HEADER PROTEIN BINDING 02-JAN-09 2KD3 TITLE NMR STRUCTURE OF THE WNT MODULATOR PROTEIN SCLEROSTIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SCLEROSTIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MSOST DELTANC, UNP RESIDUES 59-167; COMPND 5 SYNONYM: WNT MODULATOR PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)ROSETTA; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET28B KEYWDS PROTEIN, ANTAGONIST OF CYTOKINE, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR S.E.WEIDAUER,T.D.MUELLER REVDAT 3 16-MAR-22 2KD3 1 REMARK SEQADV REVDAT 2 07-APR-09 2KD3 1 JRNL REVDAT 1 10-FEB-09 2KD3 0 JRNL AUTH S.E.WEIDAUER,P.SCHMIEDER,M.BEERBAUM,W.SCHMITZ,H.OSCHKINAT, JRNL AUTH 2 T.D.MUELLER JRNL TITL NMR STRUCTURE OF THE WNT MODULATOR PROTEIN SCLEROSTIN JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 380 160 2009 JRNL REFN ISSN 0006-291X JRNL PMID 19166819 JRNL DOI 10.1016/J.BBRC.2009.01.062 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 2.0, X-PLOR NIH 2.21 REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), SCHWIETERS, KUSZEWSKI, REMARK 3 TJANDRA AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KD3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000100970. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 0.07 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM WNT MODULATOR PROTEIN-1, REMARK 210 95% H2O/5% D2O; 0.8 MM [U-95% REMARK 210 15N] WNT MODULATOR PROTEIN-2, 95% REMARK 210 H2O/5% D2O; 0.6 MM [U-95% 13C; REMARK 210 U-95% 15N] WNT MODULATOR PROTEIN- REMARK 210 3, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D CBCA(CO)NH; 3D CBCANNH; 3D REMARK 210 HBHA(CO)NH; 3D HN(CA)CO; 3D HNCO; REMARK 210 3D C(CO)NH; 3D H(CCO)NH; 3D REMARK 210 HCCH-TOCSY; 3D HCCH-COSY; 3D 1H- REMARK 210 13C NOESY; 3D 1H-15N NOESY; 3D REMARK 210 1H-15N TOCSY; 3D 1H-15N HSQC-NOE- REMARK 210 HMQC; 2D 1H-1H TOCSY; 2D DQF- REMARK 210 COSY; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AURELIA 3.8, X-PLOR NIH 2.21 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-15 REMARK 465 RES C SSSEQI REMARK 465 GLY A 32 REMARK 465 SER A 33 REMARK 465 HIS A 34 REMARK 465 MET A 35 REMARK 465 ASN A 36 REMARK 465 GLY A 37 REMARK 465 GLY A 38 REMARK 465 ARG A 39 REMARK 465 PRO A 40 REMARK 465 PRO A 41 REMARK 465 HIS A 42 REMARK 465 HIS A 43 REMARK 465 PRO A 44 REMARK 465 TYR A 45 REMARK 465 ASP A 46 REMARK 465 ALA A 47 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 O ARG A 101 H ASN A 103 1.52 REMARK 500 H ARG A 115 O LEU A 136 1.52 REMARK 500 H LEU A 121 O ARG A 130 1.58 REMARK 500 O GLY A 67 N CYS A 69 2.11 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 TYR A 53 -80.11 -110.99 REMARK 500 1 ARG A 56 -168.06 -55.36 REMARK 500 1 GLU A 57 70.98 -67.07 REMARK 500 1 PHE A 63 -79.08 -109.53 REMARK 500 1 LEU A 64 136.74 -170.72 REMARK 500 1 PRO A 68 56.23 -15.11 REMARK 500 1 ALA A 72 28.36 -147.66 REMARK 500 1 CYS A 84 24.12 -160.90 REMARK 500 1 ILE A 94 32.49 33.89 REMARK 500 1 LYS A 98 -45.76 -147.60 REMARK 500 1 TRP A 99 -84.39 -58.76 REMARK 500 1 PRO A 102 47.63 -59.44 REMARK 500 1 ASP A 112 -66.83 -107.83 REMARK 500 1 VAL A 137 84.54 -51.28 REMARK 500 2 ARG A 56 167.83 -44.21 REMARK 500 2 GLU A 57 88.32 -44.05 REMARK 500 2 PHE A 63 -83.39 -111.18 REMARK 500 2 PRO A 68 58.53 -16.57 REMARK 500 2 ALA A 72 28.30 -147.34 REMARK 500 2 ILE A 94 31.47 32.66 REMARK 500 2 LYS A 98 -32.83 164.72 REMARK 500 2 TRP A 100 132.01 -30.26 REMARK 500 2 ARG A 101 74.87 -119.47 REMARK 500 2 VAL A 137 83.22 -57.83 REMARK 500 2 SER A 139 115.14 -163.60 REMARK 500 3 TYR A 53 -83.90 -45.53 REMARK 500 3 CYS A 55 17.03 82.33 REMARK 500 3 ARG A 56 -156.65 -55.77 REMARK 500 3 PHE A 63 -79.29 -103.21 REMARK 500 3 LEU A 64 142.16 -177.46 REMARK 500 3 ASP A 66 -155.71 -150.29 REMARK 500 3 PRO A 68 59.74 -17.09 REMARK 500 3 ALA A 72 27.37 -146.93 REMARK 500 3 ALA A 93 -81.74 -119.22 REMARK 500 3 LYS A 98 20.65 -161.74 REMARK 500 3 TRP A 99 -83.60 -148.60 REMARK 500 3 ARG A 108 -116.57 -143.66 REMARK 500 3 ASP A 112 -60.14 -120.51 REMARK 500 3 ALA A 127 42.95 -83.46 REMARK 500 3 ALA A 128 53.89 -113.44 REMARK 500 3 VAL A 137 83.88 -52.83 REMARK 500 4 GLU A 57 85.35 -56.22 REMARK 500 4 HIS A 59 101.39 -169.29 REMARK 500 4 PHE A 63 -84.75 -110.01 REMARK 500 4 PRO A 68 53.42 -16.67 REMARK 500 4 ALA A 72 24.03 -148.26 REMARK 500 4 VAL A 79 79.87 -106.12 REMARK 500 4 ILE A 94 35.00 29.80 REMARK 500 4 LYS A 98 -32.90 164.77 REMARK 500 4 TRP A 99 39.66 -95.57 REMARK 500 REMARK 500 THIS ENTRY HAS 217 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 2KD3 A 36 144 UNP B2RQA5 B2RQA5_MOUSE 59 167 SEQADV 2KD3 GLY A 32 UNP B2RQA5 EXPRESSION TAG SEQADV 2KD3 SER A 33 UNP B2RQA5 EXPRESSION TAG SEQADV 2KD3 HIS A 34 UNP B2RQA5 EXPRESSION TAG SEQADV 2KD3 MET A 35 UNP B2RQA5 EXPRESSION TAG SEQRES 1 A 113 GLY SER HIS MET ASN GLY GLY ARG PRO PRO HIS HIS PRO SEQRES 2 A 113 TYR ASP ALA LYS ASP VAL SER GLU TYR SER CYS ARG GLU SEQRES 3 A 113 LEU HIS TYR THR ARG PHE LEU THR ASP GLY PRO CYS ARG SEQRES 4 A 113 SER ALA LYS PRO VAL THR GLU LEU VAL CYS SER GLY GLN SEQRES 5 A 113 CYS GLY PRO ALA ARG LEU LEU PRO ASN ALA ILE GLY ARG SEQRES 6 A 113 VAL LYS TRP TRP ARG PRO ASN GLY PRO ASP PHE ARG CYS SEQRES 7 A 113 ILE PRO ASP ARG TYR ARG ALA GLN ARG VAL GLN LEU LEU SEQRES 8 A 113 CYS PRO GLY GLY ALA ALA PRO ARG SER ARG LYS VAL ARG SEQRES 9 A 113 LEU VAL ALA SER CYS LYS CYS LYS ARG SHEET 1 A 2 THR A 65 ASP A 66 0 SHEET 2 A 2 CYS A 69 ARG A 70 -1 O CYS A 69 N ASP A 66 SHEET 1 B 2 ILE A 110 LEU A 121 0 SHEET 2 B 2 ARG A 130 LYS A 141 -1 O LEU A 136 N ARG A 115 SSBOND 1 CYS A 55 CYS A 109 1555 1555 2.03 SSBOND 2 CYS A 69 CYS A 123 1555 1555 2.03 SSBOND 3 CYS A 80 CYS A 140 1555 1555 2.03 SSBOND 4 CYS A 84 CYS A 142 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