HEADER CELL ADHESION 24-AUG-11 3ZYO TITLE CRYSTAL STRUCTURE OF THE N-TERMINAL LEUCINE RICH REPEATS AND TITLE 2 IMMUNOGLOBULIN DOMAIN OF NETRIN-G LIGAND-3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEUCINE-RICH REPEAT-CONTAINING PROTEIN 4B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL LEUCINE RICH REPEATS AND IMMUNOGLOBULIN DOMAIN, COMPND 5 RESIDUES 57-455; COMPND 6 SYNONYM: NETRIN-G3 LIGAND, NGL-3; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293S; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PHLSEC KEYWDS SYNAPSE, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR E.SEIRADAKE,C.H.COLES,P.V.PERESTENKO,K.HARLOS,R.A.J.MCILHINNEY, AUTHOR 2 A.R.ARICESCU,E.Y.JONES REVDAT 6 13-NOV-24 3ZYO 1 REMARK REVDAT 5 20-DEC-23 3ZYO 1 HETSYN REVDAT 4 29-JUL-20 3ZYO 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE REVDAT 3 16-NOV-11 3ZYO 1 JRNL REVDAT 2 26-OCT-11 3ZYO 1 JRNL REVDAT 1 05-OCT-11 3ZYO 0 JRNL AUTH E.SEIRADAKE,C.H.COLES,P.V.PERESTENKO,K.HARLOS, JRNL AUTH 2 R.A.J.MCILHINNEY,A.R.ARICESCU,E.Y.JONES JRNL TITL STRUCTURAL BASIS FOR CELL SURFACE PATTERNING THROUGH JRNL TITL 2 NETRING-NGL INTERACTIONS. JRNL REF EMBO J. V. 30 4479 2011 JRNL REFN ISSN 0261-4189 JRNL PMID 21946559 JRNL DOI 10.1038/EMBOJ.2011.346 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 10223 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) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 517 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) : 3.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.18 REMARK 3 REFLECTION IN BIN (WORKING SET) : 705 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3010 REMARK 3 BIN FREE R VALUE SET COUNT : 30 REMARK 3 BIN FREE R VALUE : 0.4690 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3100 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 87.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.43000 REMARK 3 B22 (A**2) : 3.43000 REMARK 3 B33 (A**2) : -5.15000 REMARK 3 B12 (A**2) : 1.72000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.469 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.399 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 49.006 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.931 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.889 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3183 ; 0.005 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2147 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4334 ; 0.857 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5211 ; 0.754 ; 3.004 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 388 ; 4.779 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 145 ;33.368 ;23.517 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 542 ;12.316 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ; 8.835 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 506 ; 0.051 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3492 ; 0.003 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 636 ; 0.001 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 58 A 160 REMARK 3 ORIGIN FOR THE GROUP (A): -2.9395 30.8002 9.2578 REMARK 3 T TENSOR REMARK 3 T11: 1.1121 T22: 0.2748 REMARK 3 T33: 0.9402 T12: -0.1441 REMARK 3 T13: -0.2423 T23: -0.2370 REMARK 3 L TENSOR REMARK 3 L11: 7.5366 L22: 5.6981 REMARK 3 L33: 10.9649 L12: -4.0791 REMARK 3 L13: 3.1440 L23: -2.4695 REMARK 3 S TENSOR REMARK 3 S11: -0.0457 S12: 0.2296 S13: -0.9632 REMARK 3 S21: -0.3521 S22: 0.0836 S23: -0.6132 REMARK 3 S31: 1.5557 S32: 0.4534 S33: -0.0378 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 161 A 278 REMARK 3 ORIGIN FOR THE GROUP (A): -18.3672 50.9274 12.6595 REMARK 3 T TENSOR REMARK 3 T11: 0.4059 T22: 0.3189 REMARK 3 T33: 0.2581 T12: -0.2251 REMARK 3 T13: -0.2808 T23: 0.0935 REMARK 3 L TENSOR REMARK 3 L11: 2.8146 L22: 12.7698 REMARK 3 L33: 2.2207 L12: -0.5674 REMARK 3 L13: -0.6513 L23: 2.4255 REMARK 3 S TENSOR REMARK 3 S11: 0.0313 S12: 0.2575 S13: -0.3849 REMARK 3 S21: -0.2049 S22: 0.3314 S23: -0.0405 REMARK 3 S31: 0.4912 S32: -0.4794 S33: -0.3627 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 279 A 401 REMARK 3 ORIGIN FOR THE GROUP (A): -24.1529 75.4444 16.7973 REMARK 3 T TENSOR REMARK 3 T11: 0.2287 T22: 0.3531 REMARK 3 T33: 0.1685 T12: 0.0001 REMARK 3 T13: -0.0543 T23: 0.1824 REMARK 3 L TENSOR REMARK 3 L11: 3.3843 L22: 5.3594 REMARK 3 L33: 2.9041 L12: 1.6486 REMARK 3 L13: -1.1047 L23: 0.3538 REMARK 3 S TENSOR REMARK 3 S11: 0.2505 S12: 0.2727 S13: 0.4973 REMARK 3 S21: -0.0870 S22: 0.1507 S23: 0.2791 REMARK 3 S31: -0.1808 S32: -0.6565 S33: -0.4012 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 402 A 454 REMARK 3 ORIGIN FOR THE GROUP (A): -42.9521 68.0767 21.1882 REMARK 3 T TENSOR REMARK 3 T11: 0.4008 T22: 0.9704 REMARK 3 T33: 0.9158 T12: -0.1530 REMARK 3 T13: -0.1101 T23: 0.2593 REMARK 3 L TENSOR REMARK 3 L11: 4.6391 L22: 2.8831 REMARK 3 L33: 4.1952 L12: 0.8764 REMARK 3 L13: -2.4150 L23: 0.2248 REMARK 3 S TENSOR REMARK 3 S11: 0.0887 S12: 0.5344 S13: -0.5976 REMARK 3 S21: 0.3869 S22: -0.2265 S23: 1.0246 REMARK 3 S31: 0.6184 S32: -0.8947 S33: 0.1377 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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. CLEAR ELECTRON DENSITY FOR AMINO ACID RESIDUES Q68- REMARK 3 A69 AND N335-C338 WAS NOT OBSERVED AND THESE ARE OMITTED FROM REMARK 3 THE MODEL. DISORDERED SIDECHAINS WERE MODELED STEREOCHEMICALLY REMARK 4 REMARK 4 3ZYO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1290049434. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-AUG-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0714 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10743 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 38.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 0.87000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 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: PDB ENTRY 3ZYN REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NAH2PO4, 0.1 M KH2PO4, 2M NACL, REMARK 280 0.1 M MES, PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 65.66500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 37.91171 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 58.29000 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 65.66500 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 37.91171 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 58.29000 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 65.66500 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 37.91171 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 58.29000 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 65.66500 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 37.91171 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 58.29000 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 65.66500 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 37.91171 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 58.29000 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 65.66500 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 37.91171 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 58.29000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 75.82341 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 116.58000 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 75.82341 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 116.58000 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 75.82341 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 116.58000 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 75.82341 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 116.58000 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 75.82341 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 116.58000 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 75.82341 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 116.58000 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 GLU A 54 REMARK 465 THR A 55 REMARK 465 GLY A 56 REMARK 465 THR A 57 REMARK 465 GLN A 68 REMARK 465 ALA A 69 REMARK 465 ASN A 335 REMARK 465 THR A 336 REMARK 465 THR A 337 REMARK 465 CYS A 338 REMARK 465 VAL A 455 REMARK 465 GLY A 456 REMARK 465 THR A 457 REMARK 465 LYS A 458 REMARK 465 HIS A 459 REMARK 465 HIS A 460 REMARK 465 HIS A 461 REMARK 465 HIS A 462 REMARK 465 HIS A 463 REMARK 465 HIS A 464 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 ALA A 61 -78.08 -67.61 REMARK 500 SER A 85 80.56 -69.06 REMARK 500 SER A 99 45.23 -107.69 REMARK 500 HIS A 110 15.30 59.49 REMARK 500 ASN A 146 -169.45 -110.42 REMARK 500 TYR A 158 81.08 55.96 REMARK 500 PRO A 171 43.07 -82.98 REMARK 500 PHE A 205 34.12 -92.25 REMARK 500 HIS A 288 72.58 55.14 REMARK 500 GLU A 306 -1.59 -141.79 REMARK 500 CYS A 317 79.13 -100.91 REMARK 500 ASN A 318 -163.19 -108.15 REMARK 500 GLU A 330 -80.58 -73.82 REMARK 500 VAL A 332 80.09 51.12 REMARK 500 CYS A 387 79.16 -155.48 REMARK 500 ARG A 414 -80.68 59.85 REMARK 500 ASN A 427 54.94 71.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZYN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE N-TERMINAL LEUCINE RICH REPEATS OF NETRIN- REMARK 900 G LIGAND-3 DBREF 3ZYO A 57 455 UNP P0C192 LRC4B_MOUSE 57 455 SEQADV 3ZYO GLU A 54 UNP P0C192 EXPRESSION TAG SEQADV 3ZYO THR A 55 UNP P0C192 EXPRESSION TAG SEQADV 3ZYO GLY A 56 UNP P0C192 EXPRESSION TAG SEQADV 3ZYO GLY A 456 UNP P0C192 EXPRESSION TAG SEQADV 3ZYO THR A 457 UNP P0C192 EXPRESSION TAG SEQADV 3ZYO LYS A 458 UNP P0C192 EXPRESSION TAG SEQADV 3ZYO HIS A 459 UNP P0C192 EXPRESSION TAG SEQADV 3ZYO HIS A 460 UNP P0C192 EXPRESSION TAG SEQADV 3ZYO HIS A 461 UNP P0C192 EXPRESSION TAG SEQADV 3ZYO HIS A 462 UNP P0C192 EXPRESSION TAG SEQADV 3ZYO HIS A 463 UNP P0C192 EXPRESSION TAG SEQADV 3ZYO HIS A 464 UNP P0C192 EXPRESSION TAG SEQRES 1 A 411 GLU THR GLY THR SER CYS PRO ALA ALA CYS SER CYS SER SEQRES 2 A 411 ASN GLN ALA SER ARG VAL ILE CYS THR ARG ARG GLU LEU SEQRES 3 A 411 ALA GLU VAL PRO ALA SER ILE PRO VAL ASN THR ARG TYR SEQRES 4 A 411 LEU ASN LEU GLN GLU ASN SER ILE GLN VAL ILE ARG THR SEQRES 5 A 411 ASP THR PHE LYS HIS LEU ARG HIS LEU GLU ILE LEU GLN SEQRES 6 A 411 LEU SER LYS ASN LEU VAL ARG LYS ILE GLU VAL GLY ALA SEQRES 7 A 411 PHE ASN GLY LEU PRO SER LEU ASN THR LEU GLU LEU PHE SEQRES 8 A 411 ASP ASN ARG LEU THR THR VAL PRO THR GLN ALA PHE GLU SEQRES 9 A 411 TYR LEU SER LYS LEU ARG GLU LEU TRP LEU ARG ASN ASN SEQRES 10 A 411 PRO ILE GLU SER ILE PRO SER TYR ALA PHE ASN ARG VAL SEQRES 11 A 411 PRO SER LEU ARG ARG LEU ASP LEU GLY GLU LEU LYS ARG SEQRES 12 A 411 LEU GLU TYR ILE SER GLU ALA ALA PHE GLU GLY LEU VAL SEQRES 13 A 411 ASN LEU ARG TYR LEU ASN LEU GLY MET CYS ASN LEU LYS SEQRES 14 A 411 ASP ILE PRO ASN LEU THR ALA LEU VAL ARG LEU GLU GLU SEQRES 15 A 411 LEU GLU LEU SER GLY ASN ARG LEU ASP LEU ILE ARG PRO SEQRES 16 A 411 GLY SER PHE GLN GLY LEU THR SER LEU ARG LYS LEU TRP SEQRES 17 A 411 LEU MET HIS ALA GLN VAL ALA THR ILE GLU ARG ASN ALA SEQRES 18 A 411 PHE ASP ASP LEU LYS SER LEU GLU GLU LEU ASN LEU SER SEQRES 19 A 411 HIS ASN ASN LEU MET SER LEU PRO HIS ASP LEU PHE THR SEQRES 20 A 411 PRO LEU HIS ARG LEU GLU ARG VAL HIS LEU ASN HIS ASN SEQRES 21 A 411 PRO TRP HIS CYS ASN CYS ASP VAL LEU TRP LEU SER TRP SEQRES 22 A 411 TRP LEU LYS GLU THR VAL PRO SER ASN THR THR CYS CYS SEQRES 23 A 411 ALA ARG CYS HIS ALA PRO ALA GLY LEU LYS GLY ARG TYR SEQRES 24 A 411 ILE GLY GLU LEU ASP GLN SER HIS PHE THR CYS TYR ALA SEQRES 25 A 411 PRO VAL ILE VAL GLU PRO PRO THR ASP LEU ASN VAL THR SEQRES 26 A 411 GLU GLY MET ALA ALA GLU LEU LYS CYS ARG THR GLY THR SEQRES 27 A 411 SER MET THR SER VAL ASN TRP LEU THR PRO ASN GLY THR SEQRES 28 A 411 LEU MET THR HIS GLY SER TYR ARG VAL ARG ILE SER VAL SEQRES 29 A 411 LEU HIS ASP GLY THR LEU ASN PHE THR ASN VAL THR VAL SEQRES 30 A 411 GLN ASP THR GLY GLN TYR THR CYS MET VAL THR ASN SER SEQRES 31 A 411 ALA GLY ASN THR THR ALA SER ALA THR LEU ASN VAL GLY SEQRES 32 A 411 THR LYS HIS HIS HIS HIS HIS HIS MODRES 3ZYO ASN A 376 ASN GLYCOSYLATION SITE HET ZN A1455 1 HET NAG A1456 14 HETNAM ZN ZINC ION HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 ZN ZN 2+ FORMUL 3 NAG C8 H15 N O6 HELIX 1 1 ARG A 247 GLN A 252 1 6 HELIX 2 2 ASN A 318 ASP A 320 5 3 HELIX 3 3 VAL A 321 VAL A 332 1 12 HELIX 4 4 PRO A 345 LYS A 349 5 5 HELIX 5 5 ILE A 353 LEU A 356 5 4 HELIX 6 6 ASP A 357 PHE A 361 5 5 HELIX 7 7 THR A 429 THR A 433 5 5 SHEET 1 AA 3 SER A 64 SER A 66 0 SHEET 2 AA 3 ARG A 71 ILE A 73 -1 O ARG A 71 N SER A 66 SHEET 3 AA 3 TYR A 92 ASN A 94 1 O TYR A 92 N VAL A 72 SHEET 1 AB 2 VAL A 102 ILE A 103 0 SHEET 2 AB 2 LYS A 126 ILE A 127 1 O LYS A 126 N ILE A 103 SHEET 1 AC 9 ILE A 116 GLN A 118 0 SHEET 2 AC 9 THR A 140 GLU A 142 1 O THR A 140 N LEU A 117 SHEET 3 AC 9 GLU A 164 TRP A 166 1 O GLU A 164 N LEU A 141 SHEET 4 AC 9 ARG A 188 ASP A 190 1 O ARG A 188 N LEU A 165 SHEET 5 AC 9 TYR A 213 ASN A 215 1 O TYR A 213 N LEU A 189 SHEET 6 AC 9 GLU A 235 GLU A 237 1 O GLU A 235 N LEU A 214 SHEET 7 AC 9 LYS A 259 TRP A 261 1 O LYS A 259 N LEU A 236 SHEET 8 AC 9 GLU A 283 ASN A 285 1 O GLU A 283 N LEU A 260 SHEET 9 AC 9 ARG A 307 HIS A 309 1 O ARG A 307 N LEU A 284 SHEET 1 AD 2 SER A 174 ILE A 175 0 SHEET 2 AD 2 TYR A 199 ILE A 200 1 O TYR A 199 N ILE A 175 SHEET 1 AE 2 LEU A 245 ILE A 246 0 SHEET 2 AE 2 THR A 269 ILE A 270 1 O THR A 269 N ILE A 246 SHEET 1 AF 2 TRP A 315 HIS A 316 0 SHEET 2 AF 2 CYS A 342 ALA A 344 1 N HIS A 343 O TRP A 315 SHEET 1 AG 2 VAL A 367 GLU A 370 0 SHEET 2 AG 2 ARG A 388 GLY A 390 -1 O ARG A 388 N GLU A 370 SHEET 1 AH 3 ALA A 383 LEU A 385 0 SHEET 2 AH 3 LEU A 423 PHE A 425 -1 O LEU A 423 N LEU A 385 SHEET 3 AH 3 SER A 416 VAL A 417 -1 O SER A 416 N ASN A 424 SHEET 1 AI 4 LEU A 405 MET A 406 0 SHEET 2 AI 4 SER A 395 LEU A 399 -1 O TRP A 398 N MET A 406 SHEET 3 AI 4 GLY A 434 THR A 441 -1 O THR A 437 N LEU A 399 SHEET 4 AI 4 ASN A 446 LEU A 453 -1 O THR A 447 N VAL A 440 SSBOND 1 CYS A 59 CYS A 65 1555 1555 2.03 SSBOND 2 CYS A 63 CYS A 74 1555 1555 2.04 SSBOND 3 CYS A 317 CYS A 342 1555 1555 2.02 SSBOND 4 CYS A 319 CYS A 363 1555 1555 2.04 SSBOND 5 CYS A 387 CYS A 438 1555 1555 2.03 LINK ND2 ASN A 376 C1 NAG A1456 1555 1555 1.44 CISPEP 1 ALA A 344 PRO A 345 0 -2.27 CISPEP 2 GLY A 390 THR A 391 0 0.49 CRYST1 131.330 131.330 174.870 90.00 90.00 120.00 H 3 2 18 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 0.007614 0.004396 0.000000 0.00000 SCALE2 0.000000 0.008792 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005719 0.00000