HEADER TRANSCRIPTION/DNA 22-FEB-10 2X6V TITLE CRYSTAL STRUCTURE OF HUMAN TBX5 IN THE DNA-BOUND AND DNA-FREE FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: T-BOX TRANSCRIPTION FACTOR TBX5; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: T-BOX DOMAIN, RESIDUES 51-251; COMPND 5 SYNONYM: T-BOX PROTEIN 5, HUMAN TBX5; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP)-3'; COMPND 9 CHAIN: C; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: 5'-D(*TP*AP*AP*GP*GP*TP*GP*TP*GP*AP*GP)-3'; COMPND 13 CHAIN: D; COMPND 14 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_PLASMID: PPROX HTB; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630 KEYWDS TRANSCRIPTION-DNA COMPLEX, HOLT-ORAM-SYNDROME, DEVELOPMENTAL PROTEIN, KEYWDS 2 TRANSCRIPTION REGULATION, REPRESSOR, DNA-BINDING, TRANSCRIPTION, KEYWDS 3 NUCLEAR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.PTCHELKINE,C.U.STIRNIMANN,C.GRIMM,C.W.MUELLER REVDAT 3 20-DEC-23 2X6V 1 REMARK LINK REVDAT 2 24-NOV-10 2X6V 1 JRNL REMARK REVDAT 1 28-APR-10 2X6V 0 JRNL AUTH C.U.STIRNIMANN,D.PTCHELKINE,C.GRIMM,C.W.MULLER JRNL TITL STRUCTURAL BASIS OF TBX5-DNA RECOGNITION: THE T-BOX DOMAIN JRNL TITL 2 IN ITS DNA-BOUND AND -UNBOUND FORM. JRNL REF J.MOL.BIOL. V. 400 71 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20450920 JRNL DOI 10.1016/J.JMB.2010.04.052 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 51040 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2553 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 19.7074 - 5.7209 0.92 2752 145 0.1862 0.2234 REMARK 3 2 5.7209 - 4.5593 0.99 2798 148 0.1529 0.1753 REMARK 3 3 4.5593 - 3.9884 1.00 2778 146 0.1528 0.1625 REMARK 3 4 3.9884 - 3.6262 1.00 2756 145 0.1645 0.1760 REMARK 3 5 3.6262 - 3.3677 1.00 2718 143 0.1698 0.1956 REMARK 3 6 3.3677 - 3.1700 1.00 2722 143 0.1837 0.2167 REMARK 3 7 3.1700 - 3.0118 1.00 2696 142 0.2025 0.2816 REMARK 3 8 3.0118 - 2.8811 1.00 2701 142 0.2175 0.2519 REMARK 3 9 2.8811 - 2.7705 1.00 2699 142 0.2033 0.2301 REMARK 3 10 2.7705 - 2.6752 1.00 2673 141 0.2099 0.2620 REMARK 3 11 2.6752 - 2.5917 1.00 2685 141 0.2026 0.2219 REMARK 3 12 2.5917 - 2.5178 1.00 2681 142 0.2104 0.2456 REMARK 3 13 2.5178 - 2.4516 1.00 2684 141 0.2016 0.2511 REMARK 3 14 2.4516 - 2.3919 1.00 2672 140 0.2113 0.2361 REMARK 3 15 2.3919 - 2.3376 1.00 2665 141 0.2321 0.2780 REMARK 3 16 2.3376 - 2.2880 1.00 2663 140 0.2566 0.2588 REMARK 3 17 2.2880 - 2.2423 1.00 2678 141 0.2535 0.3060 REMARK 3 18 2.2423 - 2.2000 0.94 2466 130 0.2664 0.2968 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 63.06 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.580 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.14970 REMARK 3 B22 (A**2) : -2.14970 REMARK 3 B33 (A**2) : 4.29940 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 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 : 0.009 3534 REMARK 3 ANGLE : 1.261 4870 REMARK 3 CHIRALITY : 0.072 523 REMARK 3 PLANARITY : 0.005 543 REMARK 3 DIHEDRAL : 19.791 1347 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2X6V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-FEB-10. REMARK 100 THE DEPOSITION ID IS D_1290043001. 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 : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51044 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.43000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1H6F REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 5.6, 0.2 M MGCL2, 0.2 M REMARK 280 NACL, 5% PEG 6K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 81.00000 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 162.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 121.50000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 202.50000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 40.50000 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 81.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 162.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 202.50000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 121.50000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 40.50000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.5 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, 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 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 49 REMARK 465 ALA A 50 REMARK 465 MET A 51 REMARK 465 GLU A 52 REMARK 465 GLU A 190 REMARK 465 ASN A 191 REMARK 465 ASN A 192 REMARK 465 GLY A 193 REMARK 465 PHE A 194 REMARK 465 GLY A 195 REMARK 465 SER A 196 REMARK 465 LYS A 197 REMARK 465 ASN A 198 REMARK 465 SER A 239 REMARK 465 ASP A 240 REMARK 465 ASP A 241 REMARK 465 MET A 242 REMARK 465 GLU A 243 REMARK 465 LEU A 244 REMARK 465 HIS A 245 REMARK 465 ARG A 246 REMARK 465 MET A 247 REMARK 465 SER A 248 REMARK 465 ARG A 249 REMARK 465 MET A 250 REMARK 465 GLN A 251 REMARK 465 GLY B 49 REMARK 465 ALA B 50 REMARK 465 MET B 51 REMARK 465 GLU B 190 REMARK 465 ASN B 191 REMARK 465 ASN B 192 REMARK 465 GLY B 193 REMARK 465 PHE B 194 REMARK 465 GLY B 195 REMARK 465 SER B 196 REMARK 465 LYS B 197 REMARK 465 ASN B 198 REMARK 465 ALA B 233 REMARK 465 LYS B 234 REMARK 465 GLY B 235 REMARK 465 PHE B 236 REMARK 465 ARG B 237 REMARK 465 GLY B 238 REMARK 465 SER B 239 REMARK 465 ASP B 240 REMARK 465 ASP B 241 REMARK 465 MET B 242 REMARK 465 GLU B 243 REMARK 465 LEU B 244 REMARK 465 HIS B 245 REMARK 465 ARG B 246 REMARK 465 MET B 247 REMARK 465 SER B 248 REMARK 465 ARG B 249 REMARK 465 MET B 250 REMARK 465 GLN B 251 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 DT C 1 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DT C 1 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT C 1 C7 C6 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 55 CE NZ REMARK 480 GLU A 69 CD OE1 OE2 REMARK 480 LYS A 115 CD CE NZ REMARK 480 LYS A 126 NZ REMARK 480 GLU B 69 CD REMARK 480 LYS B 115 CD CE NZ 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 C 2 O4' - C1' - N1 ANGL. DEV. = -4.7 DEGREES REMARK 500 DT C 3 O4' - C1' - N1 ANGL. DEV. = -4.8 DEGREES REMARK 500 DC C 4 O4' - C1' - N1 ANGL. DEV. = -6.1 DEGREES REMARK 500 DA C 5 O4' - C1' - N9 ANGL. DEV. = -5.9 DEGREES REMARK 500 DA C 7 O4' - C1' - N9 ANGL. DEV. = -5.2 DEGREES REMARK 500 DC C 9 O4' - C4' - C3' ANGL. DEV. = -3.0 DEGREES REMARK 500 DC C 9 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 DC C 9 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DT C 10 O4' - C1' - N1 ANGL. DEV. = -4.9 DEGREES REMARK 500 DT D 12 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG D 15 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT D 19 O4' - C1' - N1 ANGL. DEV. = -5.0 DEGREES REMARK 500 DG D 22 O4' - C1' - N9 ANGL. DEV. = 3.1 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 THR A 124 -1.75 -145.12 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 MG A1239 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 60 OE1 REMARK 620 2 SER A 86 O 123.4 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1239 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1233 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PE4 B 1234 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2X6U RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN TBX5 IN THE DNA -FREE FORM DBREF 2X6V A 49 50 PDB 2X6V 2X6V 49 50 DBREF 2X6V A 51 251 UNP Q99593 TBX5_HUMAN 51 251 DBREF 2X6V B 49 50 PDB 2X6V 2X6V 49 50 DBREF 2X6V B 51 251 UNP Q99593 TBX5_HUMAN 51 251 DBREF 2X6V C 1 11 PDB 2X6V 2X6V 1 11 DBREF 2X6V D 12 22 PDB 2X6V 2X6V 12 22 SEQRES 1 A 203 GLY ALA MET GLU GLY ILE LYS VAL PHE LEU HIS GLU ARG SEQRES 2 A 203 GLU LEU TRP LEU LYS PHE HIS GLU VAL GLY THR GLU MET SEQRES 3 A 203 ILE ILE THR LYS ALA GLY ARG ARG MET PHE PRO SER TYR SEQRES 4 A 203 LYS VAL LYS VAL THR GLY LEU ASN PRO LYS THR LYS TYR SEQRES 5 A 203 ILE LEU LEU MET ASP ILE VAL PRO ALA ASP ASP HIS ARG SEQRES 6 A 203 TYR LYS PHE ALA ASP ASN LYS TRP SER VAL THR GLY LYS SEQRES 7 A 203 ALA GLU PRO ALA MET PRO GLY ARG LEU TYR VAL HIS PRO SEQRES 8 A 203 ASP SER PRO ALA THR GLY ALA HIS TRP MET ARG GLN LEU SEQRES 9 A 203 VAL SER PHE GLN LYS LEU LYS LEU THR ASN ASN HIS LEU SEQRES 10 A 203 ASP PRO PHE GLY HIS ILE ILE LEU ASN SER MET HIS LYS SEQRES 11 A 203 TYR GLN PRO ARG LEU HIS ILE VAL LYS ALA ASP GLU ASN SEQRES 12 A 203 ASN GLY PHE GLY SER LYS ASN THR ALA PHE CYS THR HIS SEQRES 13 A 203 VAL PHE PRO GLU THR ALA PHE ILE ALA VAL THR SER TYR SEQRES 14 A 203 GLN ASN HIS LYS ILE THR GLN LEU LYS ILE GLU ASN ASN SEQRES 15 A 203 PRO PHE ALA LYS GLY PHE ARG GLY SER ASP ASP MET GLU SEQRES 16 A 203 LEU HIS ARG MET SER ARG MET GLN SEQRES 1 B 203 GLY ALA MET GLU GLY ILE LYS VAL PHE LEU HIS GLU ARG SEQRES 2 B 203 GLU LEU TRP LEU LYS PHE HIS GLU VAL GLY THR GLU MET SEQRES 3 B 203 ILE ILE THR LYS ALA GLY ARG ARG MET PHE PRO SER TYR SEQRES 4 B 203 LYS VAL LYS VAL THR GLY LEU ASN PRO LYS THR LYS TYR SEQRES 5 B 203 ILE LEU LEU MET ASP ILE VAL PRO ALA ASP ASP HIS ARG SEQRES 6 B 203 TYR LYS PHE ALA ASP ASN LYS TRP SER VAL THR GLY LYS SEQRES 7 B 203 ALA GLU PRO ALA MET PRO GLY ARG LEU TYR VAL HIS PRO SEQRES 8 B 203 ASP SER PRO ALA THR GLY ALA HIS TRP MET ARG GLN LEU SEQRES 9 B 203 VAL SER PHE GLN LYS LEU LYS LEU THR ASN ASN HIS LEU SEQRES 10 B 203 ASP PRO PHE GLY HIS ILE ILE LEU ASN SER MET HIS LYS SEQRES 11 B 203 TYR GLN PRO ARG LEU HIS ILE VAL LYS ALA ASP GLU ASN SEQRES 12 B 203 ASN GLY PHE GLY SER LYS ASN THR ALA PHE CYS THR HIS SEQRES 13 B 203 VAL PHE PRO GLU THR ALA PHE ILE ALA VAL THR SER TYR SEQRES 14 B 203 GLN ASN HIS LYS ILE THR GLN LEU LYS ILE GLU ASN ASN SEQRES 15 B 203 PRO PHE ALA LYS GLY PHE ARG GLY SER ASP ASP MET GLU SEQRES 16 B 203 LEU HIS ARG MET SER ARG MET GLN SEQRES 1 C 11 DT DC DT DC DA DC DA DC DC DT DT SEQRES 1 D 11 DT DA DA DG DG DT DG DT DG DA DG HET MG A1239 1 HET MG B1233 1 HET PE4 B1234 24 HETNAM MG MAGNESIUM ION HETNAM PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}- HETNAM 2 PE4 ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL HETSYN PE4 POLYETHYLENE GLYCOL PEG4000 FORMUL 5 MG 2(MG 2+) FORMUL 7 PE4 C16 H34 O8 FORMUL 8 HOH *368(H2 O) HELIX 1 1 GLU A 60 GLY A 71 1 12 HELIX 2 2 GLY A 145 GLN A 151 1 7 HELIX 3 3 PRO A 207 ALA A 210 5 4 HELIX 4 4 ASN A 219 ASN A 230 1 12 HELIX 5 5 PRO A 231 ARG A 237 5 7 HELIX 6 6 GLU B 60 GLY B 71 1 12 HELIX 7 7 GLY B 145 GLN B 151 1 7 HELIX 8 8 PHE B 206 ALA B 210 5 5 HELIX 9 9 ASN B 219 ASN B 230 1 12 SHEET 1 AA 3 LYS A 55 LEU A 58 0 SHEET 2 AA 3 LYS A 88 THR A 92 -1 O LYS A 90 N PHE A 57 SHEET 3 AA 3 VAL A 153 SER A 154 -1 O VAL A 153 N VAL A 89 SHEET 1 AB 8 GLU A 73 ILE A 75 0 SHEET 2 AB 8 PHE A 211 VAL A 214 1 O ILE A 212 N MET A 74 SHEET 3 AB 8 LYS A 178 VAL A 186 -1 O TYR A 179 N PHE A 211 SHEET 4 AB 8 ALA A 200 VAL A 205 -1 O CYS A 202 N ILE A 185 SHEET 5 AB 8 ALA B 200 HIS B 204 -1 O PHE B 201 N THR A 203 SHEET 6 AB 8 LYS B 178 LYS B 187 -1 O LEU B 183 N HIS B 204 SHEET 7 AB 8 PHE B 211 VAL B 214 -1 O PHE B 211 N TYR B 179 SHEET 8 AB 8 GLU B 73 ILE B 75 1 O MET B 74 N VAL B 214 SHEET 1 AC 5 GLU A 73 ILE A 75 0 SHEET 2 AC 5 PHE A 211 VAL A 214 1 O ILE A 212 N MET A 74 SHEET 3 AC 5 LYS A 178 VAL A 186 -1 O TYR A 179 N PHE A 211 SHEET 4 AC 5 LYS A 99 PRO A 108 -1 O ILE A 101 N VAL A 186 SHEET 5 AC 5 TYR A 136 VAL A 137 -1 O TYR A 136 N MET A 104 SHEET 1 AD 2 ALA A 143 THR A 144 0 SHEET 2 AD 2 LYS A 99 PRO A 108 -1 O TYR A 100 N ALA A 143 SHEET 1 AE 8 GLU A 73 ILE A 75 0 SHEET 2 AE 8 PHE A 211 VAL A 214 1 O ILE A 212 N MET A 74 SHEET 3 AE 8 LYS A 178 VAL A 186 -1 O TYR A 179 N PHE A 211 SHEET 4 AE 8 ALA A 200 VAL A 205 -1 O CYS A 202 N ILE A 185 SHEET 5 AE 8 ALA B 200 HIS B 204 -1 O PHE B 201 N THR A 203 SHEET 6 AE 8 LYS B 178 LYS B 187 -1 O LEU B 183 N HIS B 204 SHEET 7 AE 8 LYS B 99 PRO B 108 -1 O ILE B 101 N VAL B 186 SHEET 8 AE 8 TYR B 136 VAL B 137 -1 O TYR B 136 N MET B 104 SHEET 1 BA 2 ALA B 143 THR B 144 0 SHEET 2 BA 2 LYS B 99 PRO B 108 -1 O TYR B 100 N ALA B 143 SHEET 1 AF 5 GLU A 73 ILE A 75 0 SHEET 2 AF 5 PHE A 211 VAL A 214 1 O ILE A 212 N MET A 74 SHEET 3 AF 5 LYS A 178 VAL A 186 -1 O TYR A 179 N PHE A 211 SHEET 4 AF 5 LYS A 99 PRO A 108 -1 O ILE A 101 N VAL A 186 SHEET 5 AF 5 ALA A 143 THR A 144 -1 O ALA A 143 N TYR A 100 SHEET 1 AG 3 ARG A 81 ARG A 82 0 SHEET 2 AG 3 LYS A 159 THR A 161 -1 O LEU A 160 N ARG A 81 SHEET 3 AG 3 ILE A 171 ILE A 172 1 O ILE A 171 N THR A 161 SHEET 1 AH 2 HIS A 112 ALA A 117 0 SHEET 2 AH 2 LYS A 120 LYS A 126 -1 O LYS A 120 N ALA A 117 SHEET 1 BB 3 LYS B 55 LEU B 58 0 SHEET 2 BB 3 LYS B 88 THR B 92 -1 O LYS B 90 N PHE B 57 SHEET 3 BB 3 VAL B 153 SER B 154 -1 O VAL B 153 N VAL B 89 SHEET 1 BC 3 ARG B 81 ARG B 82 0 SHEET 2 BC 3 LYS B 159 THR B 161 -1 O LEU B 160 N ARG B 81 SHEET 3 BC 3 ILE B 171 ILE B 172 1 O ILE B 171 N THR B 161 SHEET 1 BD 2 HIS B 112 PHE B 116 0 SHEET 2 BD 2 TRP B 121 LYS B 126 -1 O SER B 122 N LYS B 115 SSBOND 1 CYS A 202 CYS B 202 1555 1555 2.09 LINK OE1 GLU A 60 MG MG A1239 1555 1555 2.71 LINK O SER A 86 MG MG A1239 1555 1555 2.69 LINK OE1 GLU B 60 MG MG B1233 1555 1555 2.89 CISPEP 1 GLY A 53 ILE A 54 0 -1.02 CISPEP 2 PHE A 84 PRO A 85 0 0.86 CISPEP 3 SER A 141 PRO A 142 0 -8.87 CISPEP 4 PHE B 84 PRO B 85 0 -0.89 CISPEP 5 SER B 141 PRO B 142 0 -6.53 SITE 1 AC1 3 GLU A 60 SER A 86 LYS A 88 SITE 1 AC2 2 GLU B 60 SER B 86 SITE 1 AC3 5 LEU A 103 ASP A 105 ARG A 182 ARG B 182 SITE 2 AC3 5 PHE B 201 CRYST1 118.240 118.240 243.000 90.00 90.00 120.00 P 61 2 2 24 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 0.008457 0.004883 0.000000 0.00000 SCALE2 0.000000 0.009766 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004115 0.00000