HEADER SIGNALING PROTEIN 08-OCT-14 4V2D TITLE FLRT2 LRR DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIBRONECTIN LEUCINE RICH TRANSMEMBRANE PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LRR DOMAIN, UNP RESIDUES 36-381; COMPND 5 SYNONYM: FLRT2; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PHLSEC KEYWDS SIGNALING PROTEIN, LEUCINE-RICH REPEAT, UNC5 EXPDTA X-RAY DIFFRACTION AUTHOR E.SEIRADAKE,D.DEL TORO,D.NAGEL,F.COP,R.HAERTL,T.RUFF,G.SEYIT-BREMER, AUTHOR 2 K.HARLOS,E.C.BORDER,A.ACKER-PALMER,E.Y.JONES,R.KLEIN REVDAT 2 22-JUL-15 4V2D 1 JRNL REVDAT 1 05-NOV-14 4V2D 0 JRNL AUTH E.SEIRADAKE,D.DEL TORO,D.NAGEL,F.COP,R.HAERTL,T.RUFF, JRNL AUTH 2 G.SEYIT-BREMER,K.HARLOS,E.C.BORDER,A.ACKER-PALMER,E.Y.JONES, JRNL AUTH 3 R.KLEIN JRNL TITL FLRT STRUCTURE: BALANCING REPULSION AND CELL ADHESION IN JRNL TITL 2 CORTICAL AND VASCULAR DEVELOPMENT JRNL REF NEURON V. 84 370 2014 JRNL REFN ISSN 0896-6273 JRNL PMID 25374360 JRNL DOI 10.1016/J.NEURON.2014.10.008 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.2 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0 REMARK 3 COMPLETENESS FOR RANGE (%) : 79.07 REMARK 3 NUMBER OF REFLECTIONS : 8815 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 + TEST SET) : 0.2808 REMARK 3 R VALUE (WORKING SET) : 0.2798 REMARK 3 FREE R VALUE : 0.3010 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.72 REMARK 3 FREE R VALUE TEST SET COUNT : 416 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 : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.79 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.07 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 1333 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2881 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1268 REMARK 3 BIN R VALUE (WORKING SET) : 0.2851 REMARK 3 BIN FREE R VALUE : 0.3532 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.88 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 65 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 : 2559 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 60.23 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.57 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 11.7480 REMARK 3 B22 (A**2) : -32.7722 REMARK 3 B33 (A**2) : 21.0242 REMARK 3 B12 (A**2) : 0.0000 REMARK 3 B13 (A**2) : -3.8112 REMARK 3 B23 (A**2) : 0.0000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.610 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.424 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.8354 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.7884 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2613 ; 2.00 ; HARMONIC REMARK 3 BOND ANGLES : 3553 ; 2.00 ; HARMONIC REMARK 3 TORSION ANGLES : 918 ; 2.00 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 75 ; 2.00 ; HARMONIC REMARK 3 GENERAL PLANES : 371 ; 5.00 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2613 ; 20.00 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 339 ; 5.00 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 2665 ; 4.00 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 0.96 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 1.29 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 19.41 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4V2D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-OCT-14. REMARK 100 THE PDBE ID CODE IS EBI-61948. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.968600 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2, XDS REMARK 200 DATA SCALING SOFTWARE : XIA2, XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26383 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.50 REMARK 200 RESOLUTION RANGE LOW (A) : 42.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NONE REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 78.8 REMARK 200 DATA REDUNDANCY : 2.9 REMARK 200 R MERGE (I) : 0.12 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.60 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 33.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.7 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.51 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 20.72500 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 ASN A 356 REMARK 465 LEU A 357 REMARK 465 LEU A 358 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 ASN A 110 43.21 -102.36 REMARK 500 ASP A 152 106.31 -59.58 REMARK 500 LEU A 166 44.85 -101.44 REMARK 500 ASN A 202 -6.38 69.28 REMARK 500 VAL A 211 63.32 -119.65 REMARK 500 SER A 241 53.84 -115.11 REMARK 500 GLN A 287 38.14 -95.31 REMARK 500 ASP A 315 -159.44 -137.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4V2A RELATED DB: PDB REMARK 900 HUMAN UNC5A ECTODOMAIN REMARK 900 RELATED ID: 4V2B RELATED DB: PDB REMARK 900 RAT UNC5D IG DOMAIN 1 REMARK 900 RELATED ID: 4V2C RELATED DB: PDB REMARK 900 MOUSE FLRT2 LRR DOMAIN IN COMPLEX WITH RAT UNC5D IG1 REMARK 900 DOMAIN REMARK 900 RELATED ID: 4V2E RELATED DB: PDB REMARK 900 FLRT3 LRR DOMAIN REMARK 999 REMARK 999 SEQUENCE REMARK 999 CONTAINS MUTATION E352A DBREF 4V2D A 36 361 UNP Q8BLU0 Q8BLU0_MOUSE 36 361 SEQADV 4V2D ALA A 352 UNP Q8BLU0 GLU 352 ENGINEERED MUTATION SEQRES 1 A 326 CYS PRO SER VAL CYS ARG CYS ASP ARG ASN PHE VAL TYR SEQRES 2 A 326 CYS ASN GLU ARG SER LEU THR SER VAL PRO LEU GLY ILE SEQRES 3 A 326 PRO GLU GLY VAL THR VAL LEU TYR LEU HIS ASN ASN GLN SEQRES 4 A 326 ILE ASN ASN ALA GLY PHE PRO ALA GLU LEU HIS ASN VAL SEQRES 5 A 326 GLN SER VAL HIS THR VAL TYR LEU TYR GLY ASN GLN LEU SEQRES 6 A 326 ASP GLU PHE PRO MET ASN LEU PRO LYS ASN VAL ARG VAL SEQRES 7 A 326 LEU HIS LEU GLN GLU ASN ASN ILE GLN THR ILE SER ARG SEQRES 8 A 326 ALA ALA LEU ALA GLN LEU LEU LYS LEU GLU GLU LEU HIS SEQRES 9 A 326 LEU ASP ASP ASN SER ILE SER THR VAL GLY VAL GLU ASP SEQRES 10 A 326 GLY ALA PHE ARG GLU ALA ILE SER LEU LYS LEU LEU PHE SEQRES 11 A 326 LEU SER LYS ASN HIS LEU SER SER VAL PRO VAL GLY LEU SEQRES 12 A 326 PRO VAL ASP LEU GLN GLU LEU ARG VAL ASP GLU ASN ARG SEQRES 13 A 326 ILE ALA VAL ILE SER ASP MET ALA PHE GLN ASN LEU THR SEQRES 14 A 326 SER LEU GLU ARG LEU ILE VAL ASP GLY ASN LEU LEU THR SEQRES 15 A 326 ASN LYS GLY ILE ALA GLU GLY THR PHE SER HIS LEU THR SEQRES 16 A 326 LYS LEU LYS GLU PHE SER ILE VAL ARG ASN SER LEU SER SEQRES 17 A 326 HIS PRO PRO PRO ASP LEU PRO GLY THR HIS LEU ILE ARG SEQRES 18 A 326 LEU TYR LEU GLN ASP ASN GLN ILE ASN HIS ILE PRO LEU SEQRES 19 A 326 THR ALA PHE ALA ASN LEU ARG LYS LEU GLU ARG LEU ASP SEQRES 20 A 326 ILE SER ASN ASN GLN LEU ARG MET LEU THR GLN GLY VAL SEQRES 21 A 326 PHE ASP HIS LEU SER ASN LEU LYS GLN LEU THR ALA ARG SEQRES 22 A 326 ASN ASN PRO TRP PHE CYS ASP CYS SER ILE LYS TRP VAL SEQRES 23 A 326 THR GLU TRP LEU LYS TYR ILE PRO SER SER LEU ASN VAL SEQRES 24 A 326 ARG GLY PHE MET CYS GLN GLY PRO GLU GLN VAL ARG GLY SEQRES 25 A 326 MET ALA VAL ARG ALA LEU ASN MET ASN LEU LEU SER CYS SEQRES 26 A 326 PRO HELIX 1 1 PRO A 81 HIS A 85 5 5 HELIX 2 2 SER A 125 LEU A 132 1 8 HELIX 3 3 ALA A 154 ALA A 158 5 5 HELIX 4 4 ASP A 315 SER A 317 5 3 HELIX 5 5 ILE A 318 ILE A 328 1 11 HELIX 6 6 VAL A 350 LEU A 353 5 4 SHEET 1 AA14 ARG A 41 ASP A 43 0 SHEET 2 AA14 PHE A 46 TYR A 48 -1 O PHE A 46 N ASP A 43 SHEET 3 AA14 VAL A 67 TYR A 69 1 O VAL A 67 N VAL A 47 SHEET 4 AA14 THR A 92 TYR A 94 1 O THR A 92 N LEU A 68 SHEET 5 AA14 VAL A 113 HIS A 115 1 O VAL A 113 N VAL A 93 SHEET 6 AA14 GLU A 137 HIS A 139 1 O GLU A 137 N LEU A 114 SHEET 7 AA14 LEU A 163 PHE A 165 1 O LEU A 163 N LEU A 138 SHEET 8 AA14 GLU A 184 ARG A 186 1 O GLU A 184 N LEU A 164 SHEET 9 AA14 ARG A 208 ILE A 210 1 O ARG A 208 N LEU A 185 SHEET 10 AA14 GLU A 234 SER A 236 1 O GLU A 234 N LEU A 209 SHEET 11 AA14 ARG A 256 TYR A 258 1 O ARG A 256 N PHE A 235 SHEET 12 AA14 ARG A 280 ASP A 282 1 O ARG A 280 N LEU A 257 SHEET 13 AA14 GLN A 304 THR A 306 1 O GLN A 304 N LEU A 281 SHEET 14 AA14 ASN A 333 ARG A 335 1 O ASN A 333 N LEU A 305 SHEET 1 AB 2 TRP A 312 PHE A 313 0 SHEET 2 AB 2 CYS A 339 GLY A 341 1 N GLN A 340 O TRP A 312 SSBOND 1 CYS A 36 CYS A 42 1555 1555 2.03 SSBOND 2 CYS A 40 CYS A 49 1555 1555 2.04 SSBOND 3 CYS A 314 CYS A 339 1555 1555 2.03 SSBOND 4 CYS A 316 CYS A 360 1555 1555 2.03 CISPEP 1 GLY A 341 PRO A 342 0 -1.20 CRYST1 45.120 41.450 87.350 90.00 102.91 90.00 P 1 21 1 2 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 0.022163 0.000000 0.005080 0.00000 SCALE2 0.000000 0.024125 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011745 0.00000