HEADER SIGNALING PROTEIN 24-JAN-18 6FKQ TITLE THE CRYSTAL STRUCTURE OF A FRAGMENT OF NETRIN-1 IN COMPLEX WITH A TITLE 2 FRAGMENT OF DRAXIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: NETRIN-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: EPIDIDYMIS TISSUE PROTEIN LI 131P; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: NETRIN-1 IS A PROTOTYPICAL AXON GUIDANCE CUE THAT COMPND 7 BINDS TO THE RECEPTOR DELETED IN COLORECTAL CANCER (DCC).; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DRAXIN; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: UNP RESIDUES 225-243; COMPND 12 SYNONYM: DORSAL INHIBITORY AXON GUIDANCE PROTEIN,DORSAL REPULSIVE COMPND 13 AXON GUIDANCE PROTEIN,NEUCRIN; COMPND 14 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: NTN1, NTN1L; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HEK293T; SOURCE 10 EXPRESSION_SYSTEM_ATCC_NUMBER: 293T/17 [HEK 293T/17] ATCC CRL-11268; SOURCE 11 EXPRESSION_SYSTEM_TISSUE: KIDNEY; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PXLG; SOURCE 13 MOL_ID: 2; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_COMMON: HUMAN; SOURCE 16 ORGANISM_TAXID: 9606; SOURCE 17 GENE: DRAXIN, C1ORF187, PSEC0258, UNQ3119/PRO10268; SOURCE 18 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 19 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 21 EXPRESSION_SYSTEM_CELL_LINE: HEK293T; SOURCE 22 EXPRESSION_SYSTEM_ATCC_NUMBER: (HEK 293T/17] ATCC CRL-11268; SOURCE 23 EXPRESSION_SYSTEM_TISSUE: KIDNEY; SOURCE 24 EXPRESSION_SYSTEM_PLASMID: PXLG KEYWDS AXON GUIDANCE CUE, NETRIN-1, DRAXIN, COMMISSURAL NEURON, SIGNALING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.BHOWMICK,R.MEIJERS REVDAT 4 17-JAN-24 6FKQ 1 HETSYN LINK REVDAT 3 29-JUL-20 6FKQ 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 04-APR-18 6FKQ 1 JRNL REVDAT 1 21-MAR-18 6FKQ 0 JRNL AUTH Y.LIU,T.BHOWMICK,Y.LIU,X.GAO,H.D.T.MERTENS,D.I.SVERGUN, JRNL AUTH 2 J.XIAO,Y.ZHANG,J.H.WANG,R.MEIJERS JRNL TITL STRUCTURAL BASIS FOR DRAXIN-MODULATED AXON GUIDANCE AND JRNL TITL 2 FASCICULATION BY NETRIN-1 THROUGH DCC. JRNL REF NEURON V. 97 1261 2018 JRNL REFN ISSN 1097-4199 JRNL PMID 29503192 JRNL DOI 10.1016/J.NEURON.2018.02.010 REMARK 2 REMARK 2 RESOLUTION. 3.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0155 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) : 3.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 17128 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) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 874 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) : 3.07 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1222 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.30 REMARK 3 BIN R VALUE (WORKING SET) : 0.3950 REMARK 3 BIN FREE R VALUE SET COUNT : 63 REMARK 3 BIN FREE R VALUE : 0.3380 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3420 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 155 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) : 76.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.42000 REMARK 3 B22 (A**2) : 2.42000 REMARK 3 B33 (A**2) : -7.84000 REMARK 3 B12 (A**2) : 1.21000 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): 0.826 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.387 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.375 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 23.425 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.908 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.866 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3684 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3250 ; 0.010 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4993 ; 1.881 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7507 ; 1.744 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 432 ; 8.003 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 178 ;35.405 ;22.753 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 568 ;18.113 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 37 ;17.203 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 532 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4087 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 874 ; 0.023 ; 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): 1736 ; 4.394 ; 7.334 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1735 ; 4.381 ; 7.331 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2164 ; 7.186 ;10.994 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2165 ; 7.185 ;10.998 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1948 ; 4.887 ; 7.987 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1948 ; 4.886 ; 7.987 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2830 ; 7.436 ;11.789 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3929 ;11.160 ;87.838 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3929 ;11.160 ;87.834 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 : 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 6FKQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1200008351. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-SEP-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4-5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P14 (MX2) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18063 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.070 REMARK 200 RESOLUTION RANGE LOW (A) : 54.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 32.90 REMARK 200 R MERGE (I) : 0.58700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 18.60 REMARK 200 R MERGE FOR SHELL (I) : 2.89700 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: 4URT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M AMMONIUM SULPHATE AND 0.1 M REMARK 280 SODIUM CITRATE, AT PH 4 TO PH 5, VAPOR DIFFUSION, TEMPERATURE REMARK 280 298K, VAPOR DIFFUSION, SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+1/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-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 61.29000 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 122.58000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 61.29000 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 122.58000 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 61.29000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 122.58000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 61.29000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 122.58000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -98.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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 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 O7 NAG D 3 O2 SO4 A 516 1.11 REMARK 500 ND2 ASN A 131 O5 NAG E 1 1.93 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 65 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 65 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 PRO A 129 C - N - CD ANGL. DEV. = 16.7 DEGREES REMARK 500 ARG A 182 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 PRO A 212 C - N - CA ANGL. DEV. = -10.2 DEGREES REMARK 500 CYS A 338 CA - CB - SG ANGL. DEV. = 7.3 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 HIS A 103 59.10 -144.55 REMARK 500 ASN A 116 64.71 -150.47 REMARK 500 HIS A 130 124.67 -30.58 REMARK 500 TYR A 167 -128.94 60.64 REMARK 500 ARG A 190 49.52 31.46 REMARK 500 ASP A 259 -73.30 -91.25 REMARK 500 GLU A 260 77.65 54.92 REMARK 500 ASP A 264 0.39 -65.40 REMARK 500 ASP A 270 4.75 -69.35 REMARK 500 CYS A 287 137.46 -31.99 REMARK 500 ASP A 297 -165.23 -121.71 REMARK 500 PRO A 320 136.61 -37.83 REMARK 500 HIS A 373 37.70 73.97 REMARK 500 ASP A 390 99.25 -68.96 REMARK 500 MET A 391 -177.41 -63.01 REMARK 500 LYS A 399 58.61 -118.18 REMARK 500 ASP A 405 77.49 52.91 REMARK 500 THR A 420 -12.38 78.95 REMARK 500 ARG A 436 142.09 -173.83 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 168 ARG A 169 -143.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 508 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 107 O REMARK 620 2 ASP A 110 OD1 72.7 REMARK 620 3 ASN A 112 OD1 148.9 106.5 REMARK 620 4 THR A 118 O 78.7 128.1 119.7 REMARK 620 5 THR A 118 OG1 87.6 76.5 122.9 59.6 REMARK 620 6 SER A 277 O 79.8 132.4 78.8 81.5 140.8 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4URT RELATED DB: PDB REMARK 900 NETRIN/DCC COMPLEX DBREF 6FKQ A 39 453 UNP O95631 NET1_HUMAN 39 453 DBREF 6FKQ B 225 243 UNP Q8NBI3 DRAXI_HUMAN 225 243 SEQRES 1 A 415 ASP PRO CYS SER ASP GLU ASN GLY HIS PRO ARG ARG CYS SEQRES 2 A 415 ILE PRO ASP PHE VAL ASN ALA ALA PHE GLY LYS ASP VAL SEQRES 3 A 415 ARG VAL SER SER THR CYS GLY ARG PRO PRO ALA ARG TYR SEQRES 4 A 415 CYS VAL VAL SER GLU ARG GLY GLU GLU ARG LEU ARG SER SEQRES 5 A 415 CYS HIS LEU CYS ASN ALA SER ASP PRO LYS LYS ALA HIS SEQRES 6 A 415 PRO PRO ALA PHE LEU THR ASP LEU ASN ASN PRO HIS ASN SEQRES 7 A 415 LEU THR CYS TRP GLN SER GLU ASN TYR LEU GLN PHE PRO SEQRES 8 A 415 HIS ASN VAL THR LEU THR LEU SER LEU GLY LYS LYS PHE SEQRES 9 A 415 GLU VAL THR TYR VAL SER LEU GLN PHE CYS SER PRO ARG SEQRES 10 A 415 PRO GLU SER MET ALA ILE TYR LYS SER MET ASP TYR GLY SEQRES 11 A 415 ARG THR TRP VAL PRO PHE GLN PHE TYR SER THR GLN CYS SEQRES 12 A 415 ARG LYS MET TYR ASN ARG PRO HIS ARG ALA PRO ILE THR SEQRES 13 A 415 LYS GLN ASN GLU GLN GLU ALA VAL CYS THR ASP SER HIS SEQRES 14 A 415 THR ASP MET ARG PRO LEU SER GLY GLY LEU ILE ALA PHE SEQRES 15 A 415 SER THR LEU ASP GLY ARG PRO SER ALA HIS ASP PHE ASP SEQRES 16 A 415 ASN SER PRO VAL LEU GLN ASP TRP VAL THR ALA THR ASP SEQRES 17 A 415 ILE ARG VAL ALA PHE SER ARG LEU HIS THR PHE GLY ASP SEQRES 18 A 415 GLU ASN GLU ASP ASP SER GLU LEU ALA ARG ASP SER TYR SEQRES 19 A 415 PHE TYR ALA VAL SER ASP LEU GLN VAL GLY GLY ARG CYS SEQRES 20 A 415 LYS CYS ASN GLY HIS ALA ALA ARG CYS VAL ARG ASP ARG SEQRES 21 A 415 ASP ASP SER LEU VAL CYS ASP CYS ARG HIS ASN THR ALA SEQRES 22 A 415 GLY PRO GLU CYS ASP ARG CYS LYS PRO PHE HIS TYR ASP SEQRES 23 A 415 ARG PRO TRP GLN ARG ALA THR ALA ARG GLU ALA ASN GLU SEQRES 24 A 415 CYS VAL ALA CYS ASN CYS ASN LEU HIS ALA ARG ARG CYS SEQRES 25 A 415 ARG PHE ASN MET GLU LEU TYR LYS LEU SER GLY ARG LYS SEQRES 26 A 415 SER GLY GLY VAL CYS LEU ASN CYS ARG HIS ASN THR ALA SEQRES 27 A 415 GLY ARG HIS CYS HIS TYR CYS LYS GLU GLY TYR TYR ARG SEQRES 28 A 415 ASP MET GLY LYS PRO ILE THR HIS ARG LYS ALA CYS LYS SEQRES 29 A 415 ALA CYS ASP CYS HIS PRO VAL GLY ALA ALA GLY LYS THR SEQRES 30 A 415 CYS ASN GLN THR THR GLY GLN CYS PRO CYS LYS ASP GLY SEQRES 31 A 415 VAL THR GLY ILE THR CYS ASN ARG CYS ALA LYS GLY TYR SEQRES 32 A 415 GLN GLN SER ARG SER PRO ILE ALA PRO CYS ILE LYS SEQRES 1 B 19 MET PRO THR LEU ASP MET ALA LEU PHE ASP TRP THR ASP SEQRES 2 B 19 TYR GLU ASP LEU LYS PRO HET NAG C 1 14 HET NAG C 2 14 HET NAG D 1 14 HET NAG D 2 14 HET NAG D 3 14 HET NAG E 1 14 HET NAG E 2 14 HET CA A 508 1 HET SO4 A 509 5 HET SO4 A 510 5 HET SO4 A 511 5 HET SO4 A 512 5 HET SO4 A 513 5 HET SO4 A 514 5 HET SO4 A 515 5 HET SO4 A 516 5 HET SO4 A 517 5 HET SO4 A 518 5 HET GOL A 519 6 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM CA CALCIUM ION HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL 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 HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 NAG 7(C8 H15 N O6) FORMUL 6 CA CA 2+ FORMUL 7 SO4 10(O4 S 2-) FORMUL 17 GOL C3 H8 O3 HELIX 1 AA1 ASP A 98 ALA A 102 5 5 HELIX 2 AA2 PRO A 105 ASP A 110 1 6 HELIX 3 AA3 GLN A 180 ASN A 186 1 7 HELIX 4 AA4 THR A 194 GLU A 198 5 5 HELIX 5 AA5 ASP A 231 ASN A 234 5 4 HELIX 6 AA6 SER A 235 VAL A 242 1 8 HELIX 7 AA7 ASP A 264 ASP A 270 1 7 HELIX 8 AA8 ASN A 353 SER A 360 1 8 HELIX 9 AA9 TYR B 238 LYS B 242 5 5 SHEET 1 A 2 ALA A 75 ARG A 83 0 SHEET 2 A 2 GLU A 86 CYS A 94 -1 SHEET 1 B 4 VAL A 132 SER A 137 0 SHEET 2 B 4 ASP A 246 PHE A 251 -1 SHEET 3 B 4 SER A 158 SER A 164 -1 SHEET 4 B 4 VAL A 172 SER A 178 -1 SHEET 1 C 3 LEU A 217 SER A 221 0 SHEET 2 C 3 PHE A 142 GLN A 150 -1 SHEET 3 C 3 ASP A 278 CYS A 285 -1 SHEET 1 D 2 ARG A 349 PHE A 352 0 SHEET 2 D 2 GLY A 366 LEU A 369 -1 SHEET 1 E 2 TYR A 387 ARG A 389 0 SHEET 2 E 2 CYS A 401 ALA A 403 -1 SHEET 1 F 2 ALA A 291 ARG A 296 0 SHEET 2 F 2 LEU A 302 CYS A 306 -1 SSBOND 1 CYS A 41 CYS A 51 1555 1555 2.06 SSBOND 2 CYS A 70 CYS A 94 1555 1555 2.05 SSBOND 3 CYS A 78 CYS A 91 1555 1555 2.07 SSBOND 4 CYS A 119 CYS A 152 1555 1555 2.05 SSBOND 5 CYS A 181 CYS A 203 1555 1555 2.04 SSBOND 6 CYS A 285 CYS A 294 1555 1555 2.04 SSBOND 7 CYS A 287 CYS A 304 1555 1555 2.03 SSBOND 8 CYS A 306 CYS A 315 1555 1555 2.04 SSBOND 9 CYS A 318 CYS A 338 1555 1555 2.05 SSBOND 10 CYS A 341 CYS A 350 1555 1555 2.04 SSBOND 11 CYS A 343 CYS A 368 1555 1555 2.01 SSBOND 12 CYS A 371 CYS A 380 1555 1555 2.00 SSBOND 13 CYS A 383 CYS A 401 1555 1555 2.04 SSBOND 14 CYS A 404 CYS A 416 1555 1555 2.03 SSBOND 15 CYS A 406 CYS A 423 1555 1555 2.05 SSBOND 16 CYS A 425 CYS A 434 1555 1555 2.03 SSBOND 17 CYS A 437 CYS A 451 1555 1555 2.06 LINK NH2 ARG A 65 O3 SO4 A 511 1555 1555 1.43 LINK ND2 ASN A 95 C1 NAG C 1 1555 1555 1.46 LINK CB ASP A 98 O6 NAG C 1 1555 1555 1.37 LINK ND2 ASN A 116 C1 NAG D 1 1555 1555 1.46 LINK ND2 ASN A 131 C1 NAG E 1 1555 1555 1.31 LINK NH2 ARG A 155 O4 SO4 A 509 1555 1555 1.43 LINK NH2 ARG A 248 O1 SO4 A 511 1555 1555 1.43 LINK NH2 ARG A 436 O1 SO4 A 514 1555 1555 1.42 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.45 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.48 LINK O4 NAG D 2 C1 NAG D 3 1555 1555 1.48 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.42 LINK O PHE A 107 CA CA A 508 1555 1555 2.35 LINK OD1 ASP A 110 CA CA A 508 1555 1555 2.35 LINK OD1 ASN A 112 CA CA A 508 1555 1555 2.39 LINK O THR A 118 CA CA A 508 1555 1555 2.37 LINK OG1 THR A 118 CA CA A 508 1555 1555 2.33 LINK O SER A 277 CA CA A 508 1555 1555 2.27 CISPEP 1 ARG A 72 PRO A 73 0 -10.37 CISPEP 2 PHE A 128 PRO A 129 0 -9.50 CRYST1 130.794 130.794 183.870 90.00 90.00 120.00 P 64 2 2 12 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 0.007646 0.004414 0.000000 0.00000 SCALE2 0.000000 0.008828 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005439 0.00000