HEADER CELL ADHESION 23-AUG-11 3ZYN TITLE CRYSTAL STRUCTURE OF THE N-TERMINAL LEUCINE RICH REPEATS OF NETRIN-G TITLE 2 LIGAND-3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEUCINE-RICH REPEAT-CONTAINING PROTEIN 4B; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: N-TERMINAL LEUCINE RICH REPEATS, RESIDUES 57-365; COMPND 5 SYNONYM: NETRIN-G3 LIGAND, NGL-3; COMPND 6 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 3ZYN 1 REMARK REVDAT 5 20-DEC-23 3ZYN 1 HETSYN REVDAT 4 29-JUL-20 3ZYN 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE REVDAT 3 16-NOV-11 3ZYN 1 JRNL REVDAT 2 26-OCT-11 3ZYN 1 JRNL REVDAT 1 05-OCT-11 3ZYN 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. 3.20 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) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 12344 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) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 655 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) : 3.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 809 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.20 REMARK 3 BIN R VALUE (WORKING SET) : 0.3570 REMARK 3 BIN FREE R VALUE SET COUNT : 52 REMARK 3 BIN FREE R VALUE : 0.4150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4999 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 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) : 36.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.53000 REMARK 3 B22 (A**2) : 1.66000 REMARK 3 B33 (A**2) : 1.32000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.62000 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): 0.562 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.447 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 58.717 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.907 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.851 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5145 ; 0.006 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3536 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6997 ; 0.988 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8557 ; 0.802 ; 3.004 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 620 ; 5.031 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 244 ;35.794 ;23.279 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 891 ;14.522 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 48 ;11.142 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 800 ; 0.054 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5646 ; 0.003 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1056 ; 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 57 365 B 57 365 1830 0.07 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 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 57 A 148 REMARK 3 ORIGIN FOR THE GROUP (A): -9.6994 55.8587 42.2088 REMARK 3 T TENSOR REMARK 3 T11: 0.2408 T22: 0.3575 REMARK 3 T33: 0.5578 T12: 0.1183 REMARK 3 T13: -0.0516 T23: -0.0299 REMARK 3 L TENSOR REMARK 3 L11: 4.7501 L22: 4.5314 REMARK 3 L33: 5.6511 L12: 0.1678 REMARK 3 L13: 1.5259 L23: 1.2506 REMARK 3 S TENSOR REMARK 3 S11: 0.3171 S12: 0.5141 S13: 0.3919 REMARK 3 S21: -0.3474 S22: -0.3488 S23: 1.0685 REMARK 3 S31: -0.0222 S32: -1.0100 S33: 0.0318 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 149 A 313 REMARK 3 ORIGIN FOR THE GROUP (A): 18.0864 48.4891 38.3141 REMARK 3 T TENSOR REMARK 3 T11: 0.1659 T22: 0.0399 REMARK 3 T33: 0.0758 T12: 0.0046 REMARK 3 T13: -0.0479 T23: 0.0146 REMARK 3 L TENSOR REMARK 3 L11: 6.5604 L22: 3.7324 REMARK 3 L33: 4.1206 L12: -0.4510 REMARK 3 L13: -3.4404 L23: 0.3608 REMARK 3 S TENSOR REMARK 3 S11: 0.1086 S12: 0.3247 S13: -0.1790 REMARK 3 S21: -0.1766 S22: -0.2058 S23: 0.1347 REMARK 3 S31: 0.1119 S32: -0.1146 S33: 0.0972 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 314 A 366 REMARK 3 ORIGIN FOR THE GROUP (A): 40.9611 57.4397 22.9735 REMARK 3 T TENSOR REMARK 3 T11: 0.4460 T22: 0.3805 REMARK 3 T33: 0.3994 T12: 0.0307 REMARK 3 T13: 0.0100 T23: 0.0943 REMARK 3 L TENSOR REMARK 3 L11: 1.8244 L22: 4.3915 REMARK 3 L33: 4.1954 L12: 1.4564 REMARK 3 L13: -2.3964 L23: -0.0974 REMARK 3 S TENSOR REMARK 3 S11: 0.0732 S12: 0.1588 S13: 0.1488 REMARK 3 S21: -0.4472 S22: 0.1835 S23: -0.0479 REMARK 3 S31: -0.3830 S32: -0.0746 S33: -0.2568 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 : B 55 B 100 REMARK 3 ORIGIN FOR THE GROUP (A): -1.0016 46.7685 89.0365 REMARK 3 T TENSOR REMARK 3 T11: 0.3146 T22: 0.8210 REMARK 3 T33: 0.3546 T12: 0.0303 REMARK 3 T13: 0.1340 T23: 0.0854 REMARK 3 L TENSOR REMARK 3 L11: 4.3014 L22: 4.1801 REMARK 3 L33: 11.8598 L12: -3.7253 REMARK 3 L13: -2.9949 L23: 2.5155 REMARK 3 S TENSOR REMARK 3 S11: -0.7999 S12: -0.6876 S13: -0.8205 REMARK 3 S21: 0.8197 S22: -0.0854 S23: 0.7866 REMARK 3 S31: 0.2611 S32: -0.9599 S33: 0.8852 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 101 B 313 REMARK 3 ORIGIN FOR THE GROUP (A): 21.6151 52.2490 72.1008 REMARK 3 T TENSOR REMARK 3 T11: 0.3248 T22: 0.1169 REMARK 3 T33: 0.0930 T12: -0.0232 REMARK 3 T13: -0.0456 T23: 0.0380 REMARK 3 L TENSOR REMARK 3 L11: 6.6362 L22: 1.3186 REMARK 3 L33: 2.2172 L12: -0.7977 REMARK 3 L13: -1.7271 L23: 0.4547 REMARK 3 S TENSOR REMARK 3 S11: 0.0894 S12: -0.2014 S13: 0.2079 REMARK 3 S21: -0.1175 S22: 0.0319 S23: -0.0330 REMARK 3 S31: -0.2343 S32: 0.0779 S33: -0.1213 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 314 B 366 REMARK 3 ORIGIN FOR THE GROUP (A): 54.4339 43.1478 71.6513 REMARK 3 T TENSOR REMARK 3 T11: 0.4049 T22: 0.5363 REMARK 3 T33: 0.6159 T12: -0.1123 REMARK 3 T13: -0.1534 T23: 0.2499 REMARK 3 L TENSOR REMARK 3 L11: 5.2771 L22: 0.7969 REMARK 3 L33: 1.9109 L12: -0.6955 REMARK 3 L13: 0.8756 L23: 0.7107 REMARK 3 S TENSOR REMARK 3 S11: 0.3894 S12: -0.6543 S13: -0.8178 REMARK 3 S21: 0.1255 S22: -0.0401 S23: -0.3144 REMARK 3 S31: 0.1636 S32: 0.2657 S33: -0.3493 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. REMARK 4 REMARK 4 3ZYN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1290049433. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAY-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9796 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 : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13296 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 53.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.58000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 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 2ID5 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.8 M SUCCINIC ACID PH 7.0. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 78.55000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.63000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 78.55000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 28.63000 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: 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 350 REMARK 350 BIOMOLECULE: 2 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: B 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 367 REMARK 465 LYS A 368 REMARK 465 HIS A 369 REMARK 465 HIS A 370 REMARK 465 HIS A 371 REMARK 465 HIS A 372 REMARK 465 HIS A 373 REMARK 465 HIS A 374 REMARK 465 GLU B 54 REMARK 465 THR B 367 REMARK 465 LYS B 368 REMARK 465 HIS B 369 REMARK 465 HIS B 370 REMARK 465 HIS B 371 REMARK 465 HIS B 372 REMARK 465 HIS B 373 REMARK 465 HIS B 374 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 67 -145.20 61.81 REMARK 500 GLN A 68 49.85 -92.24 REMARK 500 CYS A 74 41.05 -140.79 REMARK 500 ARG A 76 19.23 54.88 REMARK 500 GLU A 78 49.07 -103.71 REMARK 500 GLU A 97 63.75 61.41 REMARK 500 SER A 99 41.93 -105.15 REMARK 500 ASN A 139 -63.11 -103.42 REMARK 500 TYR A 158 70.04 11.38 REMARK 500 PRO A 171 40.36 -77.12 REMARK 500 ASN A 220 89.15 -61.72 REMARK 500 ARG A 242 35.25 -98.18 REMARK 500 LEU A 254 48.21 -104.61 REMARK 500 LEU A 305 109.04 -56.81 REMARK 500 ASN A 318 -169.02 -122.60 REMARK 500 THR A 337 46.61 -144.98 REMARK 500 THR B 57 33.86 -98.72 REMARK 500 ARG B 76 19.60 55.76 REMARK 500 GLU B 78 44.77 -100.49 REMARK 500 GLU B 97 63.19 61.58 REMARK 500 SER B 99 42.24 -106.55 REMARK 500 ASN B 139 -60.30 -103.43 REMARK 500 TYR B 158 69.39 13.62 REMARK 500 PRO B 171 42.62 -77.46 REMARK 500 ASN B 220 87.82 -61.60 REMARK 500 LEU B 254 56.75 -106.10 REMARK 500 ASN B 318 -166.60 -123.39 REMARK 500 THR B 337 48.04 -143.90 REMARK 500 CYS B 338 145.19 -170.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZYO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE N-TERMINAL LEUCINE RICH REPEATS AND REMARK 900 IMMUNOGLOBULIN DOMAIN OF NETRIN-G LIGAND-3 DBREF 3ZYN A 57 365 UNP P0C192 LRC4B_MOUSE 57 365 DBREF 3ZYN B 57 365 UNP P0C192 LRC4B_MOUSE 57 365 SEQADV 3ZYN GLU A 54 UNP P0C192 EXPRESSION TAG SEQADV 3ZYN THR A 55 UNP P0C192 EXPRESSION TAG SEQADV 3ZYN GLY A 56 UNP P0C192 EXPRESSION TAG SEQADV 3ZYN GLY A 366 UNP P0C192 EXPRESSION TAG SEQADV 3ZYN THR A 367 UNP P0C192 EXPRESSION TAG SEQADV 3ZYN LYS A 368 UNP P0C192 EXPRESSION TAG SEQADV 3ZYN HIS A 369 UNP P0C192 EXPRESSION TAG SEQADV 3ZYN HIS A 370 UNP P0C192 EXPRESSION TAG SEQADV 3ZYN HIS A 371 UNP P0C192 EXPRESSION TAG SEQADV 3ZYN HIS A 372 UNP P0C192 EXPRESSION TAG SEQADV 3ZYN HIS A 373 UNP P0C192 EXPRESSION TAG SEQADV 3ZYN HIS A 374 UNP P0C192 EXPRESSION TAG SEQADV 3ZYN GLU B 54 UNP P0C192 EXPRESSION TAG SEQADV 3ZYN THR B 55 UNP P0C192 EXPRESSION TAG SEQADV 3ZYN GLY B 56 UNP P0C192 EXPRESSION TAG SEQADV 3ZYN GLY B 366 UNP P0C192 EXPRESSION TAG SEQADV 3ZYN THR B 367 UNP P0C192 EXPRESSION TAG SEQADV 3ZYN LYS B 368 UNP P0C192 EXPRESSION TAG SEQADV 3ZYN HIS B 369 UNP P0C192 EXPRESSION TAG SEQADV 3ZYN HIS B 370 UNP P0C192 EXPRESSION TAG SEQADV 3ZYN HIS B 371 UNP P0C192 EXPRESSION TAG SEQADV 3ZYN HIS B 372 UNP P0C192 EXPRESSION TAG SEQADV 3ZYN HIS B 373 UNP P0C192 EXPRESSION TAG SEQADV 3ZYN HIS B 374 UNP P0C192 EXPRESSION TAG SEQRES 1 A 321 GLU THR GLY THR SER CYS PRO ALA ALA CYS SER CYS SER SEQRES 2 A 321 ASN GLN ALA SER ARG VAL ILE CYS THR ARG ARG GLU LEU SEQRES 3 A 321 ALA GLU VAL PRO ALA SER ILE PRO VAL ASN THR ARG TYR SEQRES 4 A 321 LEU ASN LEU GLN GLU ASN SER ILE GLN VAL ILE ARG THR SEQRES 5 A 321 ASP THR PHE LYS HIS LEU ARG HIS LEU GLU ILE LEU GLN SEQRES 6 A 321 LEU SER LYS ASN LEU VAL ARG LYS ILE GLU VAL GLY ALA SEQRES 7 A 321 PHE ASN GLY LEU PRO SER LEU ASN THR LEU GLU LEU PHE SEQRES 8 A 321 ASP ASN ARG LEU THR THR VAL PRO THR GLN ALA PHE GLU SEQRES 9 A 321 TYR LEU SER LYS LEU ARG GLU LEU TRP LEU ARG ASN ASN SEQRES 10 A 321 PRO ILE GLU SER ILE PRO SER TYR ALA PHE ASN ARG VAL SEQRES 11 A 321 PRO SER LEU ARG ARG LEU ASP LEU GLY GLU LEU LYS ARG SEQRES 12 A 321 LEU GLU TYR ILE SER GLU ALA ALA PHE GLU GLY LEU VAL SEQRES 13 A 321 ASN LEU ARG TYR LEU ASN LEU GLY MET CYS ASN LEU LYS SEQRES 14 A 321 ASP ILE PRO ASN LEU THR ALA LEU VAL ARG LEU GLU GLU SEQRES 15 A 321 LEU GLU LEU SER GLY ASN ARG LEU ASP LEU ILE ARG PRO SEQRES 16 A 321 GLY SER PHE GLN GLY LEU THR SER LEU ARG LYS LEU TRP SEQRES 17 A 321 LEU MET HIS ALA GLN VAL ALA THR ILE GLU ARG ASN ALA SEQRES 18 A 321 PHE ASP ASP LEU LYS SER LEU GLU GLU LEU ASN LEU SER SEQRES 19 A 321 HIS ASN ASN LEU MET SER LEU PRO HIS ASP LEU PHE THR SEQRES 20 A 321 PRO LEU HIS ARG LEU GLU ARG VAL HIS LEU ASN HIS ASN SEQRES 21 A 321 PRO TRP HIS CYS ASN CYS ASP VAL LEU TRP LEU SER TRP SEQRES 22 A 321 TRP LEU LYS GLU THR VAL PRO SER ASN THR THR CYS CYS SEQRES 23 A 321 ALA ARG CYS HIS ALA PRO ALA GLY LEU LYS GLY ARG TYR SEQRES 24 A 321 ILE GLY GLU LEU ASP GLN SER HIS PHE THR CYS TYR ALA SEQRES 25 A 321 GLY THR LYS HIS HIS HIS HIS HIS HIS SEQRES 1 B 321 GLU THR GLY THR SER CYS PRO ALA ALA CYS SER CYS SER SEQRES 2 B 321 ASN GLN ALA SER ARG VAL ILE CYS THR ARG ARG GLU LEU SEQRES 3 B 321 ALA GLU VAL PRO ALA SER ILE PRO VAL ASN THR ARG TYR SEQRES 4 B 321 LEU ASN LEU GLN GLU ASN SER ILE GLN VAL ILE ARG THR SEQRES 5 B 321 ASP THR PHE LYS HIS LEU ARG HIS LEU GLU ILE LEU GLN SEQRES 6 B 321 LEU SER LYS ASN LEU VAL ARG LYS ILE GLU VAL GLY ALA SEQRES 7 B 321 PHE ASN GLY LEU PRO SER LEU ASN THR LEU GLU LEU PHE SEQRES 8 B 321 ASP ASN ARG LEU THR THR VAL PRO THR GLN ALA PHE GLU SEQRES 9 B 321 TYR LEU SER LYS LEU ARG GLU LEU TRP LEU ARG ASN ASN SEQRES 10 B 321 PRO ILE GLU SER ILE PRO SER TYR ALA PHE ASN ARG VAL SEQRES 11 B 321 PRO SER LEU ARG ARG LEU ASP LEU GLY GLU LEU LYS ARG SEQRES 12 B 321 LEU GLU TYR ILE SER GLU ALA ALA PHE GLU GLY LEU VAL SEQRES 13 B 321 ASN LEU ARG TYR LEU ASN LEU GLY MET CYS ASN LEU LYS SEQRES 14 B 321 ASP ILE PRO ASN LEU THR ALA LEU VAL ARG LEU GLU GLU SEQRES 15 B 321 LEU GLU LEU SER GLY ASN ARG LEU ASP LEU ILE ARG PRO SEQRES 16 B 321 GLY SER PHE GLN GLY LEU THR SER LEU ARG LYS LEU TRP SEQRES 17 B 321 LEU MET HIS ALA GLN VAL ALA THR ILE GLU ARG ASN ALA SEQRES 18 B 321 PHE ASP ASP LEU LYS SER LEU GLU GLU LEU ASN LEU SER SEQRES 19 B 321 HIS ASN ASN LEU MET SER LEU PRO HIS ASP LEU PHE THR SEQRES 20 B 321 PRO LEU HIS ARG LEU GLU ARG VAL HIS LEU ASN HIS ASN SEQRES 21 B 321 PRO TRP HIS CYS ASN CYS ASP VAL LEU TRP LEU SER TRP SEQRES 22 B 321 TRP LEU LYS GLU THR VAL PRO SER ASN THR THR CYS CYS SEQRES 23 B 321 ALA ARG CYS HIS ALA PRO ALA GLY LEU LYS GLY ARG TYR SEQRES 24 B 321 ILE GLY GLU LEU ASP GLN SER HIS PHE THR CYS TYR ALA SEQRES 25 B 321 GLY THR LYS HIS HIS HIS HIS HIS HIS MODRES 3ZYN ASN A 335 ASN GLYCOSYLATION SITE MODRES 3ZYN ASN B 335 ASN GLYCOSYLATION SITE HET NAG A1367 14 HET NAG B1367 14 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 3 NAG 2(C8 H15 N O6) HELIX 1 1 PRO A 152 PHE A 156 5 5 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 ILE A 353 LEU A 356 5 4 HELIX 5 5 ASP A 357 PHE A 361 5 5 HELIX 6 6 ASN B 67 ALA B 69 5 3 HELIX 7 7 PRO B 152 PHE B 156 5 5 HELIX 8 8 ARG B 247 GLN B 252 5 6 HELIX 9 9 ASN B 318 ASP B 320 5 3 HELIX 10 10 VAL B 321 VAL B 332 1 12 HELIX 11 11 PRO B 345 LYS B 349 5 5 HELIX 12 12 ILE B 353 LEU B 356 5 4 HELIX 13 13 ASP B 357 PHE B 361 5 5 SHEET 1 AA12 SER A 64 CYS A 65 0 SHEET 2 AA12 ARG A 71 ILE A 73 -1 O ILE A 73 N SER A 64 SHEET 3 AA12 TYR A 92 ASN A 94 1 O TYR A 92 N VAL A 72 SHEET 4 AA12 ILE A 116 GLN A 118 1 O ILE A 116 N LEU A 93 SHEET 5 AA12 THR A 140 GLU A 142 1 O THR A 140 N LEU A 117 SHEET 6 AA12 GLU A 164 TRP A 166 1 O GLU A 164 N LEU A 141 SHEET 7 AA12 ARG A 188 ASP A 190 1 O ARG A 188 N LEU A 165 SHEET 8 AA12 TYR A 213 ASN A 215 1 O TYR A 213 N LEU A 189 SHEET 9 AA12 GLU A 235 GLU A 237 1 O GLU A 235 N LEU A 214 SHEET 10 AA12 LYS A 259 TRP A 261 1 O LYS A 259 N LEU A 236 SHEET 11 AA12 GLU A 283 ASN A 285 1 O GLU A 283 N LEU A 260 SHEET 12 AA12 ARG A 307 HIS A 309 1 O ARG A 307 N LEU A 284 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 2 SER A 174 ILE A 175 0 SHEET 2 AC 2 TYR A 199 ILE A 200 1 O TYR A 199 N ILE A 175 SHEET 1 AD 2 LEU A 245 ILE A 246 0 SHEET 2 AD 2 THR A 269 ILE A 270 1 O THR A 269 N ILE A 246 SHEET 1 AE 2 TRP A 315 HIS A 316 0 SHEET 2 AE 2 CYS A 342 ALA A 344 1 N HIS A 343 O TRP A 315 SHEET 1 BA12 SER B 64 CYS B 65 0 SHEET 2 BA12 ARG B 71 ILE B 73 -1 O ILE B 73 N SER B 64 SHEET 3 BA12 TYR B 92 ASN B 94 1 O TYR B 92 N VAL B 72 SHEET 4 BA12 ILE B 116 GLN B 118 1 O ILE B 116 N LEU B 93 SHEET 5 BA12 THR B 140 GLU B 142 1 O THR B 140 N LEU B 117 SHEET 6 BA12 GLU B 164 TRP B 166 1 O GLU B 164 N LEU B 141 SHEET 7 BA12 ARG B 188 ASP B 190 1 O ARG B 188 N LEU B 165 SHEET 8 BA12 TYR B 213 ASN B 215 1 O TYR B 213 N LEU B 189 SHEET 9 BA12 GLU B 235 GLU B 237 1 O GLU B 235 N LEU B 214 SHEET 10 BA12 LYS B 259 TRP B 261 1 O LYS B 259 N LEU B 236 SHEET 11 BA12 GLU B 283 ASN B 285 1 O GLU B 283 N LEU B 260 SHEET 12 BA12 ARG B 307 HIS B 309 1 O ARG B 307 N LEU B 284 SHEET 1 BB 2 VAL B 102 ILE B 103 0 SHEET 2 BB 2 LYS B 126 ILE B 127 1 O LYS B 126 N ILE B 103 SHEET 1 BC 2 SER B 174 ILE B 175 0 SHEET 2 BC 2 TYR B 199 ILE B 200 1 O TYR B 199 N ILE B 175 SHEET 1 BD 2 LEU B 245 ILE B 246 0 SHEET 2 BD 2 THR B 269 ILE B 270 1 O THR B 269 N ILE B 246 SHEET 1 BE 2 TRP B 315 HIS B 316 0 SHEET 2 BE 2 CYS B 342 ALA B 344 1 N HIS B 343 O TRP B 315 SSBOND 1 CYS A 59 CYS A 65 1555 1555 2.03 SSBOND 2 CYS A 63 CYS A 74 1555 1555 2.05 SSBOND 3 CYS A 317 CYS A 342 1555 1555 2.05 SSBOND 4 CYS A 319 CYS A 363 1555 1555 2.03 SSBOND 5 CYS B 59 CYS B 65 1555 1555 2.04 SSBOND 6 CYS B 63 CYS B 74 1555 1555 2.03 SSBOND 7 CYS B 317 CYS B 342 1555 1555 2.01 SSBOND 8 CYS B 319 CYS B 363 1555 1555 2.02 LINK ND2 ASN A 335 C1 NAG A1367 1555 1555 1.44 LINK ND2 ASN B 335 C1 NAG B1367 1555 1555 1.45 CISPEP 1 CYS A 338 CYS A 339 0 1.83 CISPEP 2 ALA A 344 PRO A 345 0 -7.01 CISPEP 3 CYS B 338 CYS B 339 0 1.71 CISPEP 4 ALA B 344 PRO B 345 0 -1.91 CRYST1 157.100 57.260 100.430 90.00 117.76 90.00 C 1 2 1 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 0.006365 0.000000 0.003350 0.00000 SCALE2 0.000000 0.017464 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011252 0.00000 MTRIX1 1 0.834300 -0.137600 -0.533800 40.15000 1 MTRIX2 1 -0.041430 -0.981300 0.188200 88.22000 1 MTRIX3 1 -0.549700 -0.134900 -0.824400 118.10000 1