HEADER TRANSCRIPTION 05-NOV-19 6TCE TITLE CRYSTAL STRUCTURE OF THE GGCT SITE-BOUND MH1 DOMAIN OF SMAD5 TITLE 2 CONTAINING A GGGS INSERTION IN THE LOOP1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 5; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MOTHERS AGAINST DPP HOMOLOG 5,JV5-1,SMAD FAMILY MEMBER 5, COMPND 5 HSMAD5; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'- COMPND 10 D(P*TP*GP*CP*AP*GP*GP*CP*TP*AP*GP*CP*CP*TP*GP*CP*A)-3'); COMPND 11 CHAIN: B; COMPND 12 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: SMAD5, MADH5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS TGF-B, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR R.PLUTA,M.J.MACIAS REVDAT 4 24-JAN-24 6TCE 1 JRNL REMARK REVDAT 3 10-FEB-21 6TCE 1 JRNL REMARK REVDAT 2 29-APR-20 6TCE 1 AUTHOR REVDAT 1 20-NOV-19 6TCE 0 JRNL AUTH L.RUIZ,Z.KACZMARSKA,T.GOMES,E.ARAGON,C.TORNER,R.FREIER, JRNL AUTH 2 B.BAGINSKI,P.MARTIN-MALPARTIDA,N.DE MARTIN GARRIDO, JRNL AUTH 3 J.A.MARQUEZ,T.N.CORDEIRO,R.PLUTA,M.J.MACIAS JRNL TITL UNVEILING THE DIMER/MONOMER PROPENSITIES OF SMAD MH1-DNA JRNL TITL 2 COMPLEXES. JRNL REF COMPUT STRUCT BIOTECHNOL J V. 19 632 2021 JRNL REFN ESSN 2001-0370 JRNL PMID 33510867 JRNL DOI 10.1016/J.CSBJ.2020.12.044 REMARK 2 REMARK 2 RESOLUTION. 2.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 (3-OCT-2019) 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) : 2.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 89.8 REMARK 3 NUMBER OF REFLECTIONS : 4823 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) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 227 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.92 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 3.00 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 45.73 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : NULL REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 439 REMARK 3 BIN R VALUE (WORKING SET) : 0.2475 REMARK 3 BIN FREE R VALUE : 0.2860 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.01 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 22 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1000 REMARK 3 NUCLEIC ACID ATOMS : 328 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 135.3 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -8.84650 REMARK 3 B22 (A**2) : -8.84650 REMARK 3 B33 (A**2) : 17.69300 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) : 0.460 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.403 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL 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 : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1393 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1945 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 448 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 179 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1389 ; 10.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 170 ; 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 : 797 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.97 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.95 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 20.83 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): -3.1405 -22.6207 -9.4397 REMARK 3 T TENSOR REMARK 3 T11: -0.005 T22: -0.1072 REMARK 3 T33: -0.2407 T12: -0.0437 REMARK 3 T13: 0.152 T23: 0.152 REMARK 3 L TENSOR REMARK 3 L11: 4.133 L22: 8.2633 REMARK 3 L33: 8.1131 L12: 1.4866 REMARK 3 L13: -1.412 L23: -0.0299 REMARK 3 S TENSOR REMARK 3 S11: 0.0981 S12: 0.5442 S13: -0.1552 REMARK 3 S21: 0.5442 S22: 0.1542 S23: 0.3937 REMARK 3 S31: -0.1552 S32: 0.3937 S33: -0.2523 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|* } REMARK 3 ORIGIN FOR THE GROUP (A): -1.8339 -26.6627 -32.2901 REMARK 3 T TENSOR REMARK 3 T11: 0.0328 T22: -0.2169 REMARK 3 T33: -0.0081 T12: 0.0423 REMARK 3 T13: 0.0267 T23: 0.1201 REMARK 3 L TENSOR REMARK 3 L11: 2.7315 L22: 4.5323 REMARK 3 L33: 4.8595 L12: -0.7172 REMARK 3 L13: -0.1509 L23: 0.7509 REMARK 3 S TENSOR REMARK 3 S11: -0.0966 S12: 0.0086 S13: -0.1094 REMARK 3 S21: 0.0086 S22: -0.3511 S23: 0.4519 REMARK 3 S31: -0.1094 S32: 0.4519 S33: 0.4477 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6TCE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1292105245. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUL-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4821 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.920 REMARK 200 RESOLUTION RANGE LOW (A) : 53.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 40.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : 2.99800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.600 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: 6FZS REMARK 200 REMARK 200 REMARK: THICK PLATE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21% PEG SMEAR MEDIUM (PEG 2000, 3350, REMARK 280 4000, AND 5000 MME), 0.05 M HEPES PH 7.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+1/2,-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 53.06150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 53.06150 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.19750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 53.06150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 20.59875 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 53.06150 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 61.79625 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 53.06150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 61.79625 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 53.06150 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 20.59875 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 53.06150 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 53.06150 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 41.19750 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 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 53.06150 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 53.06150 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 41.19750 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 53.06150 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 61.79625 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 53.06150 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 20.59875 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 53.06150 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 20.59875 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 53.06150 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 61.79625 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 53.06150 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 53.06150 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 41.19750 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: 3650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -53.06150 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -61.79625 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 5 REMARK 465 PHE A 6 REMARK 465 THR A 7 REMARK 465 GLY A 19 REMARK 465 GLY A 20 REMARK 465 GLY A 21 REMARK 465 SER A 22 REMARK 465 GLN A 23 REMARK 465 GLY A 24 REMARK 465 PRO A 137 REMARK 465 PRO A 138 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 VAL A 11 CG1 CG2 REMARK 480 LYS A 12 CG CD CE NZ REMARK 480 ARG A 13 NE CZ NH1 NH2 REMARK 480 LEU A 14 CG CD1 CD2 REMARK 480 LEU A 15 CG CD1 CD2 REMARK 480 TRP A 17 CD1 CD2 NE1 CE2 CE3 CZ2 CZ3 REMARK 480 TRP A 17 CH2 REMARK 480 LYS A 18 CE NZ REMARK 480 GLU A 26 CG CD OE1 OE2 REMARK 480 GLU A 27 CG CD OE1 OE2 REMARK 480 GLU A 28 CD OE1 OE2 REMARK 480 LYS A 29 CB CG CD CE NZ REMARK 480 GLU A 32 CG CD OE1 OE2 REMARK 480 LYS A 33 CG CD CE NZ REMARK 480 ASP A 36 CG OD1 OD2 REMARK 480 LEU A 38 CD1 CD2 REMARK 480 VAL A 39 CG1 CG2 REMARK 480 LYS A 40 CG CD CE NZ REMARK 480 LYS A 41 CB CG CD CE NZ REMARK 480 LEU A 42 CD1 CD2 REMARK 480 LYS A 43 CG CD CE NZ REMARK 480 LYS A 44 CG CD CE NZ REMARK 480 LYS A 45 CG CD CE NZ REMARK 480 LYS A 46 CD CE NZ REMARK 480 MET A 49 CG SD CE REMARK 480 LEU A 52 CG CD1 CD2 REMARK 480 GLU A 53 CB CG CD OE1 OE2 REMARK 480 LYS A 54 CB CG CD CE NZ REMARK 480 LEU A 56 CG CD1 CD2 REMARK 480 PRO A 59 CB CG CD REMARK 480 GLN A 61 CB CG CD OE1 NE2 REMARK 480 LYS A 64 CD CE NZ REMARK 480 VAL A 66 CG1 CG2 REMARK 480 ILE A 68 CG2 CD1 REMARK 480 ARG A 70 CZ NH1 NH2 REMARK 480 ARG A 81 CG CD NE CZ NH1 NH2 REMARK 480 VAL A 92 CG1 CG2 REMARK 480 LEU A 104 CG CD1 CD2 REMARK 480 LYS A 105 CB CG CD CE NZ REMARK 480 LEU A 107 CG CD1 CD2 REMARK 480 ILE A 109 CG1 CG2 REMARK 480 GLU A 111 CD OE1 OE2 REMARK 480 LYS A 117 CG CD CE NZ REMARK 480 ILE A 123 CG2 CD1 REMARK 480 LYS A 129 CB CG CD CE NZ REMARK 480 GLU A 132 CD OE1 OE2 REMARK 480 DT B 1 P OP1 OP2 O5' 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 DA B 4 O3' DA B 4 C3' -0.039 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 DC B 15 O4' - C1' - N1 ANGL. DEV. = 2.0 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 TRP A 17 44.16 -93.05 REMARK 500 PRO A 62 107.23 -56.92 REMARK 500 ARG A 94 -62.55 -167.99 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 110 SG 135.8 REMARK 620 3 CYS A 122 SG 107.1 114.2 REMARK 620 4 HIS A 127 ND1 114.8 89.2 78.0 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6FZS RELATED DB: PDB REMARK 900 WT PROTEIN REMARK 900 RELATED ID: 6TBZ RELATED DB: PDB REMARK 900 MUTANT PROTEIN DBREF 6TCE A 5 138 UNP Q99717 SMAD5_HUMAN 9 138 DBREF 6TCE B 1 16 PDB 6TCE 6TCE 1 16 SEQADV 6TCE GLY A 19 UNP Q99717 INSERTION SEQADV 6TCE GLY A 20 UNP Q99717 INSERTION SEQADV 6TCE GLY A 21 UNP Q99717 INSERTION SEQADV 6TCE SER A 22 UNP Q99717 INSERTION SEQRES 1 A 134 SER PHE THR SER PRO ALA VAL LYS ARG LEU LEU GLY TRP SEQRES 2 A 134 LYS GLY GLY GLY SER GLN GLY ASP GLU GLU GLU LYS TRP SEQRES 3 A 134 ALA GLU LYS ALA VAL ASP ALA LEU VAL LYS LYS LEU LYS SEQRES 4 A 134 LYS LYS LYS GLY ALA MET GLU GLU LEU GLU LYS ALA LEU SEQRES 5 A 134 SER SER PRO GLY GLN PRO SER LYS CYS VAL THR ILE PRO SEQRES 6 A 134 ARG SER LEU ASP GLY ARG LEU GLN VAL SER HIS ARG LYS SEQRES 7 A 134 GLY LEU PRO HIS VAL ILE TYR CYS ARG VAL TRP ARG TRP SEQRES 8 A 134 PRO ASP LEU GLN SER HIS HIS GLU LEU LYS PRO LEU ASP SEQRES 9 A 134 ILE CYS GLU PHE PRO PHE GLY SER LYS GLN LYS GLU VAL SEQRES 10 A 134 CYS ILE ASN PRO TYR HIS TYR LYS ARG VAL GLU SER PRO SEQRES 11 A 134 VAL LEU PRO PRO SEQRES 1 B 16 DT DG DC DA DG DG DC DT DA DG DC DC DT SEQRES 2 B 16 DG DC DA HET ZN A 201 1 HETNAM ZN ZINC ION FORMUL 3 ZN ZN 2+ HELIX 1 AA1 SER A 8 GLY A 16 1 9 HELIX 2 AA2 GLU A 26 LYS A 44 1 19 HELIX 3 AA3 ALA A 48 SER A 57 1 10 HELIX 4 AA4 LEU A 84 ARG A 94 1 11 HELIX 5 AA5 SER A 100 HIS A 102 5 3 SHEET 1 AA1 2 THR A 67 PRO A 69 0 SHEET 2 AA1 2 GLU A 120 CYS A 122 -1 O VAL A 121 N ILE A 68 SHEET 1 AA2 2 LEU A 76 VAL A 78 0 SHEET 2 AA2 2 ARG A 81 GLY A 83 -1 O GLY A 83 N LEU A 76 SHEET 1 AA3 2 LEU A 104 PRO A 106 0 SHEET 2 AA3 2 TYR A 128 ARG A 130 -1 O LYS A 129 N LYS A 105 LINK SG CYS A 65 ZN ZN A 201 1555 1555 2.17 LINK SG CYS A 110 ZN ZN A 201 1555 1555 2.36 LINK SG CYS A 122 ZN ZN A 201 1555 1555 2.53 LINK ND1 HIS A 127 ZN ZN A 201 1555 1555 2.01 SITE 1 AC1 4 CYS A 65 CYS A 110 CYS A 122 HIS A 127 CRYST1 106.123 106.123 82.395 90.00 90.00 90.00 I 41 2 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 0.009423 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009423 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012137 0.00000