PDB Short entry for 1W8A 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 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: 293-EBNA; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PCEP-PU KEYWDS SIGNALING PROTEIN, SECRETED PROTEIN, AXON GUIDANCE, LEUCINE-RICH KEYWDS 2 REPEAT GLYCOPROTEIN, EGF-LIKE DOMAIN, SIGNAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.A.HOWITT,N.J.CLOUT,E.HOHENESTER REVDAT 5 13-DEC-23 1W8A 1 REMARK REVDAT 4 08-NOV-17 1W8A 1 SOURCE REMARK REVDAT 3 24-FEB-09 1W8A 1 VERSN 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 DISSECTION OF JRNL TITL 2 THE LEUCINE-RICH REPEAT REGION OF SLIT. JRNL REF EMBO J. V. 23 4406 2004 JRNL REFN ISSN 0261-4189 JRNL PMID 15496984 JRNL DOI 10.1038/SJ.EMBOJ.7600446 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)) : 10000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.8 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 : 5 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) : 1.500 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1W8A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-SEP-04. REMARK 100 THE DEPOSITION ID IS D_1290021081. 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 : 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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 (%): 44.19 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 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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. (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 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 ASN A 698 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LEU A 697 C O 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 MET A 546 38.60 -94.58 REMARK 500 ASP A 567 63.70 -100.17 REMARK 500 SER A 587 78.04 -108.84 REMARK 500 ARG A 604 70.42 43.69 REMARK 500 ALA A 618 56.23 -102.04 REMARK 500 ASN A 629 -169.13 -124.38 REMARK 500 ASN A 653 -152.06 -112.33 REMARK 500 LEU A 666 75.48 -108.02 REMARK 500 ASN A 682 -163.98 -125.29 REMARK 500 LYS A 694 -74.21 -87.16 REMARK 500 SER A 696 97.25 62.32 REMARK 500 ASN A 698 9.36 -69.68 REMARK 500 ALA A 706 -59.47 -140.86 REMARK 500 PRO A 707 87.22 -64.27 REMARK 500 SER A 708 -56.41 -18.89 REMARK 500 ARG A 711 151.32 -41.81 REMARK 500 ASP A 712 4.00 53.83 REMARK 500 HIS A 720 -13.51 -48.54 REMARK 500 SER A 726 120.26 175.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OZN RELATED DB: PDB REMARK 900 NOGO RECEPTOR LIGAND BINDING DOMAIN 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 1555 1555 2.03 SSBOND 2 CYS A 547 CYS A 556 1555 1555 2.03 SSBOND 3 CYS A 657 CYS A 733 1555 1555 2.01 SSBOND 4 CYS A 681 CYS A 704 1555 1555 2.03 SSBOND 5 CYS A 683 CYS A 725 1555 1555 2.02 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