PDB Short entry for 4AJV HEADER SIGNALING PROTEIN 20-FEB-12 4AJV TITLE STRUCTURE OF MOUSE ZP-C DOMAIN OF TGF-BETA-RECEPTOR-3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSFORMING GROWTH FACTOR BETA RECEPTOR TYPE 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ZP-C DOMAIN, RESIDUES 591-757; COMPND 5 SYNONYM: TGF-BETA RECEPTOR TYPE 3, TGFR-3, BETAGLYCAN, TRANSFORMING COMPND 6 GROWTH FACTOR BETA RECEPTOR III, TGF-BETA RECEPTOR TYPE III; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK 293 EBNA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PCEP4-PU BM40 KEYWDS SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR U.DIESTEL,M.RESCH,K.MEINHARDT,S.WEILER,T.V.HELLMANN,J.NICKEL, AUTHOR 2 J.EICHLER,Y.A.MULLER REVDAT 2 17-JUL-13 4AJV 1 JRNL REVDAT 1 27-FEB-13 4AJV 0 JRNL AUTH U.DIESTEL,M.RESCH,K.MEINHARDT,S.WEILER,T.V.HELLMANN, JRNL AUTH 2 T.D.MUELLER,J.NICKEL,J.EICHLER,Y.A.MULLER JRNL TITL IDENTIFICATION OF A NOVEL TGF-BETA-BINDING SITE IN THE ZONA JRNL TITL 2 PELLUCIDA C-TERMINAL (ZP-C) DOMAIN OF TGF-BETA-RECEPTOR-3 JRNL TITL 3 (TGFR-3). JRNL REF PLOS ONE V. 8 67214 2013 JRNL REFN ISSN 1932-6203 JRNL PMID 23826237 JRNL DOI 10.1371/JOURNAL.PONE.0067214 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT 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) : 2.700 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.318 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.99 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.28 REMARK 3 NUMBER OF REFLECTIONS : 4959 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.2242 REMARK 3 R VALUE (WORKING SET) : 0.2200 REMARK 3 FREE R VALUE : 0.2958 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.5 REMARK 3 FREE R VALUE TEST SET COUNT : 271 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 38.3221 - 3.4017 0.99 2400 129 0.2094 0.2649 REMARK 3 2 3.4017 - 2.7002 1.00 2288 142 0.2461 0.3686 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.11 REMARK 3 K_SOL : 0.363 REMARK 3 B_SOL : 67.046 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.43 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.60 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.1 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.0 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -10.6555 REMARK 3 B22 (A**2) : 21.8371 REMARK 3 B33 (A**2) : -11.1816 REMARK 3 B12 (A**2) : 0.0000 REMARK 3 B13 (A**2) : 0.0000 REMARK 3 B23 (A**2) : 0.0000 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 : 0.017 1241 REMARK 3 ANGLE : 1.753 1681 REMARK 3 CHIRALITY : 0.090 193 REMARK 3 PLANARITY : 0.009 215 REMARK 3 DIHEDRAL : 17.933 450 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: RESIDUES 730-744 COULD NOT BE MODELED REMARK 4 REMARK 4 4AJV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-FEB-12. REMARK 100 THE PDBE ID CODE IS EBI-51376. 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 : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD (MX-225) REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4960 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.70 REMARK 200 RESOLUTION RANGE LOW (A) : 38.32 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.5 REMARK 200 R MERGE (I) : 0.10 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.20 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.6 REMARK 200 R MERGE FOR SHELL (I) : 0.64 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.30 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 3QW9 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 6 TO 7, 0.2 M REMARK 280 AMMONIUM ACETATE, 20 TO 30 % PEG 3350 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 24.83000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.12000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.41000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.12000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.83000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.41000 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 SER A 730 REMARK 465 LEU A 731 REMARK 465 ASP A 732 REMARK 465 ALA A 733 REMARK 465 THR A 734 REMARK 465 MET A 735 REMARK 465 ILE A 736 REMARK 465 TRP A 737 REMARK 465 THR A 738 REMARK 465 MET A 739 REMARK 465 MET A 740 REMARK 465 GLN A 741 REMARK 465 ASN A 742 REMARK 465 LYS A 743 REMARK 465 LYS A 744 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 745 OG1 CG2 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 SER A 664 O HOH A 2005 2.11 REMARK 500 OD2 ASP A 683 NH2 ARG A 711 2.07 REMARK 500 OG1 THR A 697 O HOH A 2008 1.99 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 ARG A 648 NE - CZ - NH1 ANGL. DEV. = 5.0 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 ASP A 600 30.62 -82.50 REMARK 500 PHE A 602 50.19 38.64 REMARK 500 VAL A 609 110.36 -5.08 REMARK 500 ASN A 615 -2.39 80.05 REMARK 500 MET A 649 -165.46 -61.73 REMARK 500 ILE A 658 -1.14 66.91 REMARK 500 PHE A 746 39.58 -93.56 REMARK 500 REMARK 500 REMARK: NULL DBREF 4AJV A 591 757 UNP O88393 TGBR3_MOUSE 591 757 SEQRES 1 A 167 THR PHE ASN MET GLU LEU TYR ASN THR ASP LEU PHE LEU SEQRES 2 A 167 VAL PRO SER PRO GLY VAL PHE SER VAL ALA GLU ASN GLU SEQRES 3 A 167 HIS VAL TYR VAL GLU VAL SER VAL THR LYS ALA ASP GLN SEQRES 4 A 167 ASP LEU GLY PHE ALA ILE GLN THR CYS PHE ILE SER PRO SEQRES 5 A 167 TYR SER ASN PRO ASP ARG MET SER ASP TYR THR ILE ILE SEQRES 6 A 167 GLU ASN ILE CYS PRO LYS ASP ASP SER VAL LYS PHE TYR SEQRES 7 A 167 SER SER LYS ARG VAL HIS PHE PRO ILE PRO HIS ALA GLU SEQRES 8 A 167 VAL ASP LYS LYS ARG PHE SER PHE VAL PHE LYS SER VAL SEQRES 9 A 167 PHE ASN THR SER LEU LEU PHE LEU HIS CYS GLU LEU THR SEQRES 10 A 167 LEU CYS SER ARG ASN LYS GLY SER GLN LYS LEU PRO LYS SEQRES 11 A 167 CYS VAL THR PRO ASP ASP ALA CYS THR SER LEU ASP ALA SEQRES 12 A 167 THR MET ILE TRP THR MET MET GLN ASN LYS LYS THR PHE SEQRES 13 A 167 THR LYS PRO LEU ALA VAL VAL LEU GLN VAL ASP FORMUL 2 HOH *9(H2 O) SHEET 1 AA 4 PHE A 592 TYR A 597 0 SHEET 2 AA 4 HIS A 617 LYS A 626 -1 O TYR A 619 N TYR A 597 SHEET 3 AA 4 ALA A 680 VAL A 690 -1 O GLU A 681 N LYS A 626 SHEET 4 AA 4 LYS A 666 PHE A 675 -1 O LYS A 666 N SER A 688 SHEET 1 AB 6 PHE A 610 VAL A 612 0 SHEET 2 AB 6 THR A 747 VAL A 756 1 O VAL A 753 N PHE A 610 SHEET 3 AB 6 LEU A 699 SER A 710 -1 O LEU A 700 N LEU A 754 SHEET 4 AB 6 LEU A 631 SER A 641 -1 O GLY A 632 N CYS A 709 SHEET 5 AB 6 THR A 653 GLU A 656 -1 N ILE A 654 O CYS A 638 SHEET 6 AB 6 CYS A 659 PRO A 660 -1 O CYS A 659 N GLU A 656 SSBOND 1 CYS A 638 CYS A 704 1555 1555 2.03 SSBOND 2 CYS A 659 CYS A 728 1555 1555 2.02 SSBOND 3 CYS A 709 CYS A 721 1555 1555 2.02 CRYST1 49.660 56.820 60.240 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 0.020137 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017599 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016600 0.00000