[Scop | Full Entry | Seq (local cached copy) | More Options ]
HEADER SIGNALING PROTEIN 17-SEP-04 1W8A TITLE THIRD LRR DOMAIN OF DROSOPHILA SLIT COMPND MOL_ID: 1; COMPND 2 MOLECULE: SLIT PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: THIRD LRR DOMAIN, RESIDUES 542-733; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 4 EXPRESSION_SYSTEM_CELL_LINE: 293-EBNA; SOURCE 5 EXPRESSION_SYSTEM_PLASMID: PCEP-PU KEYWDS SECRETED PROTEIN, AXON GUIDANCE, LEUCINE-RICH REPEAT KEYWDS 2 GLYCOPROTEIN, EGF-LIKE DOMAIN, SIGNAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.A.HOWITT,N.J.CLOUT,E.HOHENESTER REVDAT 2 20-DEC-06 1W8A 1 JRNL REVDAT 1 25-OCT-04 1W8A 0 JRNL AUTH J.A.HOWITT,N.J.CLOUT,E.HOHENESTER JRNL TITL BINDING SITE FOR ROBO RECEPTORS REVEALED BY JRNL TITL 2 DISSECTION OF THE LEUCINE-RICH REPEAT REGION OF JRNL TITL 3 SLIT. JRNL REF EMBO J. V. 23 4406 2004 JRNL REFN ASTM EMJODG UK ISSN 0261-4189 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.80 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 4705 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) : 0.199 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 493 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 : 1465 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : NULL 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) : -8.41700 REMARK 3 B22 (A**2) : 0.52800 REMARK 3 B33 (A**2) : 7.88900 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.61000 REMARK 3 B23 (A**2) : 0.00000 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) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.50 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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) : 0.817 ; 1.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.441 ; 1.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.239 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.480 ; 3.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.29 REMARK 3 BSOL : 21.61 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1W8A COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.103 (2007-05-31) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY EBI . REMARK 100 THE EBI ID CODE IS EBI-21081 . REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 293.0 REMARK 200 PH : NULL 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 RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4705 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.19000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1OZN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 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 3555 1/2+X,1/2+Y,Z REMARK 290 4555 1/2-X,1/2+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 SMTRY1 3 1.000000 0.000000 0.000000 60.60650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.92600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 60.60650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.92600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 APPLY THE FOLLOWING TO CHAINS: A, Z 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 GLU A 728 REMARK 465 ASN A 729 REMARK 465 SER A 730 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 MET A 659 SD MET A 659 CE 0.042 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS A 549 N - CA - C ANGL. DEV. = 9.9 DEGREES REMARK 500 ASN A 653 N - CA - C ANGL. DEV. =-10.6 DEGREES REMARK 500 SER A 668 N - CA - C ANGL. DEV. = 9.8 DEGREES DBREF 1W8A A 542 733 UNP P24014 SLIT_DROME 542 733 SEQRES 1 A 192 ASP CYS PRO ALA MET CYS HIS CYS GLU GLY THR THR VAL SEQRES 2 A 192 ASP CYS THR GLY ARG GLY LEU LYS GLU ILE PRO ARG ASP SEQRES 3 A 192 ILE PRO LEU HIS THR THR GLU LEU LEU LEU ASN ASP ASN SEQRES 4 A 192 GLU LEU GLY ARG ILE SER SER ASP GLY LEU PHE GLY ARG SEQRES 5 A 192 LEU PRO HIS LEU VAL LYS LEU GLU LEU LYS ARG ASN GLN SEQRES 6 A 192 LEU THR GLY ILE GLU PRO ASN ALA PHE GLU GLY ALA SER SEQRES 7 A 192 HIS ILE GLN GLU LEU GLN LEU GLY GLU ASN LYS ILE LYS SEQRES 8 A 192 GLU ILE SER ASN LYS MET PHE LEU GLY LEU HIS GLN LEU SEQRES 9 A 192 LYS THR LEU ASN LEU TYR ASP ASN GLN ILE SER CYS VAL SEQRES 10 A 192 MET PRO GLY SER PHE GLU HIS LEU ASN SER LEU THR SER SEQRES 11 A 192 LEU ASN LEU ALA SER ASN PRO PHE ASN CYS ASN CYS HIS SEQRES 12 A 192 LEU ALA TRP PHE ALA GLU TRP LEU ARG LYS LYS SER LEU SEQRES 13 A 192 ASN GLY GLY ALA ALA ARG CYS GLY ALA PRO SER LYS VAL SEQRES 14 A 192 ARG ASP VAL GLN ILE LYS ASP LEU PRO HIS SER GLU PHE SEQRES 15 A 192 LYS CYS SER SER GLU ASN SER GLU GLY CYS FORMUL 2 HOH *5(H2 O) HELIX 1 1 LEU A 590 LEU A 594 5 5 HELIX 2 2 ASN A 682 HIS A 684 5 3 HELIX 3 3 LEU A 685 SER A 696 1 12 HELIX 4 4 ASN A 698 ALA A 702 5 5 HELIX 5 5 ILE A 715 LEU A 718 5 4 SHEET 1 AA 7 HIS A 548 GLU A 550 0 SHEET 2 AA 7 THR A 553 ASP A 555 -1 O THR A 553 N GLU A 550 SHEET 3 AA 7 GLU A 574 LEU A 576 1 O GLU A 574 N VAL A 554 SHEET 4 AA 7 LYS A 599 GLU A 601 1 O LYS A 599 N LEU A 575 SHEET 5 AA 7 GLU A 623 GLN A 625 1 O GLU A 623 N LEU A 600 SHEET 6 AA 7 THR A 647 ASN A 649 1 O THR A 647 N LEU A 624 SHEET 7 AA 7 SER A 671 ASN A 673 1 O SER A 671 N LEU A 648 SHEET 1 AB 2 GLU A 633 ILE A 634 0 SHEET 2 AB 2 CYS A 657 VAL A 658 1 O CYS A 657 N ILE A 634 SSBOND 1 CYS A 543 CYS A 549 SSBOND 2 CYS A 547 CYS A 556 SSBOND 3 CYS A 657 CYS A 733 SSBOND 4 CYS A 681 CYS A 704 SSBOND 5 CYS A 683 CYS A 725 CRYST1 121.213 31.852 49.526 90.00 100.72 90.00 C 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 0.008250 0.000000 0.001562 0.00000 SCALE2 0.000000 0.031395 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020550 0.00000