HEADER STRUCTURAL PROTEIN 02-DEC-03 1ROW TITLE STRUCTURE OF SSP-19, AN MSP-DOMAIN PROTEIN LIKE FAMILY MEMBER IN TITLE 2 CAENORHABDITIS ELEGANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: MSP-DOMAIN PROTEIN LIKE FAMILY MEMBER; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SSP-19; SPERM-SPECIFIC FAMILY, CLASS P SSP-19; HYPOTHETICAL COMPND 5 PROTEIN C55C2.2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_TAXID: 6239; SOURCE 4 STRAIN: BRISTOL N2 (CLONE C55C2); SOURCE 5 CELL: SPERM; SOURCE 6 GENE: SSP-19; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS BETA BARREL, STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE INITIATIVE, KEYWDS 2 SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS, SECSG, STRUCTURAL KEYWDS 3 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.SCHORMANN,J.SYMERSKY,M.CARSON,M.LUO,G.LIN,S.LI,S.QIU,A.ARABASHI, AUTHOR 2 B.BUNZEL,D.LUO,L.NAGY,R.GRAY,C.-H.LUAN,J.ZHANG,S.LU,L.DELUCAS, AUTHOR 3 SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS (SECSG) REVDAT 6 23-AUG-23 1ROW 1 REMARK REVDAT 5 11-OCT-17 1ROW 1 REMARK REVDAT 4 24-FEB-09 1ROW 1 VERSN REVDAT 3 01-FEB-05 1ROW 1 AUTHOR KEYWDS REMARK REVDAT 2 28-SEP-04 1ROW 1 JRNL HEADER REMARK REVDAT 1 23-DEC-03 1ROW 0 JRNL AUTH N.SCHORMANN,J.SYMERSKY,M.LUO JRNL TITL STRUCTURE OF SPERM-SPECIFIC PROTEIN SSP-19 FROM JRNL TITL 2 CAENORHABDITIS ELEGANS. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 60 1840 2004 JRNL REFN ISSN 0907-4449 JRNL PMID 15388931 JRNL DOI 10.1107/S0907444904017846 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 525587.120 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 85.9 REMARK 3 NUMBER OF REFLECTIONS : 11037 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 560 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.012 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 65.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1214 REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE : 0.3150 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 56 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.042 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1514 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 157 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -8.10000 REMARK 3 B22 (A**2) : -8.84000 REMARK 3 B33 (A**2) : 16.94000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -4.09000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.13 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.26 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 28.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.980 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.260 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.730 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.120 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.810 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 53.68 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: IN INITIAL STAGES RESTRAINED NCS WAS REMARK 3 USED, BUT LATER THE TWO MONOMERS WERE REFINED INDEPENDENTLY REMARK 4 REMARK 4 1ROW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-DEC-03. REMARK 100 THE DEPOSITION ID IS D_1000020919. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-OCT-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11037 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.2 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : 0.04800 REMARK 200 FOR THE DATA SET : 33.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 60.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.06600 REMARK 200 R SYM FOR SHELL (I) : 0.06600 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: HOMOLOGY MODEL (SWISS MODEL)BASED ON PDB ENTRY REMARK 200 1M1S REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.7M LITHIUM SULFATE, 0.05M MES, 0.1M REMARK 280 MAGNESIUM CHLORIDE, PH 5.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 15.92400 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: THE BIOLOGICAL UNIT IS A MONOMER 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A 1 REMARK 465 SER A 2 REMARK 465 MET B 1 REMARK 465 SER B 2 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 VAL A 17 CB CG1 CG2 REMARK 470 VAL B 17 CB CG1 CG2 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 VAL A 17 -169.69 170.96 REMARK 500 ALA A 83 -89.83 11.28 REMARK 500 VAL B 17 -173.10 172.92 REMARK 500 ASP B 84 -0.20 73.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1M1S RELATED DB: PDB REMARK 900 STRUCTURE OF WR4, A C. ELEGANS MSP FAMILY MEMBER REMARK 900 RELATED ID: C55C2.2 RELATED DB: TARGETDB DBREF 1ROW A 1 109 UNP O01829 O01829_CAEEL 1 109 DBREF 1ROW B 1 109 UNP O01829 O01829_CAEEL 1 109 SEQRES 1 A 109 MET SER LEU THR ALA ASP PRO PRO ALA CYS THR VAL PRO SEQRES 2 A 109 ALA ALA GLY VAL SER SER THR HIS LYS LEU VAL ASN GLY SEQRES 3 A 109 GLY ALA GLU LYS ILE VAL PHE LYS ILE LYS SER SER ASN SEQRES 4 A 109 ASN ASN GLU TYR ARG ILE ALA PRO VAL PHE GLY PHE VAL SEQRES 5 A 109 ASP PRO SER GLY SER LYS ASP VAL VAL ILE THR ARG THR SEQRES 6 A 109 ALA GLY ALA PRO LYS GLU ASP LYS LEU VAL VAL HIS PHE SEQRES 7 A 109 ALA SER ALA PRO ALA ASP ALA THR ASP ALA GLN ALA ALA SEQRES 8 A 109 PHE VAL ALA VAL ALA PRO ALA GLY THR VAL THR ILE PRO SEQRES 9 A 109 MET SER ALA THR ALA SEQRES 1 B 109 MET SER LEU THR ALA ASP PRO PRO ALA CYS THR VAL PRO SEQRES 2 B 109 ALA ALA GLY VAL SER SER THR HIS LYS LEU VAL ASN GLY SEQRES 3 B 109 GLY ALA GLU LYS ILE VAL PHE LYS ILE LYS SER SER ASN SEQRES 4 B 109 ASN ASN GLU TYR ARG ILE ALA PRO VAL PHE GLY PHE VAL SEQRES 5 B 109 ASP PRO SER GLY SER LYS ASP VAL VAL ILE THR ARG THR SEQRES 6 B 109 ALA GLY ALA PRO LYS GLU ASP LYS LEU VAL VAL HIS PHE SEQRES 7 B 109 ALA SER ALA PRO ALA ASP ALA THR ASP ALA GLN ALA ALA SEQRES 8 B 109 PHE VAL ALA VAL ALA PRO ALA GLY THR VAL THR ILE PRO SEQRES 9 B 109 MET SER ALA THR ALA FORMUL 3 HOH *157(H2 O) HELIX 1 1 ASP A 87 VAL A 93 1 7 HELIX 2 2 ASP B 87 ALA B 94 1 8 SHEET 1 A 4 THR A 4 ASP A 6 0 SHEET 2 A 4 VAL A 17 ASN A 25 -1 O VAL A 24 N THR A 4 SHEET 3 A 4 GLY A 56 ARG A 64 -1 O ILE A 62 N SER A 19 SHEET 4 A 4 TYR A 43 ALA A 46 -1 N ALA A 46 O VAL A 61 SHEET 1 B 5 CYS A 10 PRO A 13 0 SHEET 2 B 5 GLY A 99 THR A 108 1 O PRO A 104 N CYS A 10 SHEET 3 B 5 LYS A 70 SER A 80 -1 N LEU A 74 O ILE A 103 SHEET 4 B 5 ILE A 31 SER A 37 -1 N LYS A 36 O VAL A 75 SHEET 5 B 5 PHE A 49 VAL A 52 -1 O GLY A 50 N PHE A 33 SHEET 1 C 4 THR B 4 ASP B 6 0 SHEET 2 C 4 VAL B 17 VAL B 24 -1 O VAL B 24 N THR B 4 SHEET 3 C 4 SER B 57 ARG B 64 -1 O ILE B 62 N SER B 19 SHEET 4 C 4 TYR B 43 ALA B 46 -1 N ALA B 46 O VAL B 61 SHEET 1 D 5 CYS B 10 PRO B 13 0 SHEET 2 D 5 GLY B 99 THR B 108 1 O SER B 106 N CYS B 10 SHEET 3 D 5 LYS B 70 SER B 80 -1 N ASP B 72 O MET B 105 SHEET 4 D 5 ILE B 31 SER B 37 -1 N LYS B 36 O VAL B 75 SHEET 5 D 5 PHE B 49 VAL B 52 -1 O VAL B 52 N ILE B 31 CISPEP 1 ASP A 6 PRO A 7 0 0.00 CISPEP 2 ALA A 46 PRO A 47 0 -0.13 CISPEP 3 ASP B 6 PRO B 7 0 0.06 CISPEP 4 ALA B 46 PRO B 47 0 0.07 CRYST1 52.354 31.848 55.577 90.00 97.67 90.00 P 1 21 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 0.019101 0.000000 0.002572 0.00000 SCALE2 0.000000 0.031399 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018155 0.00000