HEADER TRANSCRIPTION 05-APR-17 5NM9 TITLE CRYSTAL STRUCTURE OF THE PLACOZOA TRICHOPLAX ADHAERENS SMAD4-MH1 BOUND TITLE 2 TO THE GGCGC SITE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: MH1 DOMAIN, UNP RESIDUES 33-174; COMPND 5 SYNONYM: SMAD4, MOTHERS AGAINST DPP HOMOLOG,SMAD FAMILY MEMBER; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'- COMPND 9 D(P*AP*TP*GP*CP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*GP*CP*AP*T)-3'); COMPND 10 CHAIN: C, D; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRICHOPLAX ADHAERENS; SOURCE 3 ORGANISM_TAXID: 10228; SOURCE 4 GENE: TRIADDRAFT_30731; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606 KEYWDS SMADS, TRANSCRIPTION FACTOR, DNA COMPLEX, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR Z.KACZMARSKA,R.FREIER,J.A.MARQUEZ,M.J.MACIAS REVDAT 3 17-JAN-24 5NM9 1 REMARK REVDAT 2 27-DEC-17 5NM9 1 JRNL REVDAT 1 15-NOV-17 5NM9 0 JRNL AUTH P.MARTIN-MALPARTIDA,M.BATET,Z.KACZMARSKA,R.FREIER,T.GOMES, JRNL AUTH 2 E.ARAGON,Y.ZOU,Q.WANG,Q.XI,L.RUIZ,A.VEA,J.A.MARQUEZ, JRNL AUTH 3 J.MASSAGUE,M.J.MACIAS JRNL TITL STRUCTURAL BASIS FOR GENOME WIDE RECOGNITION OF 5-BP GC JRNL TITL 2 MOTIFS BY SMAD TRANSCRIPTION FACTORS. JRNL REF NAT COMMUN V. 8 2070 2017 JRNL REFN ESSN 2041-1723 JRNL PMID 29234012 JRNL DOI 10.1038/S41467-017-02054-6 REMARK 2 REMARK 2 RESOLUTION. 2.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.2 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.46 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 16190 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) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.850 REMARK 3 FREE R VALUE TEST SET COUNT : 786 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.000 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.43 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.60 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.97 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2894 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2280 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2772 REMARK 3 BIN R VALUE (WORKING SET) : 0.2280 REMARK 3 BIN FREE R VALUE : 0.2330 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.22 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 122 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1897 REMARK 3 NUCLEIC ACID ATOMS : 738 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 19 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 77.62 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 82.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -8.65960 REMARK 3 B22 (A**2) : 1.76980 REMARK 3 B33 (A**2) : 6.88980 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) : 0.400 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.390 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.248 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.369 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.246 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2763 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 3894 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 844 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 41 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 324 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2763 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 2 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 364 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 2750 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.02 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.76 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 22.82 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): -13.0932 13.9927 -20.1989 REMARK 3 T TENSOR REMARK 3 T11: 0.0691 T22: -0.2818 REMARK 3 T33: -0.1319 T12: -0.0118 REMARK 3 T13: 0.0078 T23: -0.0008 REMARK 3 L TENSOR REMARK 3 L11: 3.5264 L22: 7.7624 REMARK 3 L33: 8.5836 L12: -0.1678 REMARK 3 L13: -0.8054 L23: 1.0652 REMARK 3 S TENSOR REMARK 3 S11: -0.1143 S12: -0.0579 S13: 0.2141 REMARK 3 S21: 0.4163 S22: -0.0368 S23: 0.2776 REMARK 3 S31: -0.2634 S32: 0.1420 S33: 0.1511 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|* } REMARK 3 ORIGIN FOR THE GROUP (A): -13.0488 46.0105 -19.9128 REMARK 3 T TENSOR REMARK 3 T11: 0.2634 T22: -0.2852 REMARK 3 T33: -0.1360 T12: -0.0135 REMARK 3 T13: -0.0776 T23: -0.0008 REMARK 3 L TENSOR REMARK 3 L11: 3.3699 L22: 5.7638 REMARK 3 L33: 6.3020 L12: -0.0324 REMARK 3 L13: 0.6143 L23: 0.1007 REMARK 3 S TENSOR REMARK 3 S11: 0.1747 S12: -0.1260 S13: -0.1816 REMARK 3 S21: 0.2771 S22: -0.0234 S23: -0.3941 REMARK 3 S31: 0.2618 S32: 0.0397 S33: -0.1514 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { C|* } REMARK 3 ORIGIN FOR THE GROUP (A): -12.5091 -9.9977 -20.1817 REMARK 3 T TENSOR REMARK 3 T11: 0.2502 T22: -0.3651 REMARK 3 T33: -0.2904 T12: 0.0064 REMARK 3 T13: 0.3040 T23: -0.1277 REMARK 3 L TENSOR REMARK 3 L11: 6.0263 L22: 11.8419 REMARK 3 L33: 4.6894 L12: -4.1270 REMARK 3 L13: -1.2742 L23: 2.3195 REMARK 3 S TENSOR REMARK 3 S11: -0.0386 S12: -0.2935 S13: -0.0427 REMARK 3 S21: 0.7702 S22: 0.5280 S23: 0.2098 REMARK 3 S31: 0.9474 S32: 0.4699 S33: -0.4894 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: { D|* } REMARK 3 ORIGIN FOR THE GROUP (A): -13.2886 -8.7672 -19.4949 REMARK 3 T TENSOR REMARK 3 T11: 0.5057 T22: -0.3469 REMARK 3 T33: -0.2042 T12: -0.0074 REMARK 3 T13: 0.3040 T23: -0.0687 REMARK 3 L TENSOR REMARK 3 L11: 6.6782 L22: 6.7111 REMARK 3 L33: 3.5649 L12: -3.3319 REMARK 3 L13: -1.1480 L23: 0.1606 REMARK 3 S TENSOR REMARK 3 S11: 0.1912 S12: -0.4864 S13: 0.4705 REMARK 3 S21: 1.0260 S22: 0.6374 S23: -0.1609 REMARK 3 S31: -0.1036 S32: -0.1666 S33: -0.8286 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5NM9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-APR-17. REMARK 100 THE DEPOSITION ID IS D_1200004330. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-NOV-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976250 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.800 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: 5MEY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4.8% PEG 4000, 0.1 M SODIUM ACETATE PH REMARK 280 4.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 18.57500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.52000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.49000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 72.52000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.57500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.49000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -76.98000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 APPLY THE FOLLOWING TO CHAINS: A, C, D REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 76.98000 REMARK 350 BIOMT3 2 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 -2 REMARK 465 PRO A -1 REMARK 465 GLY A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 ALA A 3 REMARK 465 SER A 4 REMARK 465 GLY A 5 REMARK 465 SER A 6 REMARK 465 GLY A 7 REMARK 465 ASP A 8 REMARK 465 ILE A 131 REMARK 465 SER A 132 REMARK 465 PRO A 133 REMARK 465 GLY A 134 REMARK 465 TYR A 135 REMARK 465 ASN A 136 REMARK 465 VAL A 137 REMARK 465 THR A 138 REMARK 465 ASP A 139 REMARK 465 ILE A 140 REMARK 465 GLY B -2 REMARK 465 PRO B -1 REMARK 465 GLY B 0 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 ALA B 3 REMARK 465 SER B 4 REMARK 465 GLY B 5 REMARK 465 SER B 6 REMARK 465 GLY B 7 REMARK 465 ILE B 131 REMARK 465 SER B 132 REMARK 465 PRO B 133 REMARK 465 GLY B 134 REMARK 465 TYR B 135 REMARK 465 ASN B 136 REMARK 465 VAL B 137 REMARK 465 THR B 138 REMARK 465 ASP B 139 REMARK 465 ILE B 140 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 THR A 10 OG1 CG2 REMARK 470 LEU A 11 CG CD1 CD2 REMARK 470 ARG A 45 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 62 CG CD OE1 NE2 REMARK 470 LYS A 64 CG CD CE NZ REMARK 470 LEU A 72 CG CD1 CD2 REMARK 470 LYS A 81 CG CD CE NZ REMARK 470 ASP A 97 CG OD1 OD2 REMARK 470 LYS A 100 CG CD CE NZ REMARK 470 LYS A 104 CG CD CE NZ REMARK 470 LYS A 107 CG CD CE NZ REMARK 470 LEU A 108 CG CD1 CD2 REMARK 470 LYS B 31 CG CD CE NZ REMARK 470 ARG B 32 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 42 CG CD CE NZ REMARK 470 ARG B 45 CG CD NE CZ NH1 NH2 REMARK 470 LEU B 72 CG CD1 CD2 REMARK 470 LYS B 100 CG CD CE NZ REMARK 470 LYS B 104 CG CD CE NZ REMARK 470 LYS B 107 CG 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 D 16 O4' - C1' - N1 ANGL. DEV. = 2.3 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 ARG A 94 -60.51 -132.17 REMARK 500 ALA B 9 -33.78 74.09 REMARK 500 ARG B 94 -59.26 -124.69 REMARK 500 ASN B 101 46.59 -104.38 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 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 65 SG REMARK 620 2 CYS A 109 SG 114.1 REMARK 620 3 CYS A 121 SG 106.4 113.7 REMARK 620 4 HIS A 126 ND1 103.0 108.2 110.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 65 SG REMARK 620 2 CYS B 109 SG 117.2 REMARK 620 3 CYS B 121 SG 111.2 111.8 REMARK 620 4 HIS B 126 ND1 98.8 108.7 107.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5MF0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SMAD4-MH1 BOUND TO THE GGCCG SITE. REMARK 900 RELATED ID: 5MEZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SMAD4-MH1 BOUND TO THE GGCT SITE. REMARK 900 RELATED ID: 5MEY RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SMAD4-MH1 BOUND TO THE GGCGC SITE. DBREF 5NM9 A 1 140 UNP B3S7S5 B3S7S5_TRIAD 1 140 DBREF 5NM9 B 1 140 UNP B3S7S5 B3S7S5_TRIAD 1 140 DBREF 5NM9 C 1 18 PDB 5NM9 5NM9 1 18 DBREF 5NM9 D 1 18 PDB 5NM9 5NM9 1 18 SEQADV 5NM9 GLY A -2 UNP B3S7S5 EXPRESSION TAG SEQADV 5NM9 PRO A -1 UNP B3S7S5 EXPRESSION TAG SEQADV 5NM9 GLY A 0 UNP B3S7S5 EXPRESSION TAG SEQADV 5NM9 GLY B -2 UNP B3S7S5 EXPRESSION TAG SEQADV 5NM9 PRO B -1 UNP B3S7S5 EXPRESSION TAG SEQADV 5NM9 GLY B 0 UNP B3S7S5 EXPRESSION TAG SEQRES 1 A 143 GLY PRO GLY MET SER ALA SER GLY SER GLY ASP ALA THR SEQRES 2 A 143 LEU GLY ILE VAL HIS THR LEU MET CYS HIS ARG GLN GLY SEQRES 3 A 143 GLY GLU SER GLU ASN PHE ALA LYS ARG ALA VAL GLU SER SEQRES 4 A 143 LEU VAL LYS LYS LEU LYS ASP LYS ARG ASP GLU LEU ASP SEQRES 5 A 143 ALA LEU ILE THR ALA VAL THR SER ASN GLY ILE GLN GLN SEQRES 6 A 143 SER LYS CYS VAL THR ILE ALA ARG THR LEU ASP GLY ARG SEQRES 7 A 143 LEU GLN VAL ALA GLY LYS LYS GLY PHE PRO HIS VAL ILE SEQRES 8 A 143 TYR SER ARG ILE TRP ARG TRP PRO ASP LEU HIS LYS ASN SEQRES 9 A 143 GLU LEU LYS HIS ILE LYS LEU CYS LYS PHE ALA PHE ASP SEQRES 10 A 143 LEU LYS LEU ASP HIS VAL CYS VAL ASN PRO TYR HIS TYR SEQRES 11 A 143 GLU ARG VAL ILE SER PRO GLY TYR ASN VAL THR ASP ILE SEQRES 1 B 143 GLY PRO GLY MET SER ALA SER GLY SER GLY ASP ALA THR SEQRES 2 B 143 LEU GLY ILE VAL HIS THR LEU MET CYS HIS ARG GLN GLY SEQRES 3 B 143 GLY GLU SER GLU ASN PHE ALA LYS ARG ALA VAL GLU SER SEQRES 4 B 143 LEU VAL LYS LYS LEU LYS ASP LYS ARG ASP GLU LEU ASP SEQRES 5 B 143 ALA LEU ILE THR ALA VAL THR SER ASN GLY ILE GLN GLN SEQRES 6 B 143 SER LYS CYS VAL THR ILE ALA ARG THR LEU ASP GLY ARG SEQRES 7 B 143 LEU GLN VAL ALA GLY LYS LYS GLY PHE PRO HIS VAL ILE SEQRES 8 B 143 TYR SER ARG ILE TRP ARG TRP PRO ASP LEU HIS LYS ASN SEQRES 9 B 143 GLU LEU LYS HIS ILE LYS LEU CYS LYS PHE ALA PHE ASP SEQRES 10 B 143 LEU LYS LEU ASP HIS VAL CYS VAL ASN PRO TYR HIS TYR SEQRES 11 B 143 GLU ARG VAL ILE SER PRO GLY TYR ASN VAL THR ASP ILE SEQRES 1 C 18 DA DT DG DC DG DG DG DC DG DC DG DC DC SEQRES 2 C 18 DC DG DC DA DT SEQRES 1 D 18 DA DT DG DC DG DG DG DC DG DC DG DC DC SEQRES 2 D 18 DC DG DC DA DT HET ZN A 201 1 HET ZN B 201 1 HETNAM ZN ZINC ION FORMUL 5 ZN 2(ZN 2+) FORMUL 7 HOH *19(H2 O) HELIX 1 AA1 ALA A 9 CYS A 19 1 11 HELIX 2 AA2 SER A 26 LEU A 41 1 16 HELIX 3 AA3 LYS A 44 SER A 57 1 14 HELIX 4 AA4 PHE A 84 ARG A 94 1 11 HELIX 5 AA5 ALA A 112 LYS A 116 5 5 HELIX 6 AA6 ASN A 123 TYR A 125 5 3 HELIX 7 AA7 ALA B 9 HIS B 20 1 12 HELIX 8 AA8 SER B 26 LEU B 41 1 16 HELIX 9 AA9 LYS B 44 SER B 57 1 14 HELIX 10 AB1 PHE B 84 ARG B 94 1 11 HELIX 11 AB2 ALA B 112 LYS B 116 5 5 HELIX 12 AB3 ASN B 123 TYR B 125 5 3 SHEET 1 AA1 2 THR A 67 ALA A 69 0 SHEET 2 AA1 2 HIS A 119 CYS A 121 -1 O VAL A 120 N ILE A 68 SHEET 1 AA2 2 LEU A 76 VAL A 78 0 SHEET 2 AA2 2 LYS A 81 GLY A 83 -1 O GLY A 83 N LEU A 76 SHEET 1 AA3 2 LEU A 103 HIS A 105 0 SHEET 2 AA3 2 TYR A 127 ARG A 129 -1 O GLU A 128 N LYS A 104 SHEET 1 AA4 2 THR B 67 ALA B 69 0 SHEET 2 AA4 2 HIS B 119 CYS B 121 -1 O VAL B 120 N ILE B 68 SHEET 1 AA5 2 LEU B 76 VAL B 78 0 SHEET 2 AA5 2 LYS B 81 GLY B 83 -1 O GLY B 83 N LEU B 76 SHEET 1 AA6 2 LEU B 103 HIS B 105 0 SHEET 2 AA6 2 TYR B 127 ARG B 129 -1 O GLU B 128 N LYS B 104 LINK SG CYS A 65 ZN ZN A 201 1555 1555 2.14 LINK SG CYS A 109 ZN ZN A 201 1555 1555 2.32 LINK SG CYS A 121 ZN ZN A 201 1555 1555 2.52 LINK ND1 HIS A 126 ZN ZN A 201 1555 1555 2.15 LINK SG CYS B 65 ZN ZN B 201 1555 1555 2.16 LINK SG CYS B 109 ZN ZN B 201 1555 1555 2.23 LINK SG CYS B 121 ZN ZN B 201 1555 1555 2.35 LINK ND1 HIS B 126 ZN ZN B 201 1555 1555 2.23 SITE 1 AC1 4 CYS A 65 CYS A 109 CYS A 121 HIS A 126 SITE 1 AC2 4 CYS B 65 CYS B 109 CYS B 121 HIS B 126 CRYST1 37.150 76.980 145.040 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 0.026918 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012990 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006895 0.00000