PDB Short entry for 4XJJ HEADER CYTOKINE RECEPTOR 08-JAN-15 4XJJ TITLE EXTRACELLULAR DOMAIN OF TYPE II TRANSFORMING GROWTH FACTOR BETA TITLE 2 RECEPTOR IN COMPLEX WITH 2-(2-HYDROXYETHYL)NDSB-201 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TGF-BETA RECEPTOR TYPE-2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIGAND BINDING DOMAIN (UNP REISUDES 50-159); 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: PET24A KEYWDS TYPE II TRANSFORMING GROWTH FACTOR BETA RECEPTOR, NDSB-201, KEYWDS 2 TRANSFORMING GROWTH FACTOR BETA, KINASE, EXTRACELLULAR DOMAIN, KEYWDS 3 CYTOKINE RECEPTOR EXPDTA X-RAY DIFFRACTION AUTHOR K.WANGKANONT,K.T.FOREST,L.L.KIESSLING REVDAT 2 27-SEP-23 4XJJ 1 SOURCE KEYWDS REMARK REVDAT 1 24-JUN-15 4XJJ 0 JRNL AUTH K.WANGKANONT,K.T.FOREST,L.L.KIESSLING JRNL TITL EXTRACELLULAR DOMAIN OF TYPE II TRANSFORMING GROWTH FACTOR JRNL TITL 2 BETA RECEPTOR IN COMPLEX WITH 2-(2-HYDROXYETHYL)NDSB-201 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 21988 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1099 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 27.7420 - 2.7990 1.00 2781 146 0.1603 0.1720 REMARK 3 2 2.7990 - 2.2219 1.00 2652 140 0.1771 0.2162 REMARK 3 3 2.2219 - 1.9412 1.00 2628 138 0.1454 0.1937 REMARK 3 4 1.9412 - 1.7637 1.00 2588 137 0.1354 0.1585 REMARK 3 5 1.7637 - 1.6373 1.00 2618 138 0.1199 0.1943 REMARK 3 6 1.6373 - 1.5408 1.00 2585 135 0.1251 0.1641 REMARK 3 7 1.5408 - 1.4636 1.00 2559 135 0.1362 0.2035 REMARK 3 8 1.4636 - 1.4000 0.96 2478 130 0.1631 0.1914 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.420 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.14 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.10 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 : 0.006 943 REMARK 3 ANGLE : 1.091 1273 REMARK 3 CHIRALITY : 0.047 137 REMARK 3 PLANARITY : 0.004 168 REMARK 3 DIHEDRAL : 13.719 360 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 4XJJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000205791. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAR-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-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : C(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22047 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 13.80 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 11.80 REMARK 200 R MERGE FOR SHELL (I) : 0.51900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 2.5.6 REMARK 200 STARTING MODEL: 1M9Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 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 17.58500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.17050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.18650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.17050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.58500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.18650 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 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 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 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: 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 -143.33 53.36 REMARK 500 PHE A 126 48.79 -100.32 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 41D A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4P7U RELATED DB: PDB DBREF 4XJJ A 27 136 UNP P37173 TGFR2_HUMAN 50 159 SEQADV 4XJJ MET A 25 UNP P37173 EXPRESSION TAG SEQADV 4XJJ ALA A 26 UNP P37173 EXPRESSION TAG SEQADV 4XJJ THR A 97 UNP P37173 LYS 120 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 41D A 201 16 HETNAM 41D 3-[2-(2-HYDROXYETHYL)PYRIDINIUM-1-YL]PROPANE-1- HETNAM 2 41D SULFONATE FORMUL 2 41D C10 H15 N O4 S FORMUL 3 HOH *111(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 GLU A 108 CYS A 115 -1 O PHE A 111 N TRP A 65 SHEET 5 AA2 5 LYS A 101 LYS A 105 -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 2.04 SSBOND 3 CYS A 38 CYS A 44 1555 1555 2.03 SSBOND 4 CYS A 54 CYS A 78 1555 1555 2.05 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 7 GLN A 41 TRP A 65 PHE A 111 PHE A 126 SITE 2 AC1 7 HOH A 317 HOH A 335 HOH A 393 CRYST1 35.170 40.373 76.341 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 0.028433 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024769 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013099 0.00000