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
(ATOM LINES ARE NOT SHOWN.)
END
