 7 C 134 VAL ALA ARG PHE ASN ASP LEU ARG PHE VAL GLY ARG SER SEQRES 8 C 134 GLY ARG GLY LYS SER PHE THR LEU THR ILE THR VAL PHE SEQRES 9 C 134 THR ASN PRO PRO GLN VAL ALA THR TYR HIS ARG ALA ILE SEQRES 10 C 134 LYS ILE THR VAL ASP GLY PRO ARG GLU PRO ARG ARG HIS SEQRES 11 C 134 ARG GLN LYS LEU SEQRES 1 D 134 PRO ARG VAL VAL PRO ASP GLN ARG SER LYS PHE GLU ASN SEQRES 2 D 134 GLU GLU PHE PHE ARG LYS LEU SER ARG GLU CYS GLU ILE SEQRES 3 D 134 LYS TYR THR GLY PHE ARG ASP ARG PRO HIS GLU GLU ARG SEQRES 4 D 134 GLN ALA ARG PHE GLN ASN ALA CYS ARG ASP GLY ARG SER SEQRES 5 D 134 GLU ILE ALA PHE VAL ALA THR GLY THR ASN LEU SER LEU SEQRES 6 D 134 GLN PHE PHE PRO ALA SER TRP GLN GLY GLU GLN ARG GLN SEQRES 7 D 134 THR PRO SER ARG GLU TYR VAL ASP LEU GLU ARG GLU ALA SEQRES 8 D 134 GLY LYS VAL TYR LEU LYS ALA PRO MET ILE LEU ASN GLY SEQRES 9 D 134 VAL CYS VAL ILE TRP LYS GLY TRP ILE ASP LEU GLN ARG SEQRES 10 D 134 LEU ASP GLY MET GLY CYS LEU GLU PHE ASP GLU GLU ARG SEQRES 11 D 134 ALA GLN GLN GLU SEQRES 1 E 10 DG DT DT DG DC DG DG DT DT DG SEQRES 1 F 10 DC DA DA DC DC DG DC DA DA DC SEQRES 1 G 10 DG DT DT DG DC DG DG DT DT DG SEQRES 1 H 10 DC DA DA DC DC DG DC DA DA DC FORMUL 9 HOH *56(H2 O) HELIX 1 1 ASP B 7 GLU B 15 1 9 HELIX 2 2 GLU B 15 LYS B 20 1 6 HELIX 3 3 PRO B 36 ASP B 50 1 15 HELIX 4 4 ASP B 128 GLU B 135 1 8 HELIX 5 5 ASP D 7 GLU D 15 1 9 HELIX 6 6 GLU D 15 ARG D 23 1 9 HELIX 7 7 PRO D 36 ASP D 50 1 15 HELIX 8 8 ASP D 128 GLU D 135 1 8 SHEET 1 AA 9 LEU A 62 ARG A 64 0 SHEET 2 AA 9 PHE A 70 SER A 73 -1 O CYS A 72 N VAL A 63 SHEET 3 AA 9 LYS A 90 ALA A 93 -1 O LYS A 90 N SER A 73 SHEET 4 AA 9 VAL A 128 ARG A 130 -1 O ALA A 129 N VAL A 91 SHEET 5 AA 9 THR A 121 LYS A 125 -1 O ALA A 123 N ARG A 130 SHEET 6 AA 9 LEU A 102 GLY A 108 -1 O VAL A 103 N ALA A 122 SHEET 7 AA 9 PHE A 146 VAL A 152 -1 O THR A 147 N GLY A 108 SHEET 8 AA 9 GLN A 158 THR A 169 -1 O GLN A 158 N VAL A 152 SHEET 9 AA 9 HIS A 78 ARG A 80 1 O TRP A 79 N THR A 169 SHEET 1 AB 9 LEU A 62 ARG A 64 0 SHEET 2 AB 9 PHE A 70 SER A 73 -1 O CYS A 72 N VAL A 63 SHEET 3 AB 9 LYS A 90 ALA A 93 -1 O LYS A 90 N SER A 73 SHEET 4 AB 9 VAL A 128 ARG A 130 -1 O ALA A 129 N VAL A 91 SHEET 5 AB 9 THR A 121 LYS A 125 -1 O ALA A 123 N ARG A 130 SHEET 6 AB 9 LEU A 102 GLY A 108 -1 O VAL A 103 N ALA A 122 SHEET 7 AB 9 PHE A 146 VAL A 152 -1 O THR A 147 N GLY A 108 SHEET 8 AB 9 GLN A 158 THR A 169 -1 O GLN A 158 N VAL A 152 SHEET 9 AB 9 LYS B 94 LEU B 103 1 O ILE B 102 N VAL A 159 SHEET 1 AC 2 LEU A 117 ARG A 118 0 SHEET 2 AC 2 ARG A 135 PHE A 136 -1 O ARG A 135 N ARG A 118 SHEET 1 CA 9 LEU C 62 ARG C 64 0 SHEET 2 CA 9 PHE C 70 SER C 73 -1 O CYS C 72 N VAL C 63 SHEET 3 CA 9 LYS C 90 ALA C 93 -1 O LYS C 90 N SER C 73 SHEET 4 CA 9 VAL C 128 ARG C 130 -1 O ALA C 129 N VAL C 91 SHEET 5 CA 9 THR C 121 LYS C 125 -1 O ALA C 123 N ARG C 130 SHEET 6 CA 9 LEU C 102 GLY C 108 -1 O VAL C 103 N ALA C 122 SHEET 7 CA 9 PHE C 146 VAL C 152 -1 O THR C 147 N GLY C 108 SHEET 8 CA 9 GLN C 158 THR C 169 -1 O GLN C 158 N VAL C 152 SHEET 9 CA 9 HIS C 78 ARG C 80 1 O TRP C 79 N THR C 169 SHEET 1 CB 9 LEU C 62 ARG C 64 0 SHEET 2 CB 9 PHE C 70 SER C 73 -1 O CYS C 72 N VAL C 63 SHEET 3 CB 9 LYS C 90 ALA C 93 -1 O LYS C 90 N SER C 73 SHEET 4 CB 9 VAL C 128 ARG C 130 -1 O ALA C 129 N VAL C 91 SHEET 5 CB 9 THR C 121 LYS C 125 -1 O ALA C 123 N ARG C 130 SHEET 6 CB 9 LEU C 102 GLY C 108 -1 O VAL C 103 N ALA C 122 SHEET 7 CB 9 PHE C 146 VAL C 152 -1 O THR C 147 N GLY C 108 SHEET 8 CB 9 GLN C 158 THR C 169 -1 O GLN C 158 N VAL C 152 SHEET 9 CB 9 LYS D 94 LEU D 103 1 O ILE D 102 N VAL C 159 SHEET 1 CC 2 LEU C 117 ARG C 118 0 SHEET 2 CC 2 ARG C 135 PHE C 136 -1 O ARG C 135 N ARG C 118 CISPEP 1 ASN A 155 PRO A 156 0 -0.15 CISPEP 2 ASN C 155 PRO C 156 0 -0.31 CRYST1 115.033 115.033 133.925 90.00 90.00 90.00 P 43 21 2 16 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 0.008693 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008693 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007467 0.00000