HEADER SIGNALING PROTEIN 27-MAR-14 4P7U TITLE EXTRACELLULAR DOMAIN OF TYPE II TRANSFORMING GROWTH FACTOR BETA TITLE 2 RECEPTOR IN COMPLEX WITH NDSB-201 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TGF-BETA RECEPTOR TYPE-2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EXTRACELLULAR DOMAIN, UNP RESIDUES 74-175; COMPND 5 SYNONYM: TGFR-2,TGF-BETA TYPE II RECEPTOR,TRANSFORMING GROWTH FACTOR- COMPND 6 BETA RECEPTOR TYPE II,TBETAR-II; COMPND 7 EC: 2.7.11.30; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TGFBR2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET24 KEYWDS NDSB-201, TYPE II TRANSFORMING GROWTH FACTOR BETA RECEPTOR, SIGNALING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.WANGKANONT,K.T.FOREST REVDAT 5 27-SEP-23 4P7U 1 REMARK HETSYN REVDAT 4 25-DEC-19 4P7U 1 REMARK REVDAT 3 13-SEP-17 4P7U 1 REMARK REVDAT 2 30-SEP-15 4P7U 1 JRNL REMARK REVDAT 1 24-JUN-15 4P7U 0 JRNL AUTH K.WANGKANONT,K.T.FOREST,L.L.KIESSLING JRNL TITL THE NON-DETERGENT SULFOBETAINE-201 ACTS AS A PHARMACOLOGICAL JRNL TITL 2 CHAPERONE TO PROMOTE FOLDING AND CRYSTALLIZATION OF THE TYPE JRNL TITL 3 II TGF-BETA RECEPTOR EXTRACELLULAR DOMAIN. JRNL REF PROTEIN EXPR.PURIF. V. 115 19 2015 JRNL REFN ESSN 1096-0279 JRNL PMID 26073093 JRNL DOI 10.1016/J.PEP.2015.06.001 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 17020 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1703 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 21.4412 - 3.4335 1.00 1390 155 0.1651 0.1893 REMARK 3 2 3.4335 - 2.7270 1.00 1313 147 0.1737 0.2159 REMARK 3 3 2.7270 - 2.3828 1.00 1282 142 0.1773 0.2245 REMARK 3 4 2.3828 - 2.1652 1.00 1301 144 0.1709 0.2023 REMARK 3 5 2.1652 - 2.0101 1.00 1269 142 0.1651 0.1962 REMARK 3 6 2.0101 - 1.8917 1.00 1283 143 0.1614 0.2118 REMARK 3 7 1.8917 - 1.7970 1.00 1262 139 0.1744 0.2220 REMARK 3 8 1.7970 - 1.7188 0.99 1259 140 0.1720 0.2015 REMARK 3 9 1.7188 - 1.6526 0.99 1239 137 0.1818 0.2278 REMARK 3 10 1.6526 - 1.5956 1.00 1228 138 0.1644 0.1798 REMARK 3 11 1.5956 - 1.5458 0.99 1277 141 0.1805 0.2246 REMARK 3 12 1.5458 - 1.5020 0.97 1214 135 0.1944 0.2418 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.160 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.007 949 REMARK 3 ANGLE : 1.181 1286 REMARK 3 CHIRALITY : 0.081 136 REMARK 3 PLANARITY : 0.005 170 REMARK 3 DIHEDRAL : 14.485 370 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 4P7U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAR-14. REMARK 100 THE DEPOSITION ID IS D_1000200841. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17064 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 22.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.41900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 1M9Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM CITRATE, 30% PEG 2000, REMARK 280 PH 5.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 16.78700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.91850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.23150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.91850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.78700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.23150 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: BIOLOGICAL UNIT IS THE SAME AS ASYM. 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 MET A 25 REMARK 465 GLU A 128 REMARK 465 GLU A 129 REMARK 465 TYR A 130 REMARK 465 ASN A 131 REMARK 465 THR A 132 REMARK 465 SER A 133 REMARK 465 ASN A 134 REMARK 465 PRO A 135 REMARK 465 ASP A 136 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 O LYS A 105 O HOH A 352 2.18 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 ASP A 32 -147.82 56.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 1PS A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1M9Z RELATED DB: PDB REMARK 900 1M9Z CONTAINS THE SAME PROTEIN WITHOUT NDSB-201 REMARK 900 RELATED ID: 1PLO RELATED DB: PDB REMARK 900 1PLO CONTAINS THE SOLUTION NMR STRUCTURE OF THE SAME PROTEIN REMARK 900 WITHOUT NDSB-201 REMARK 900 RELATED ID: 4XJJ RELATED DB: PDB DBREF 4P7U A 27 136 UNP P37173 TGFR2_HUMAN 75 184 SEQADV 4P7U MET A 25 UNP P37173 INITIATING METHIONINE SEQADV 4P7U ALA A 26 UNP P37173 ENGINEERED MUTATION SEQADV 4P7U THR A 97 UNP P37173 LYS 145 ENGINEERED MUTATION SEQRES 1 A 112 MET ALA LEU CYS LYS PHE CYS ASP VAL ARG PHE SER THR SEQRES 2 A 112 CYS ASP ASN GLN LYS SER CYS MET SER ASN CYS SER ILE SEQRES 3 A 112 THR SER ILE CYS GLU LYS PRO GLN GLU VAL CYS VAL ALA SEQRES 4 A 112 VAL TRP ARG LYS ASN ASP GLU ASN ILE THR LEU GLU THR SEQRES 5 A 112 VAL CYS HIS ASP PRO LYS LEU PRO TYR HIS ASP PHE ILE SEQRES 6 A 112 LEU GLU ASP ALA ALA SER PRO THR CYS ILE MET LYS GLU SEQRES 7 A 112 LYS LYS LYS PRO GLY GLU THR PHE PHE MET CYS SER CYS SEQRES 8 A 112 SER SER ASP GLU CYS ASN ASP ASN ILE ILE PHE SER GLU SEQRES 9 A 112 GLU TYR ASN THR SER ASN PRO ASP HET 1PS A 201 26 HETNAM 1PS 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE HETSYN 1PS 1-(3-SULFOPROPYL) PYRIDINIUM; PPS FORMUL 2 1PS C8 H11 N O3 S FORMUL 3 HOH *90(H2 O) HELIX 1 AA1 GLU A 119 ASN A 121 5 3 SHEET 1 AA1 2 LEU A 27 LYS A 29 0 SHEET 2 AA1 2 THR A 51 ILE A 53 -1 O SER A 52 N CYS A 28 SHEET 1 AA2 5 ASP A 32 PHE A 35 0 SHEET 2 AA2 5 ILE A 72 HIS A 79 -1 O LEU A 74 N ARG A 34 SHEET 3 AA2 5 VAL A 60 LYS A 67 -1 N VAL A 60 O HIS A 79 SHEET 4 AA2 5 THR A 109 CYS A 115 -1 O PHE A 111 N TRP A 65 SHEET 5 AA2 5 LYS A 101 LYS A 103 -1 N LYS A 103 O PHE A 110 SHEET 1 AA3 3 SER A 43 MET A 45 0 SHEET 2 AA3 3 ASN A 123 ILE A 125 -1 O ILE A 124 N CYS A 44 SHEET 3 AA3 3 CYS A 98 ILE A 99 1 N CYS A 98 O ILE A 125 SSBOND 1 CYS A 28 CYS A 61 1555 1555 2.03 SSBOND 2 CYS A 31 CYS A 48 1555 1555 2.02 SSBOND 3 CYS A 38 CYS A 44 1555 1555 2.01 SSBOND 4 CYS A 54 CYS A 78 1555 1555 2.06 SSBOND 5 CYS A 98 CYS A 113 1555 1555 2.05 SSBOND 6 CYS A 115 CYS A 120 1555 1555 2.05 SITE 1 AC1 5 GLN A 41 TRP A 65 THR A 109 PHE A 111 SITE 2 AC1 5 PHE A 126 CRYST1 33.574 40.463 75.837 90.00 90.00 90.00 P 21 21 21 4 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 0.029785 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024714 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013186 0.00000