HEADER IMMUNE SYSTEM 02-JUL-18 6A77 TITLE CRYSTAL STRUCTURE OF THE FIFTH IMMUNOGLOBULIN DOMAIN (IG5) OF HUMAN TITLE 2 ROBO1 IN COMPLEX WITH THE FAB FRAGMENT OF MURINE MONOCLONAL ANTIBODY TITLE 3 B5209B 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; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: LIGHT CHAIN OF THE ANTI-HUMAN ROBO1 ANTIBODY B5209B FAB; COMPND 8 CHAIN: L; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: HEAVY CHAIN OF THE ANTI-HUMAN ROBO1 ANTIBODY B5209B FAB; COMPND 12 CHAIN: H; COMPND 13 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: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 10 ORGANISM_TAXID: 10090; SOURCE 11 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 14 MOL_ID: 3; SOURCE 15 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 16 ORGANISM_TAXID: 10090; SOURCE 17 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 19 EXPRESSION_SYSTEM_CELL_LINE: HEK293 KEYWDS HEPATOCELLULAR CARCINOMA ANTIGEN, ANGIOGENESIS, IMMUNE SYSTEM, KEYWDS 2 ANTIBODY DRUG EXPDTA X-RAY DIFFRACTION AUTHOR E.MIZOHATA,T.NAKAYAMA,Y.KADO,T.INOUE REVDAT 2 20-MAR-19 6A77 1 JRNL REVDAT 1 30-JAN-19 6A77 0 JRNL AUTH T.YAMASHITA,E.MIZOHATA,S.NAGATOISHI,T.WATANABE,M.NAKAKIDO, JRNL AUTH 2 H.IWANARI,Y.MOCHIZUKI,T.NAKAYAMA,Y.KADO,Y.YOKOTA, JRNL AUTH 3 H.MATSUMURA,T.KAWAMURA,T.KODAMA,T.HAMAKUBO,T.INOUE, JRNL AUTH 4 H.FUJITANI,K.TSUMOTO JRNL TITL AFFINITY IMPROVEMENT OF A CANCER-TARGETED ANTIBODY THROUGH JRNL TITL 2 ALANINE-INDUCED ADJUSTMENT OF ANTIGEN-ANTIBODY INTERFACE. JRNL REF STRUCTURE V. 27 519 2019 JRNL REFN ISSN 1878-4186 JRNL PMID 30595454 JRNL DOI 10.1016/J.STR.2018.11.002 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 39899 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) : 0.240 REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2048 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2975 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.46 REMARK 3 BIN R VALUE (WORKING SET) : 0.4510 REMARK 3 BIN FREE R VALUE SET COUNT : 145 REMARK 3 BIN FREE R VALUE : 0.4660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3931 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 159 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.87000 REMARK 3 B22 (A**2) : -1.87000 REMARK 3 B33 (A**2) : 3.74000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.204 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.183 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.182 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.349 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4039 ; 0.019 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 3624 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5501 ; 2.102 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8459 ; 1.118 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 519 ; 7.996 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 152 ;37.743 ;24.079 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 647 ;18.583 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;17.350 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 632 ; 0.130 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4461 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 794 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2079 ; 5.469 ; 5.635 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2078 ; 5.468 ; 5.633 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2594 ; 7.332 ; 8.418 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2595 ; 7.331 ; 8.420 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1960 ; 5.586 ; 5.910 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1961 ; 5.584 ; 5.912 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2906 ; 7.599 ; 8.715 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 16281 ;10.524 ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 16230 ;10.522 ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6A77 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1300008266. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42067 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 97.1 REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 56.9000 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 (%) : NULL 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 : NULL 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: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM CITRATE TRIBASIC REMARK 280 DIHYDRATE (PH 5.6), 10% (W/V) PEG 8000, 10% (V/V) 2-PROPANOL, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 61.37800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 50.28300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 50.28300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 92.06700 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 50.28300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 50.28300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 30.68900 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 50.28300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.28300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 92.06700 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 50.28300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.28300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 30.68900 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 61.37800 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, L, H 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 CYS H 134A REMARK 465 GLY H 134B REMARK 465 ASP H 134C REMARK 465 THR H 134D REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NE ARG L 38 O LYS L 42 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH L 351 O HOH L 351 7555 1.21 REMARK 500 REMARK 500 REMARK: NULL 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 PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 76 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG L 108 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP L 170 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 23 -11.72 79.51 REMARK 500 VAL A 37 125.27 -39.13 REMARK 500 ASP A 45 53.26 39.70 REMARK 500 GLN A 52 -18.74 -39.41 REMARK 500 LEU A 59 -169.88 -101.18 REMARK 500 THR A 83 129.74 -176.24 REMARK 500 ALA L 51 -35.96 67.78 REMARK 500 ALA L 84 170.42 177.19 REMARK 500 SER L 127 0.24 -68.70 REMARK 500 GLU L 154 149.71 -33.38 REMARK 500 SER H 139 -39.01 76.49 REMARK 500 SER H 154 99.65 87.04 REMARK 500 ASN H 160 59.02 31.65 REMARK 500 GLU H 216 -77.08 -125.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 8 PRO A 9 -146.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 119 DISTANCE = 7.24 ANGSTROMS REMARK 525 HOH A 120 DISTANCE = 8.08 ANGSTROMS REMARK 525 HOH A 121 DISTANCE = 9.29 ANGSTROMS REMARK 525 HOH L 369 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH L 370 DISTANCE = 6.79 ANGSTROMS REMARK 525 HOH L 371 DISTANCE = 6.94 ANGSTROMS REMARK 525 HOH L 372 DISTANCE = 6.96 ANGSTROMS REMARK 525 HOH L 373 DISTANCE = 7.48 ANGSTROMS REMARK 525 HOH L 374 DISTANCE = 7.56 ANGSTROMS REMARK 525 HOH L 375 DISTANCE = 8.48 ANGSTROMS REMARK 525 HOH L 376 DISTANCE = 8.64 ANGSTROMS REMARK 525 HOH L 377 DISTANCE = 8.92 ANGSTROMS REMARK 525 HOH H 355 DISTANCE = 6.51 ANGSTROMS REMARK 525 HOH H 356 DISTANCE = 6.73 ANGSTROMS REMARK 525 HOH H 357 DISTANCE = 7.22 ANGSTROMS REMARK 525 HOH H 358 DISTANCE = 8.39 ANGSTROMS REMARK 525 HOH H 359 DISTANCE = 8.78 ANGSTROMS REMARK 525 HOH H 360 DISTANCE = 9.37 ANGSTROMS REMARK 525 HOH H 361 DISTANCE = 9.89 ANGSTROMS DBREF 6A77 A 9 97 UNP Q9Y6N7 ROBO1_HUMAN 455 543 DBREF 6A77 L 1 211 PDB 6A77 6A77 1 211 DBREF 6A77 H -1 217 PDB 6A77 6A77 -1 217 SEQADV 6A77 MET A 7 UNP Q9Y6N7 EXPRESSION TAG SEQADV 6A77 GLY A 8 UNP Q9Y6N7 EXPRESSION TAG SEQRES 1 A 91 MET GLY PRO VAL ILE ARG GLN GLY PRO VAL ASN GLN THR SEQRES 2 A 91 VAL ALA VAL ASP GLY THR PHE VAL LEU SER CYS VAL ALA SEQRES 3 A 91 THR GLY SER PRO VAL PRO THR ILE LEU TRP ARG LYS ASP SEQRES 4 A 91 GLY VAL LEU VAL SER THR GLN ASP SER ARG ILE LYS GLN SEQRES 5 A 91 LEU GLU ASN GLY VAL LEU GLN ILE ARG TYR ALA LYS LEU SEQRES 6 A 91 GLY ASP THR GLY ARG TYR THR CYS ILE ALA SER THR PRO SEQRES 7 A 91 SER GLY GLU ALA THR TRP SER ALA TYR ILE GLU VAL GLN SEQRES 1 L 211 ASP ILE GLN MET THR GLN SER PRO ALA SER LEU SER ALA SEQRES 2 L 211 SER VAL GLY GLU THR VAL THR ILE THR CYS GLY ALA SER SEQRES 3 L 211 GLU ASN ILE TYR GLY ALA LEU THR TRP TYR GLN ARG LYS SEQRES 4 L 211 GLN GLY LYS SER PRO GLN LEU LEU ILE TYR GLY ALA ILE SEQRES 5 L 211 ASN LEU ALA ASP ASP LYS SER SER ARG PHE SER GLY SER SEQRES 6 L 211 GLY SER GLY ARG GLN TYR SER LEU LYS ILE SER SER LEU SEQRES 7 L 211 HIS PRO ASP ASP VAL ALA THR TYR TYR CYS GLN ASN VAL SEQRES 8 L 211 LEU SER THR PRO PHE THR PHE GLY SER GLY THR LYS LEU SEQRES 9 L 211 GLU ILE LYS ARG ALA ASP ALA ALA PRO THR VAL SER ILE SEQRES 10 L 211 PHE PRO PRO SER SER GLU GLN LEU THR SER GLY GLY ALA SEQRES 11 L 211 SER VAL VAL CYS PHE LEU ASN ASN PHE TYR PRO LYS ASP SEQRES 12 L 211 ILE ASN VAL LYS TRP LYS ILE ASP GLY SER GLU ARG GLN SEQRES 13 L 211 ASN GLY VAL LEU ASN SER TRP THR ASP GLN ASP SER LYS SEQRES 14 L 211 ASP SER THR TYR SER MET SER SER THR LEU THR LEU THR SEQRES 15 L 211 LYS ASP GLU TYR GLU ARG HIS ASN SER TYR THR CYS GLU SEQRES 16 L 211 ALA THR HIS LYS THR SER THR SER PRO ILE VAL LYS SER SEQRES 17 L 211 PHE ASN ARG SEQRES 1 H 221 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY VAL VAL GLN SEQRES 2 H 221 PRO GLY GLY SER LEU LYS LEU SER CYS ALA ALA SER GLY SEQRES 3 H 221 PHE THR PHE SER THR TYR ASP MET SER TRP VAL ARG GLN SEQRES 4 H 221 THR PRO ASP LYS ARG LEU GLU LEU VAL ALA THR ILE ASN SEQRES 5 H 221 SER ASN GLY GLY SER THR TYR TYR PRO ASP SER VAL LYS SEQRES 6 H 221 GLY ARG PHE THR SER SER ARG ASP ASN ALA LYS ASN ILE SEQRES 7 H 221 LEU TYR LEU GLN MET SER SER LEU LYS SER GLU ASP THR SEQRES 8 H 221 ALA MET TYR TYR CYS ALA ARG GLU ALA LEU LEU ARG PRO SEQRES 9 H 221 PRO TYR TYR ALA LEU ASP TYR TRP GLY GLN GLY THR SER SEQRES 10 H 221 VAL THR VAL SER SER ALA LYS THR THR PRO PRO SER VAL SEQRES 11 H 221 TYR PRO LEU ALA PRO GLY CYS GLY ASP THR THR GLY SER SEQRES 12 H 221 SER VAL THR LEU GLY CYS LEU VAL LYS GLY TYR PHE PRO SEQRES 13 H 221 GLU SER VAL THR VAL THR TRP ASN SER GLY SER LEU SER SEQRES 14 H 221 SER SER VAL HIS THR PHE PRO ALA LEU LEU GLN SER GLY SEQRES 15 H 221 LEU TYR THR MET SER SER SER VAL THR VAL PRO SER SER SEQRES 16 H 221 THR TRP PRO SER GLN THR VAL THR CYS SER VAL ALA HIS SEQRES 17 H 221 PRO ALA SER SER THR THR VAL ASP LYS LYS LEU GLU PRO FORMUL 4 HOH *159(H2 O) HELIX 1 AA1 LYS A 70 THR A 74 5 5 HELIX 2 AA2 HIS L 79 VAL L 83 5 5 HELIX 3 AA3 SER L 121 SER L 127 1 7 HELIX 4 AA4 LYS L 183 ARG L 188 1 6 HELIX 5 AA5 THR H 26 TYR H 30 5 5 HELIX 6 AA6 PRO H 59 LYS H 63 5 5 HELIX 7 AA7 LYS H 85 THR H 89 5 5 HELIX 8 AA8 SER H 161 SER H 163 5 3 HELIX 9 AA9 LEU H 164 SER H 166 5 3 HELIX 10 AB1 PRO H 205 SER H 208 5 4 SHEET 1 AA1 2 VAL A 10 GLN A 13 0 SHEET 2 AA1 2 VAL A 31 THR A 33 -1 O VAL A 31 N ARG A 12 SHEET 1 AA2 5 GLN A 18 ALA A 21 0 SHEET 2 AA2 5 GLY A 86 GLN A 97 1 O GLU A 95 N GLN A 18 SHEET 3 AA2 5 GLY A 75 THR A 83 -1 N TYR A 77 O ALA A 92 SHEET 4 AA2 5 THR A 39 LYS A 44 -1 N THR A 39 O SER A 82 SHEET 5 AA2 5 VAL A 47 LEU A 48 -1 O VAL A 47 N LYS A 44 SHEET 1 AA3 3 PHE A 26 SER A 29 0 SHEET 2 AA3 3 VAL A 63 ILE A 66 -1 O LEU A 64 N LEU A 28 SHEET 3 AA3 3 ILE A 56 GLN A 58 -1 N LYS A 57 O GLN A 65 SHEET 1 AA4 4 MET L 4 SER L 7 0 SHEET 2 AA4 4 VAL L 19 ALA L 25 -1 O GLY L 24 N THR L 5 SHEET 3 AA4 4 GLN L 70 ILE L 75 -1 O LEU L 73 N ILE L 21 SHEET 4 AA4 4 PHE L 62 SER L 67 -1 N SER L 63 O LYS L 74 SHEET 1 AA5 6 SER L 10 SER L 14 0 SHEET 2 AA5 6 THR L 102 LYS L 107 1 O GLU L 105 N LEU L 11 SHEET 3 AA5 6 ALA L 84 ASN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 AA5 6 LEU L 33 ARG L 38 -1 N ARG L 38 O THR L 85 SHEET 5 AA5 6 GLN L 45 TYR L 49 -1 O LEU L 47 N TRP L 35 SHEET 6 AA5 6 ASN L 53 LEU L 54 -1 O ASN L 53 N TYR L 49 SHEET 1 AA6 4 THR L 114 PHE L 118 0 SHEET 2 AA6 4 GLY L 129 PHE L 139 -1 O PHE L 135 N SER L 116 SHEET 3 AA6 4 TYR L 173 THR L 182 -1 O TYR L 173 N PHE L 139 SHEET 4 AA6 4 VAL L 159 TRP L 163 -1 N LEU L 160 O THR L 178 SHEET 1 AA7 4 SER L 153 ARG L 155 0 SHEET 2 AA7 4 ASN L 145 ILE L 150 -1 N ILE L 150 O SER L 153 SHEET 3 AA7 4 SER L 191 HIS L 198 -1 O THR L 197 N ASN L 145 SHEET 4 AA7 4 SER L 201 ASN L 210 -1 O ILE L 205 N ALA L 196 SHEET 1 AA8 4 GLN H 1 SER H 5 0 SHEET 2 AA8 4 LEU H 16 SER H 23 -1 O SER H 19 N SER H 5 SHEET 3 AA8 4 ILE H 76 MET H 81 -1 O MET H 81 N LEU H 16 SHEET 4 AA8 4 PHE H 66 ASP H 71 -1 N THR H 67 O GLN H 80 SHEET 1 AA9 6 GLY H 8 VAL H 10 0 SHEET 2 AA9 6 THR H 114 VAL H 118 1 O THR H 117 N GLY H 8 SHEET 3 AA9 6 ALA H 90 GLU H 97 -1 N TYR H 92 O THR H 114 SHEET 4 AA9 6 MET H 32 GLN H 37 -1 N VAL H 35 O TYR H 93 SHEET 5 AA9 6 LEU H 43 ILE H 49 -1 O GLU H 44 N ARG H 36 SHEET 6 AA9 6 THR H 56 TYR H 57 -1 O TYR H 57 N THR H 48 SHEET 1 AB1 4 GLY H 8 VAL H 10 0 SHEET 2 AB1 4 THR H 114 VAL H 118 1 O THR H 117 N GLY H 8 SHEET 3 AB1 4 ALA H 90 GLU H 97 -1 N TYR H 92 O THR H 114 SHEET 4 AB1 4 LEU H 107 TRP H 110 -1 O TYR H 109 N ARG H 96 SHEET 1 AB2 4 SER H 127 LEU H 131 0 SHEET 2 AB2 4 SER H 140 TYR H 150 -1 O LEU H 146 N TYR H 129 SHEET 3 AB2 4 LEU H 179 PRO H 189 -1 O MET H 182 N VAL H 147 SHEET 4 AB2 4 VAL H 168 GLN H 176 -1 N GLN H 176 O LEU H 179 SHEET 1 AB3 3 THR H 156 TRP H 159 0 SHEET 2 AB3 3 THR H 199 HIS H 204 -1 O SER H 201 N THR H 158 SHEET 3 AB3 3 THR H 209 LYS H 214 -1 O VAL H 211 N VAL H 202 SSBOND 1 CYS A 30 CYS A 79 1555 1555 1.99 SSBOND 2 CYS L 23 CYS L 88 1555 1555 2.10 SSBOND 3 CYS L 134 CYS L 194 1555 1555 2.06 SSBOND 4 CYS H 20 CYS H 94 1555 1555 2.10 SSBOND 5 CYS H 145 CYS H 200 1555 1555 2.03 CISPEP 1 MET A 7 GLY A 8 0 9.84 CISPEP 2 SER A 35 PRO A 36 0 -4.17 CISPEP 3 SER L 7 PRO L 8 0 -17.40 CISPEP 4 THR L 94 PRO L 95 0 -8.31 CISPEP 5 TYR L 140 PRO L 141 0 4.35 CISPEP 6 ARG H 101 PRO H 102 0 -10.29 CISPEP 7 PHE H 151 PRO H 152 0 -3.47 CISPEP 8 TRP H 193 PRO H 194 0 6.58 CRYST1 100.566 100.566 122.756 90.00 90.00 90.00 P 43 21 2 8 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 0.009944 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009944 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008146 0.00000