HEADER SIGNALING PROTEIN INHIBITOR 29-SEP-05 2D3J TITLE NMR STRUCTURE OF THE WIF DOMAIN FROM HUMAN WIF-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: WNT INHIBITORY FACTOR-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: WIF DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS PALMITOYL GROUP, RECOGNITION DOMAIN, SIGNALING PROTEIN INHIBITOR EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR E.LIEPINSH,L.BANYAI,L.PATTHY,G.OTTING REVDAT 3 09-MAR-22 2D3J 1 REMARK SEQADV REVDAT 2 24-FEB-09 2D3J 1 VERSN REVDAT 1 25-APR-06 2D3J 0 JRNL AUTH E.LIEPINSH,L.BANYAI,L.PATTHY,G.OTTING JRNL TITL NMR STRUCTURE OF THE WIF DOMAIN OF THE HUMAN WNT-INHIBITORY JRNL TITL 2 FACTOR-1 JRNL REF J.MOL.BIOL. V. 357 942 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16476441 JRNL DOI 10.1016/J.JMB.2006.01.047 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5, OPAL 2.6 REMARK 3 AUTHORS : GUENTERT (DYANA), LUGINBUEHL (OPAL) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON 1755 NOE REMARK 3 RESTRAINTS AND 413 DIHEDRAL ANGLE RESTRAINTS. REMARK 4 REMARK 4 2D3J COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-SEP-05. REMARK 100 THE DEPOSITION ID IS D_1000024942. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 301 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : NO BUFFER ADDED REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.4MM U-15N WIF DOMAIN; 0.7MM U REMARK 210 -15N/13C WIF DOMAIN; 0.4MM U-15N REMARK 210 WIF DOMAIN REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 2D REMARK 210 NOESY; DQF-COSY; 2D TOCSY; HNCA, REMARK 210 CBCA(CO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DMX; UNITY REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 HG SER A 2 OD2 ASP A 6 1.55 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 4 ASN A 146 C - N - CA ANGL. DEV. = 16.1 DEGREES REMARK 500 5 LEU A 5 C - N - CA ANGL. DEV. = 16.3 DEGREES REMARK 500 5 LYS A 38 C - N - CA ANGL. DEV. = 16.1 DEGREES REMARK 500 5 LYS A 38 CB - CA - C ANGL. DEV. = 12.2 DEGREES REMARK 500 5 GLY A 71 C - N - CA ANGL. DEV. = 13.0 DEGREES REMARK 500 7 ASN A 146 C - N - CA ANGL. DEV. = 16.9 DEGREES REMARK 500 9 LYS A 38 C - N - CA ANGL. DEV. = 15.9 DEGREES REMARK 500 10 LYS A 38 C - N - CA ANGL. DEV. = 17.1 DEGREES REMARK 500 10 LYS A 38 CB - CA - C ANGL. DEV. = 12.6 DEGREES REMARK 500 12 ARG A 52 CD - NE - CZ ANGL. DEV. = 8.8 DEGREES REMARK 500 15 TYR A 13 CB - CG - CD1 ANGL. DEV. = -3.8 DEGREES REMARK 500 17 GLY A 71 C - N - CA ANGL. DEV. = 13.3 DEGREES REMARK 500 19 MET A 4 C - N - CA ANGL. DEV. = 17.2 DEGREES REMARK 500 19 GLU A 10 CA - CB - CG ANGL. DEV. = 13.4 DEGREES REMARK 500 19 LYS A 38 C - N - CA ANGL. DEV. = 15.8 DEGREES REMARK 500 20 ASN A 146 C - N - CA ANGL. DEV. = 16.3 DEGREES REMARK 500 20 ASN A 146 N - CA - CB ANGL. DEV. = 11.5 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 1 MET A 4 164.53 -44.47 REMARK 500 1 ILE A 25 15.73 -150.88 REMARK 500 1 ILE A 33 -65.83 -91.95 REMARK 500 1 LYS A 38 37.53 -80.32 REMARK 500 1 MET A 39 129.12 -37.78 REMARK 500 1 PRO A 41 33.23 -73.52 REMARK 500 1 ALA A 73 37.05 -80.82 REMARK 500 1 LEU A 82 92.75 -170.29 REMARK 500 1 ALA A 107 109.26 -50.92 REMARK 500 1 ILE A 140 -38.25 -140.64 REMARK 500 1 ASN A 146 -16.19 172.80 REMARK 500 1 ALA A 147 97.62 -61.83 REMARK 500 1 ALA A 156 113.08 -165.32 REMARK 500 2 ILE A 25 14.90 -146.85 REMARK 500 2 LYS A 38 37.23 -73.30 REMARK 500 2 MET A 39 117.66 -38.09 REMARK 500 2 PRO A 41 36.59 -74.72 REMARK 500 2 ARG A 52 -11.07 -47.44 REMARK 500 2 PRO A 54 -70.86 -68.22 REMARK 500 2 ALA A 73 37.24 -73.77 REMARK 500 2 LEU A 82 92.66 -170.28 REMARK 500 2 ALA A 107 108.19 -43.04 REMARK 500 2 ILE A 140 -39.03 -140.01 REMARK 500 2 ASN A 146 -16.53 172.65 REMARK 500 2 ALA A 147 98.20 -56.22 REMARK 500 3 LEU A 5 113.37 -177.00 REMARK 500 3 GLN A 7 113.83 -170.60 REMARK 500 3 ILE A 25 20.83 -155.71 REMARK 500 3 LYS A 38 37.63 -64.86 REMARK 500 3 MET A 39 113.75 -37.82 REMARK 500 3 ALA A 49 113.88 -176.62 REMARK 500 3 GLN A 51 -66.62 -176.48 REMARK 500 3 ARG A 52 -16.49 -158.42 REMARK 500 3 ALA A 70 78.26 -67.43 REMARK 500 3 GLU A 74 113.36 -38.81 REMARK 500 3 LYS A 87 -32.38 -138.55 REMARK 500 3 ILE A 89 21.77 -76.81 REMARK 500 3 ALA A 107 108.70 -49.05 REMARK 500 3 ILE A 140 -38.39 -139.08 REMARK 500 3 ASN A 146 -11.48 172.40 REMARK 500 3 ALA A 147 75.08 -63.38 REMARK 500 4 ILE A 25 18.39 -154.51 REMARK 500 4 LYS A 38 37.61 -75.73 REMARK 500 4 MET A 39 131.92 -37.84 REMARK 500 4 PRO A 41 39.60 -74.79 REMARK 500 4 ALA A 73 37.10 -83.48 REMARK 500 4 LEU A 82 92.94 -170.30 REMARK 500 4 ALA A 107 105.25 -54.26 REMARK 500 4 LYS A 119 -75.69 -112.47 REMARK 500 4 ILE A 140 -33.87 -140.48 REMARK 500 REMARK 500 THIS ENTRY HAS 276 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 1 SER A 2 1 -125.45 REMARK 500 GLY A 1 SER A 2 2 143.36 REMARK 500 GLY A 1 SER A 2 5 144.87 REMARK 500 GLY A 1 SER A 2 6 140.74 REMARK 500 GLY A 1 SER A 2 9 136.20 REMARK 500 GLY A 1 SER A 2 10 136.67 REMARK 500 GLY A 1 SER A 2 13 135.35 REMARK 500 GLY A 1 SER A 2 16 142.52 REMARK 500 GLY A 1 SER A 2 17 120.51 REMARK 500 GLY A 1 SER A 2 19 130.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 PHE A 149 0.08 SIDE CHAIN REMARK 500 2 ARG A 52 0.08 SIDE CHAIN REMARK 500 2 PHE A 149 0.09 SIDE CHAIN REMARK 500 4 ARG A 47 0.10 SIDE CHAIN REMARK 500 4 ARG A 83 0.08 SIDE CHAIN REMARK 500 4 PHE A 149 0.08 SIDE CHAIN REMARK 500 6 TYR A 13 0.12 SIDE CHAIN REMARK 500 6 ARG A 22 0.14 SIDE CHAIN REMARK 500 6 ARG A 83 0.08 SIDE CHAIN REMARK 500 7 ARG A 47 0.12 SIDE CHAIN REMARK 500 8 ARG A 47 0.08 SIDE CHAIN REMARK 500 8 ARG A 83 0.08 SIDE CHAIN REMARK 500 8 PHE A 149 0.08 SIDE CHAIN REMARK 500 9 PHE A 149 0.08 SIDE CHAIN REMARK 500 10 ARG A 22 0.13 SIDE CHAIN REMARK 500 10 ARG A 47 0.12 SIDE CHAIN REMARK 500 10 ARG A 83 0.09 SIDE CHAIN REMARK 500 11 ARG A 83 0.08 SIDE CHAIN REMARK 500 12 ARG A 22 0.10 SIDE CHAIN REMARK 500 13 ARG A 47 0.10 SIDE CHAIN REMARK 500 15 ARG A 47 0.16 SIDE CHAIN REMARK 500 15 ARG A 52 0.08 SIDE CHAIN REMARK 500 18 ARG A 52 0.09 SIDE CHAIN REMARK 500 18 ARG A 83 0.10 SIDE CHAIN REMARK 500 20 PHE A 42 0.08 SIDE CHAIN REMARK 500 20 PHE A 150 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2D3J A 8 157 UNP Q9Y5W5 WIF1_HUMAN 32 181 SEQADV 2D3J GLY A 1 UNP Q9Y5W5 CLONING ARTIFACT SEQADV 2D3J SER A 2 UNP Q9Y5W5 CLONING ARTIFACT SEQADV 2D3J HIS A 3 UNP Q9Y5W5 CLONING ARTIFACT SEQADV 2D3J MET A 4 UNP Q9Y5W5 CLONING ARTIFACT SEQADV 2D3J LEU A 5 UNP Q9Y5W5 CLONING ARTIFACT SEQADV 2D3J ASP A 6 UNP Q9Y5W5 CLONING ARTIFACT SEQADV 2D3J GLN A 7 UNP Q9Y5W5 CLONING ARTIFACT SEQRES 1 A 157 GLY SER HIS MET LEU ASP GLN GLN GLU GLU SER LEU TYR SEQRES 2 A 157 LEU TRP ILE ASP ALA HIS GLN ALA ARG VAL LEU ILE GLY SEQRES 3 A 157 PHE GLU GLU ASP ILE LEU ILE VAL SER GLU GLY LYS MET SEQRES 4 A 157 ALA PRO PHE THR HIS ASP PHE ARG LYS ALA GLN GLN ARG SEQRES 5 A 157 MET PRO ALA ILE PRO VAL ASN ILE HIS SER MET ASN PHE SEQRES 6 A 157 THR TRP GLN ALA ALA GLY GLN ALA GLU TYR PHE TYR GLU SEQRES 7 A 157 PHE LEU SER LEU ARG SER LEU ASP LYS GLY ILE MET ALA SEQRES 8 A 157 ASP PRO THR VAL ASN VAL PRO LEU LEU GLY THR VAL PRO SEQRES 9 A 157 HIS LYS ALA SER VAL VAL GLN VAL GLY PHE PRO CYS LEU SEQRES 10 A 157 GLY LYS GLN ASP GLY VAL ALA ALA PHE GLU VAL ASP VAL SEQRES 11 A 157 ILE VAL MET ASN SER GLU GLY ASN THR ILE LEU GLN THR SEQRES 12 A 157 PRO GLN ASN ALA ILE PHE PHE LYS THR CYS LEU GLN ALA SEQRES 13 A 157 GLU HELIX 1 1 ASP A 17 GLY A 26 1 10 HELIX 2 2 PRO A 41 LYS A 48 1 8 SHEET 1 A 5 ILE A 31 VAL A 34 0 SHEET 2 A 5 TYR A 13 ILE A 16 -1 N ILE A 16 O ILE A 31 SHEET 3 A 5 SER A 62 GLN A 68 -1 O THR A 66 N TRP A 15 SHEET 4 A 5 SER A 108 GLY A 113 -1 O VAL A 110 N PHE A 65 SHEET 5 A 5 THR A 94 VAL A 95 -1 N THR A 94 O GLY A 113 SHEET 1 B 5 ALA A 55 ILE A 56 0 SHEET 2 B 5 ILE A 148 CYS A 153 1 O THR A 152 N ILE A 56 SHEET 3 B 5 GLY A 122 MET A 133 -1 N ALA A 124 O LYS A 151 SHEET 4 B 5 TYR A 75 SER A 84 -1 N PHE A 76 O MET A 133 SHEET 5 B 5 LEU A 100 VAL A 103 -1 O GLY A 101 N TYR A 77 SHEET 1 C 4 ALA A 55 ILE A 56 0 SHEET 2 C 4 ILE A 148 CYS A 153 1 O THR A 152 N ILE A 56 SHEET 3 C 4 GLY A 122 MET A 133 -1 N ALA A 124 O LYS A 151 SHEET 4 C 4 THR A 139 GLN A 142 -1 O ILE A 140 N VAL A 132 SSBOND 1 CYS A 116 CYS A 153 1555 1555 2.03 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1