HEADER IMMUNE SYSTEM 02-JUL-18 6A78 TITLE CRYSTAL STRUCTURE OF THE FIFTH IMMUNOGLOBULIN DOMAIN (IG5) OF HUMAN TITLE 2 ROBO1 IN COMPLEX WITH THE SCFV FRAGMENT OF MURINE MONOCLONAL ANTIBODY TITLE 3 B5209B COMPND MOL_ID: 1; COMPND 2 MOLECULE: ROUNDABOUT HOMOLOG 1; COMPND 3 CHAIN: A, B; 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 REGION OF THE ANTI-HUMAN ROBO1 ANTIBODY B5209B COMPND 8 SCFV; COMPND 9 CHAIN: L, M; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: HEAVY CHAIN AND LINKER REGION OF THE ANTI-HUMAN ROBO1 COMPND 13 ANTIBODY B5209B SCFV; COMPND 14 CHAIN: H, I; COMPND 15 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: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 15 ORGANISM_TAXID: 10090; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HEPATOCELLULAR CARCINOMA ANTIGEN, ANGIOGENESIS, IMMUNE SYSTEM, KEYWDS 2 ANTIBODY DRUG, SINGLE CHAIN FV FRAGMENT EXPDTA X-RAY DIFFRACTION AUTHOR E.MIZOHATA,T.NAKAYAMA,Y.KADO,T.INOUE REVDAT 2 20-MAR-19 6A78 1 JRNL REVDAT 1 30-JAN-19 6A78 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. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 37871 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) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.239 REMARK 3 FREE R VALUE : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1979 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2722 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.64 REMARK 3 BIN R VALUE (WORKING SET) : 0.3740 REMARK 3 BIN FREE R VALUE SET COUNT : 157 REMARK 3 BIN FREE R VALUE : 0.4150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4869 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 323 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.58000 REMARK 3 B22 (A**2) : -0.87000 REMARK 3 B33 (A**2) : 1.45000 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): 0.290 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.230 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.185 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.612 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.941 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.913 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5047 ; 0.017 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 4598 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6864 ; 1.834 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10685 ; 1.057 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 652 ; 8.930 ; 5.015 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 202 ;37.063 ;23.713 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 825 ;17.887 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;17.111 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 778 ; 0.107 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5613 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1027 ; 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): 2580 ; 2.095 ; 2.540 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2579 ; 2.089 ; 2.539 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3221 ; 3.306 ; 3.793 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3222 ; 3.306 ; 3.795 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2467 ; 2.690 ; 2.781 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2459 ; 2.691 ; 2.772 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3626 ; 4.235 ; 4.050 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 20469 ; 6.911 ;47.850 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 20356 ; 6.868 ;47.831 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 6A78 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_1300008267. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39986 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : 95.1 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 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 (%): 49.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 85MM TRIS-HCL (PH 8.5), 27.5% (W/V) REMARK 280 PEG 4000, 170MM LITHIUM SULFATE MONOHYDRATE, 670MM SODIUM REMARK 280 THIOCYANATE, 15% (V/V) GLYCEROL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 35.34500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 74.97150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.34500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 74.97150 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 3430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 3460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, M, I 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH L 311 LIES ON A SPECIAL POSITION. REMARK 375 HOH M 318 LIES ON A SPECIAL POSITION. REMARK 375 HOH M 326 LIES ON A SPECIAL POSITION. REMARK 375 HOH M 356 LIES ON A SPECIAL POSITION. 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 MET A 7 REMARK 465 ASP L -2 REMARK 465 ILE L -1 REMARK 465 ALA L 108 REMARK 465 ALA L 109 REMARK 465 SER H 120 REMARK 465 ALA H 121 REMARK 465 GLY H 122 REMARK 465 GLY H 123 REMARK 465 GLY H 124 REMARK 465 GLY H 125 REMARK 465 SER H 126 REMARK 465 GLY H 127 REMARK 465 GLY H 128 REMARK 465 GLY H 129 REMARK 465 GLY H 130 REMARK 465 SER H 131 REMARK 465 GLY H 132 REMARK 465 GLY H 133 REMARK 465 GLY H 134 REMARK 465 GLY H 135 REMARK 465 SER H 136 REMARK 465 MET B 7 REMARK 465 ASP M -2 REMARK 465 ALA M 109 REMARK 465 ALA I 121 REMARK 465 GLY I 122 REMARK 465 GLY I 123 REMARK 465 GLY I 124 REMARK 465 GLY I 125 REMARK 465 SER I 126 REMARK 465 GLY I 127 REMARK 465 GLY I 128 REMARK 465 GLY I 129 REMARK 465 GLY I 130 REMARK 465 SER I 131 REMARK 465 GLY I 132 REMARK 465 GLY I 133 REMARK 465 GLY I 134 REMARK 465 GLY I 135 REMARK 465 SER I 136 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 NH2 ARG A 76 O HOH A 101 2.14 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 346 O HOH L 346 2655 1.76 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 M 69 NE - CZ - NH2 ANGL. DEV. = 3.5 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 -12.38 76.05 REMARK 500 THR A 51 24.19 -65.33 REMARK 500 ALA L 51 -36.27 75.68 REMARK 500 ASP L 57 41.89 -105.52 REMARK 500 SER L 77 67.08 65.92 REMARK 500 ASP B 23 -12.50 73.35 REMARK 500 THR B 51 6.87 -64.45 REMARK 500 LEU M 0 -27.34 96.37 REMARK 500 LEU M 47 -62.46 -109.53 REMARK 500 ALA M 51 -36.61 73.71 REMARK 500 ASP M 57 37.77 -99.30 REMARK 500 SER M 77 64.57 68.75 REMARK 500 ALA I 90 161.58 174.71 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 GLN A 52 ASP A 53 147.16 REMARK 500 VAL H 118 SER H 119 147.78 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 142 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH L 358 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH H 257 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH H 258 DISTANCE = 6.52 ANGSTROMS REMARK 525 HOH H 259 DISTANCE = 7.43 ANGSTROMS REMARK 525 HOH B 137 DISTANCE = 5.98 ANGSTROMS REMARK 525 HOH B 138 DISTANCE = 6.11 ANGSTROMS REMARK 525 HOH B 139 DISTANCE = 7.82 ANGSTROMS REMARK 525 HOH M 363 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH M 364 DISTANCE = 6.77 ANGSTROMS REMARK 525 HOH M 365 DISTANCE = 8.16 ANGSTROMS REMARK 525 HOH I 258 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH I 259 DISTANCE = 6.29 ANGSTROMS REMARK 525 HOH I 260 DISTANCE = 7.53 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 L 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 M 201 DBREF 6A78 A 9 97 UNP Q9Y6N7 ROBO1_HUMAN 455 543 DBREF 6A78 L -2 109 PDB 6A78 6A78 -2 109 DBREF 6A78 H -1 136 PDB 6A78 6A78 -1 136 DBREF 6A78 B 9 97 UNP Q9Y6N7 ROBO1_HUMAN 455 543 DBREF 6A78 M -2 109 PDB 6A78 6A78 -2 109 DBREF 6A78 I -1 136 PDB 6A78 6A78 -1 136 SEQADV 6A78 MET A 7 UNP Q9Y6N7 EXPRESSION TAG SEQADV 6A78 GLY A 8 UNP Q9Y6N7 EXPRESSION TAG SEQADV 6A78 MET B 7 UNP Q9Y6N7 EXPRESSION TAG SEQADV 6A78 GLY B 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 112 ASP ILE LEU ASP ILE GLN MET THR GLN SER PRO ALA SER SEQRES 2 L 112 LEU SER ALA SER VAL GLY GLU THR VAL THR ILE THR CYS SEQRES 3 L 112 GLY ALA SER GLU ASN ILE TYR GLY ALA LEU THR TRP TYR SEQRES 4 L 112 GLN ARG LYS GLN GLY LYS SER PRO GLN LEU LEU ILE TYR SEQRES 5 L 112 GLY ALA ILE ASN LEU ALA ASP ASP LYS SER SER ARG PHE SEQRES 6 L 112 SER GLY SER GLY SER GLY ARG GLN TYR SER LEU LYS ILE SEQRES 7 L 112 SER SER LEU HIS PRO ASP ASP VAL ALA THR TYR TYR CYS SEQRES 8 L 112 GLN ASN VAL LEU SER THR PRO PHE THR PHE GLY SER GLY SEQRES 9 L 112 THR LYS LEU GLU ILE LYS ALA ALA SEQRES 1 H 138 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY VAL VAL GLN SEQRES 2 H 138 PRO GLY GLY SER LEU LYS LEU SER CYS ALA ALA SER GLY SEQRES 3 H 138 PHE THR PHE SER THR TYR ASP MET SER TRP VAL ARG GLN SEQRES 4 H 138 THR PRO ASP LYS ARG LEU GLU LEU VAL ALA THR ILE ASN SEQRES 5 H 138 SER ASN GLY GLY SER THR TYR TYR PRO ASP SER VAL LYS SEQRES 6 H 138 GLY ARG PHE THR SER SER ARG ASP ASN ALA LYS ASN ILE SEQRES 7 H 138 LEU TYR LEU GLN MET SER SER LEU LYS SER GLU ASP THR SEQRES 8 H 138 ALA MET TYR TYR CYS ALA ARG GLU ALA LEU LEU ARG PRO SEQRES 9 H 138 PRO TYR TYR ALA LEU ASP TYR TRP GLY GLN GLY THR SER SEQRES 10 H 138 VAL THR VAL SER SER ALA GLY GLY GLY GLY SER GLY GLY SEQRES 11 H 138 GLY GLY SER GLY GLY GLY GLY SER SEQRES 1 B 91 MET GLY PRO VAL ILE ARG GLN GLY PRO VAL ASN GLN THR SEQRES 2 B 91 VAL ALA VAL ASP GLY THR PHE VAL LEU SER CYS VAL ALA SEQRES 3 B 91 THR GLY SER PRO VAL PRO THR ILE LEU TRP ARG LYS ASP SEQRES 4 B 91 GLY VAL LEU VAL SER THR GLN ASP SER ARG ILE LYS GLN SEQRES 5 B 91 LEU GLU ASN GLY VAL LEU GLN ILE ARG TYR ALA LYS LEU SEQRES 6 B 91 GLY ASP THR GLY ARG TYR THR CYS ILE ALA SER THR PRO SEQRES 7 B 91 SER GLY GLU ALA THR TRP SER ALA TYR ILE GLU VAL GLN SEQRES 1 M 112 ASP ILE LEU ASP ILE GLN MET THR GLN SER PRO ALA SER SEQRES 2 M 112 LEU SER ALA SER VAL GLY GLU THR VAL THR ILE THR CYS SEQRES 3 M 112 GLY ALA SER GLU ASN ILE TYR GLY ALA LEU THR TRP TYR SEQRES 4 M 112 GLN ARG LYS GLN GLY LYS SER PRO GLN LEU LEU ILE TYR SEQRES 5 M 112 GLY ALA ILE ASN LEU ALA ASP ASP LYS SER SER ARG PHE SEQRES 6 M 112 SER GLY SER GLY SER GLY ARG GLN TYR SER LEU LYS ILE SEQRES 7 M 112 SER SER LEU HIS PRO ASP ASP VAL ALA THR TYR TYR CYS SEQRES 8 M 112 GLN ASN VAL LEU SER THR PRO PHE THR PHE GLY SER GLY SEQRES 9 M 112 THR LYS LEU GLU ILE LYS ALA ALA SEQRES 1 I 138 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY VAL VAL GLN SEQRES 2 I 138 PRO GLY GLY SER LEU LYS LEU SER CYS ALA ALA SER GLY SEQRES 3 I 138 PHE THR PHE SER THR TYR ASP MET SER TRP VAL ARG GLN SEQRES 4 I 138 THR PRO ASP LYS ARG LEU GLU LEU VAL ALA THR ILE ASN SEQRES 5 I 138 SER ASN GLY GLY SER THR TYR TYR PRO ASP SER VAL LYS SEQRES 6 I 138 GLY ARG PHE THR SER SER ARG ASP ASN ALA LYS ASN ILE SEQRES 7 I 138 LEU TYR LEU GLN MET SER SER LEU LYS SER GLU ASP THR SEQRES 8 I 138 ALA MET TYR TYR CYS ALA ARG GLU ALA LEU LEU ARG PRO SEQRES 9 I 138 PRO TYR TYR ALA LEU ASP TYR TRP GLY GLN GLY THR SER SEQRES 10 I 138 VAL THR VAL SER SER ALA GLY GLY GLY GLY SER GLY GLY SEQRES 11 I 138 GLY GLY SER GLY GLY GLY GLY SER HET SO4 L 201 5 HET SO4 M 201 5 HETNAM SO4 SULFATE ION FORMUL 7 SO4 2(O4 S 2-) FORMUL 9 HOH *323(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 THR H 26 TYR H 30 5 5 HELIX 4 AA4 LYS H 85 THR H 89 5 5 HELIX 5 AA5 LYS B 70 THR B 74 5 5 HELIX 6 AA6 HIS M 79 VAL M 83 5 5 HELIX 7 AA7 THR I 26 TYR I 30 5 5 HELIX 8 AA8 LYS I 85 THR I 89 5 5 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 GLN A 13 SHEET 1 AA2 5 GLN A 18 ALA A 21 0 SHEET 2 AA2 5 GLU A 87 GLN A 97 1 O GLN A 97 N VAL A 20 SHEET 3 AA2 5 GLY A 75 SER A 82 -1 N TYR A 77 O ALA A 92 SHEET 4 AA2 5 THR A 39 LYS A 44 -1 N LEU A 41 O ILE A 80 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 ILE A 66 N PHE A 26 SHEET 3 AA3 3 ILE A 56 LEU A 59 -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 ILE L 75 N VAL L 19 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 ALA L 13 0 SHEET 2 AA5 6 THR L 102 ILE L 106 1 O GLU L 105 N LEU L 11 SHEET 3 AA5 6 ALA L 84 ASN L 90 -1 N ALA L 84 O LEU L 104 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 GLN L 45 N GLN L 37 SHEET 6 AA5 6 ASN L 53 LEU L 54 -1 O ASN L 53 N TYR L 49 SHEET 1 AA6 4 GLN H 1 SER H 5 0 SHEET 2 AA6 4 LEU H 16 SER H 23 -1 O ALA H 21 N VAL H 3 SHEET 3 AA6 4 ILE H 76 MET H 81 -1 O MET H 81 N LEU H 16 SHEET 4 AA6 4 PHE H 66 ASP H 71 -1 N THR H 67 O GLN H 80 SHEET 1 AA7 6 GLY H 8 VAL H 10 0 SHEET 2 AA7 6 THR H 114 VAL H 118 1 O THR H 117 N GLY H 8 SHEET 3 AA7 6 ALA H 90 GLU H 97 -1 N TYR H 92 O THR H 114 SHEET 4 AA7 6 MET H 32 GLN H 37 -1 N VAL H 35 O TYR H 93 SHEET 5 AA7 6 LEU H 43 ILE H 49 -1 O VAL H 46 N TRP H 34 SHEET 6 AA7 6 THR H 56 TYR H 57 -1 O TYR H 57 N THR H 48 SHEET 1 AA8 4 GLY H 8 VAL H 10 0 SHEET 2 AA8 4 THR H 114 VAL H 118 1 O THR H 117 N GLY H 8 SHEET 3 AA8 4 ALA H 90 GLU H 97 -1 N TYR H 92 O THR H 114 SHEET 4 AA8 4 LEU H 107 TRP H 110 -1 O TYR H 109 N ARG H 96 SHEET 1 AA9 2 VAL B 10 GLN B 13 0 SHEET 2 AA9 2 VAL B 31 THR B 33 -1 O VAL B 31 N GLN B 13 SHEET 1 AB1 5 GLN B 18 ALA B 21 0 SHEET 2 AB1 5 GLU B 87 GLN B 97 1 O GLU B 95 N VAL B 20 SHEET 3 AB1 5 GLY B 75 SER B 82 -1 N TYR B 77 O ALA B 92 SHEET 4 AB1 5 THR B 39 LYS B 44 -1 N ARG B 43 O THR B 78 SHEET 5 AB1 5 VAL B 47 LEU B 48 -1 O VAL B 47 N LYS B 44 SHEET 1 AB2 3 PHE B 26 SER B 29 0 SHEET 2 AB2 3 VAL B 63 ILE B 66 -1 O ILE B 66 N PHE B 26 SHEET 3 AB2 3 ILE B 56 GLN B 58 -1 N LYS B 57 O GLN B 65 SHEET 1 AB3 4 MET M 4 SER M 7 0 SHEET 2 AB3 4 VAL M 19 ALA M 25 -1 O THR M 22 N SER M 7 SHEET 3 AB3 4 GLN M 70 ILE M 75 -1 O ILE M 75 N VAL M 19 SHEET 4 AB3 4 PHE M 62 SER M 67 -1 N SER M 63 O LYS M 74 SHEET 1 AB4 6 SER M 10 ALA M 13 0 SHEET 2 AB4 6 THR M 102 ILE M 106 1 O GLU M 105 N LEU M 11 SHEET 3 AB4 6 ALA M 84 ASN M 90 -1 N ALA M 84 O LEU M 104 SHEET 4 AB4 6 LEU M 33 ARG M 38 -1 N ARG M 38 O THR M 85 SHEET 5 AB4 6 GLN M 45 TYR M 49 -1 O LEU M 47 N TRP M 35 SHEET 6 AB4 6 ASN M 53 LEU M 54 -1 O ASN M 53 N TYR M 49 SHEET 1 AB5 4 GLN I 1 SER I 5 0 SHEET 2 AB5 4 LEU I 16 SER I 23 -1 O ALA I 21 N VAL I 3 SHEET 3 AB5 4 ILE I 76 MET I 81 -1 O MET I 81 N LEU I 16 SHEET 4 AB5 4 PHE I 66 ASP I 71 -1 N THR I 67 O GLN I 80 SHEET 1 AB6 6 GLY I 8 VAL I 10 0 SHEET 2 AB6 6 THR I 114 VAL I 118 1 O THR I 117 N GLY I 8 SHEET 3 AB6 6 ALA I 90 GLU I 97 -1 N TYR I 92 O THR I 114 SHEET 4 AB6 6 MET I 32 GLN I 37 -1 N VAL I 35 O TYR I 93 SHEET 5 AB6 6 LEU I 43 ILE I 49 -1 O ALA I 47 N TRP I 34 SHEET 6 AB6 6 THR I 56 TYR I 57 -1 O TYR I 57 N THR I 48 SHEET 1 AB7 4 GLY I 8 VAL I 10 0 SHEET 2 AB7 4 THR I 114 VAL I 118 1 O THR I 117 N GLY I 8 SHEET 3 AB7 4 ALA I 90 GLU I 97 -1 N TYR I 92 O THR I 114 SHEET 4 AB7 4 LEU I 107 TRP I 110 -1 O TYR I 109 N ARG I 96 SSBOND 1 CYS A 30 CYS A 79 1555 1555 2.02 SSBOND 2 CYS L 23 CYS L 88 1555 1555 2.17 SSBOND 3 CYS H 20 CYS H 94 1555 1555 2.04 SSBOND 4 CYS B 30 CYS B 79 1555 1555 2.04 SSBOND 5 CYS M 23 CYS M 88 1555 1555 2.17 SSBOND 6 CYS I 20 CYS I 94 1555 1555 2.05 CISPEP 1 SER A 35 PRO A 36 0 -2.62 CISPEP 2 SER L 7 PRO L 8 0 -14.46 CISPEP 3 THR L 94 PRO L 95 0 0.44 CISPEP 4 ARG H 101 PRO H 102 0 -10.85 CISPEP 5 SER B 35 PRO B 36 0 -3.74 CISPEP 6 SER M 7 PRO M 8 0 -7.80 CISPEP 7 THR M 94 PRO M 95 0 -7.89 CISPEP 8 LYS M 107 ALA M 108 0 -4.30 CISPEP 9 ARG I 101 PRO I 102 0 -2.36 SITE 1 AC1 6 LYS H 41 ARG L 38 GLN L 40 HOH L 303 SITE 2 AC1 6 HOH L 312 HOH L 316 SITE 1 AC2 5 LYS I 41 ARG M 38 GLN M 40 HOH M 302 SITE 2 AC2 5 HOH M 310 CRYST1 70.690 149.943 66.153 90.00 90.00 90.00 P 21 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 0.014146 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006669 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015116 0.00000