HEADER SIGNALING PROTEIN 01-MAY-01 1IJY TITLE CRYSTAL STRUCTURE OF THE CYSTEINE-RICH DOMAIN OF MOUSE FRIZZLED 8 TITLE 2 (MFZ8) COMPND MOL_ID: 1; COMPND 2 MOLECULE: FRIZZLED HOMOLOG 8; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CYSTEINE-RICH DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: FZD8; SOURCE 6 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 9 EXPRESSION_SYSTEM_CELL: OVARY CELLS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PSGHV0 KEYWDS WNT RECEPTOR, FRIZZLED PROTEIN STRUCTURE, CYSTEINE-RICH, SIGNALING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.E.DANN III,J.C.HSIEH,A.RATTNER,D.SHARMA,J.NATHANS,D.J.LEAHY REVDAT 7 30-OCT-24 1IJY 1 REMARK REVDAT 6 16-AUG-23 1IJY 1 REMARK REVDAT 5 27-OCT-21 1IJY 1 SEQADV REVDAT 4 28-MAY-14 1IJY 1 AUTHOR VERSN REVDAT 3 24-FEB-09 1IJY 1 VERSN REVDAT 2 01-APR-03 1IJY 1 JRNL REVDAT 1 11-JUL-01 1IJY 0 JRNL AUTH C.E.DANN III,J.C.HSIEH,A.RATTNER,D.SHARMA,J.NATHANS, JRNL AUTH 2 D.J.LEAHY JRNL TITL INSIGHTS INTO WNT BINDING AND SIGNALLING FROM THE STRUCTURES JRNL TITL 2 OF TWO FRIZZLED CYSTEINE-RICH DOMAINS. JRNL REF NATURE V. 412 86 2001 JRNL REFN ISSN 0028-0836 JRNL PMID 11452312 JRNL DOI 10.1038/35083601 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 48062 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 4898 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1978 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 279 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IJY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-MAY-01. REMARK 100 THE DEPOSITION ID IS D_1000013349. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAR-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9197 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48062 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.43700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1IJX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, HEPES, PH 7.3, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 GLY A -1 REMARK 465 SER A 0 REMARK 465 ALA A 1 REMARK 465 SER A 2 REMARK 465 ALA A 3 REMARK 465 LYS A 4 REMARK 465 THR A 127 REMARK 465 ASP A 128 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 ALA B 1 REMARK 465 SER B 2 REMARK 465 ALA B 3 REMARK 465 LYS B 4 REMARK 465 THR B 127 REMARK 465 ASP B 128 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 LYS A 74 48.73 -80.96 REMARK 500 LEU B 6 84.09 51.33 REMARK 500 CYS B 16 37.08 -95.63 REMARK 500 LYS B 74 60.74 -107.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IJX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CYSTEINE-RICH DOMAIN OF SECRETED FRIZZLED- REMARK 900 RELATED PROTEIN 3 (SFRP-3;FZB) DBREF 1IJY A 1 128 UNP Q61091 FZD8_MOUSE 28 155 DBREF 1IJY B 1 128 UNP Q61091 FZD8_MOUSE 28 155 SEQADV 1IJY GLY A -1 UNP Q61091 CLONING ARTIFACT SEQADV 1IJY SER A 0 UNP Q61091 CLONING ARTIFACT SEQADV 1IJY GLU A 22 UNP Q61091 ASN 49 ENGINEERED MUTATION SEQADV 1IJY GLU A 125 UNP Q61091 ASN 152 ENGINEERED MUTATION SEQADV 1IJY GLY B -1 UNP Q61091 CLONING ARTIFACT SEQADV 1IJY SER B 0 UNP Q61091 CLONING ARTIFACT SEQADV 1IJY GLU B 22 UNP Q61091 ASN 49 ENGINEERED MUTATION SEQADV 1IJY GLU B 125 UNP Q61091 ASN 152 ENGINEERED MUTATION SEQRES 1 A 130 GLY SER ALA SER ALA LYS GLU LEU ALA CYS GLN GLU ILE SEQRES 2 A 130 THR VAL PRO LEU CYS LYS GLY ILE GLY TYR GLU TYR THR SEQRES 3 A 130 TYR MET PRO ASN GLN PHE ASN HIS ASP THR GLN ASP GLU SEQRES 4 A 130 ALA GLY LEU GLU VAL HIS GLN PHE TRP PRO LEU VAL GLU SEQRES 5 A 130 ILE GLN CYS SER PRO ASP LEU LYS PHE PHE LEU CYS SER SEQRES 6 A 130 MET TYR THR PRO ILE CYS LEU GLU ASP TYR LYS LYS PRO SEQRES 7 A 130 LEU PRO PRO CYS ARG SER VAL CYS GLU ARG ALA LYS ALA SEQRES 8 A 130 GLY CYS ALA PRO LEU MET ARG GLN TYR GLY PHE ALA TRP SEQRES 9 A 130 PRO ASP ARG MET ARG CYS ASP ARG LEU PRO GLU GLN GLY SEQRES 10 A 130 ASN PRO ASP THR LEU CYS MET ASP TYR GLU ARG THR ASP SEQRES 1 B 130 GLY SER ALA SER ALA LYS GLU LEU ALA CYS GLN GLU ILE SEQRES 2 B 130 THR VAL PRO LEU CYS LYS GLY ILE GLY TYR GLU TYR THR SEQRES 3 B 130 TYR MET PRO ASN GLN PHE ASN HIS ASP THR GLN ASP GLU SEQRES 4 B 130 ALA GLY LEU GLU VAL HIS GLN PHE TRP PRO LEU VAL GLU SEQRES 5 B 130 ILE GLN CYS SER PRO ASP LEU LYS PHE PHE LEU CYS SER SEQRES 6 B 130 MET TYR THR PRO ILE CYS LEU GLU ASP TYR LYS LYS PRO SEQRES 7 B 130 LEU PRO PRO CYS ARG SER VAL CYS GLU ARG ALA LYS ALA SEQRES 8 B 130 GLY CYS ALA PRO LEU MET ARG GLN TYR GLY PHE ALA TRP SEQRES 9 B 130 PRO ASP ARG MET ARG CYS ASP ARG LEU PRO GLU GLN GLY SEQRES 10 B 130 ASN PRO ASP THR LEU CYS MET ASP TYR GLU ARG THR ASP FORMUL 3 HOH *279(H2 O) HELIX 1 1 VAL A 13 LYS A 17 5 5 HELIX 2 2 THR A 34 HIS A 43 1 10 HELIX 3 3 PHE A 45 GLN A 52 1 8 HELIX 4 4 ASP A 56 THR A 66 1 11 HELIX 5 5 CYS A 80 TYR A 98 1 19 HELIX 6 6 PRO A 103 ARG A 107 5 5 HELIX 7 7 ARG A 107 LEU A 111 5 5 HELIX 8 8 VAL B 13 LYS B 17 5 5 HELIX 9 9 THR B 34 HIS B 43 1 10 HELIX 10 10 PHE B 45 GLN B 52 1 8 HELIX 11 11 ASP B 56 THR B 66 1 11 HELIX 12 12 CYS B 80 TYR B 98 1 19 HELIX 13 13 PRO B 103 ARG B 107 5 5 SHEET 1 A 2 GLN A 9 GLU A 10 0 SHEET 2 A 2 TYR A 23 THR A 24 -1 N THR A 24 O GLN A 9 SHEET 1 B 2 GLN B 9 GLU B 10 0 SHEET 2 B 2 TYR B 23 THR B 24 -1 N THR B 24 O GLN B 9 SSBOND 1 CYS A 8 CYS A 69 1555 1555 2.04 SSBOND 2 CYS A 16 CYS A 62 1555 1555 2.03 SSBOND 3 CYS A 53 CYS A 91 1555 1555 2.04 SSBOND 4 CYS A 80 CYS A 121 1555 1555 2.03 SSBOND 5 CYS A 84 CYS A 108 1555 1555 2.04 SSBOND 6 CYS B 8 CYS B 69 1555 1555 2.04 SSBOND 7 CYS B 16 CYS B 62 1555 1555 2.03 SSBOND 8 CYS B 53 CYS B 91 1555 1555 2.03 SSBOND 9 CYS B 80 CYS B 121 1555 1555 2.04 SSBOND 10 CYS B 84 CYS B 108 1555 1555 2.03 CISPEP 1 MET A 26 PRO A 27 0 -0.19 CISPEP 2 MET B 26 PRO B 27 0 -0.04 CRYST1 55.690 36.370 57.940 90.00 98.82 90.00 P 1 2 1 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 0.017957 0.000000 0.002786 0.00000 SCALE2 0.000000 0.027495 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017466 0.00000