HEADER SIGNALING PROTEIN 01-JUN-17 5O5I TITLE ROBO1 IG5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ROUNDABOUT HOMOLOG 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DELETED IN U TWENTY TWENTY,H-ROBO-1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ROBO1, DUTT1; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HEK293T; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PTT3 KEYWDS NEURONAL RECEPTOR, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.ALEKSANDROVA,I.GUTSCHE,E.KANDIAH,S.V.AVILOV,M.V.PETOUKHOV, AUTHOR 2 E.SEIRADAKE,A.A.MCCARTHY REVDAT 4 17-JAN-24 5O5I 1 REMARK REVDAT 3 02-MAY-18 5O5I 1 REMARK REVDAT 2 14-FEB-18 5O5I 1 JRNL REVDAT 1 17-JAN-18 5O5I 0 JRNL AUTH N.ALEKSANDROVA,I.GUTSCHE,E.KANDIAH,S.V.AVILOV,M.V.PETOUKHOV, JRNL AUTH 2 E.SEIRADAKE,A.A.MCCARTHY JRNL TITL ROBO1 FORMS A COMPACT DIMER-OF-DIMERS ASSEMBLY. JRNL REF STRUCTURE V. 26 320 2018 JRNL REFN ISSN 1878-4186 JRNL PMID 29307485 JRNL DOI 10.1016/J.STR.2017.12.003 REMARK 2 REMARK 2 RESOLUTION. 3.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 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) : 3.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 2081 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) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.810 REMARK 3 FREE R VALUE TEST SET COUNT : 100 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) : 3.01 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 3.37 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.66 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 586 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2378 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 554 REMARK 3 BIN R VALUE (WORKING SET) : 0.2326 REMARK 3 BIN FREE R VALUE : 0.3198 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.46 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 : 689 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 8 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 74.92 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.12150 REMARK 3 B22 (A**2) : -2.12150 REMARK 3 B33 (A**2) : 4.24310 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.410 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.427 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 : 0.923 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.859 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 716 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 982 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 241 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 17 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 106 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 716 ; 20.000 ; 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 : 100 ; 5.000 ; 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 : 785 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.13 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.32 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 18.70 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): 27.1298 -28.4573 6.1192 REMARK 3 T TENSOR REMARK 3 T11: -0.2587 T22: -0.0934 REMARK 3 T33: 0.0796 T12: -0.1788 REMARK 3 T13: 0.1951 T23: -0.0983 REMARK 3 L TENSOR REMARK 3 L11: 7.6549 L22: 14.8721 REMARK 3 L33: 6.0750 L12: 0.5879 REMARK 3 L13: 0.6084 L23: -3.5043 REMARK 3 S TENSOR REMARK 3 S11: 0.4310 S12: -0.3811 S13: -0.4810 REMARK 3 S21: 0.1940 S22: 0.0360 S23: 0.4532 REMARK 3 S31: -0.7193 S32: 0.0980 S33: -0.4671 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5O5I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1200005231. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-SEP-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9393 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : TOROIDAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 2 NOVEMBER 2014 REMARK 200 DATA SCALING SOFTWARE : XSCALE 2 NOVEMBER 2014 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2082 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 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: 2V9Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 100 MM SODIUM ACETATE,, REMARK 280 PH 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 8.94333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.88667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 13.41500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 22.35833 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 4.47167 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 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 GLN A 459 CB CG CD OE1 NE2 REMARK 480 LYS A 503 CD CE NZ REMARK 480 LYS A 516 CD CE NZ REMARK 480 GLN A 543 CB CG CD OE1 NE2 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 ASP A 469 -0.84 78.19 REMARK 500 LEU A 505 -62.78 -29.97 REMARK 500 REMARK 500 REMARK: NULL DBREF 5O5I A 454 543 UNP Q9Y6N7 ROBO1_HUMAN 454 543 SEQADV 5O5I ALA A 544 UNP Q9Y6N7 EXPRESSION TAG SEQADV 5O5I GLY A 545 UNP Q9Y6N7 EXPRESSION TAG SEQRES 1 A 92 PRO PRO VAL ILE ARG GLN GLY PRO VAL ASN GLN THR VAL SEQRES 2 A 92 ALA VAL ASP GLY THR PHE VAL LEU SER CYS VAL ALA THR SEQRES 3 A 92 GLY SER PRO VAL PRO THR ILE LEU TRP ARG LYS ASP GLY SEQRES 4 A 92 VAL LEU VAL SER THR GLN ASP SER ARG ILE LYS GLN LEU SEQRES 5 A 92 GLU ASN GLY VAL LEU GLN ILE ARG TYR ALA LYS LEU GLY SEQRES 6 A 92 ASP THR GLY ARG TYR THR CYS ILE ALA SER THR PRO SER SEQRES 7 A 92 GLY GLU ALA THR TRP SER ALA TYR ILE GLU VAL GLN ALA SEQRES 8 A 92 GLY FORMUL 2 HOH *8(H2 O) HELIX 1 AA1 LYS A 516 THR A 520 5 5 SHEET 1 AA1 2 VAL A 456 GLN A 459 0 SHEET 2 AA1 2 VAL A 477 THR A 479 -1 O THR A 479 N VAL A 456 SHEET 1 AA2 5 GLN A 464 ALA A 467 0 SHEET 2 AA2 5 GLY A 532 GLN A 543 1 O GLU A 541 N VAL A 466 SHEET 3 AA2 5 GLY A 521 THR A 529 -1 N TYR A 523 O ALA A 538 SHEET 4 AA2 5 THR A 485 LYS A 490 -1 N LEU A 487 O ILE A 526 SHEET 5 AA2 5 VAL A 493 LEU A 494 -1 O VAL A 493 N LYS A 490 SHEET 1 AA3 3 PHE A 472 SER A 475 0 SHEET 2 AA3 3 VAL A 509 ILE A 512 -1 O ILE A 512 N PHE A 472 SHEET 3 AA3 3 ILE A 502 GLU A 506 -1 N LYS A 503 O GLN A 511 SSBOND 1 CYS A 476 CYS A 525 1555 1555 2.02 CISPEP 1 SER A 481 PRO A 482 0 5.47 CRYST1 80.820 80.820 26.830 90.00 90.00 120.00 P 61 6 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 0.012373 0.007144 0.000000 0.00000 SCALE2 0.000000 0.014287 0.000000 0.00000 SCALE3 0.000000 0.000000 0.037272 0.00000