HEADER APOPTOSIS 21-FEB-14 4OVE TITLE X-RAY CRYSTAL STRUCTURE OF MOUSE NETRIN-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NETRIN-1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: NTN1; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 9 EXPRESSION_SYSTEM_ORGAN: KIDNEY; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PCEP-PU KEYWDS SIMILAR TO LAMININ GAMMA-1, DOMAIN VI: BETA-SANDWICH JELLY-ROLL, KEYWDS 2 DOMAINS V-1, V-2, V-3: LAMININ-TYPE EPIDERMAL GROWTH FACTOR, KEYWDS 3 STRUCTURAL CALCIUM, AXON GUIDANCE CUE, SURVIVAL FACTOR, NEOGENIN, KEYWDS 4 DCC, UNC5A, UNC5B, UNC5C, UNC5D, DSCAM, EXTRACELLULAR MATRIX, KEYWDS 5 APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR M.MEIER,D.NIKODEMUS,R.REUTEN,T.R.PATEL,G.ORRISS,N.OKUN,M.KOCH, AUTHOR 2 J.STETEFELD REVDAT 5 29-JUL-20 4OVE 1 COMPND REMARK SEQADV HETNAM REVDAT 5 2 1 SSBOND LINK SITE ATOM REVDAT 4 25-OCT-17 4OVE 1 REMARK REVDAT 3 17-FEB-16 4OVE 1 JRNL REVDAT 2 11-MAR-15 4OVE 1 SHEET REVDAT 1 25-FEB-15 4OVE 0 JRNL AUTH M.GRANDIN,M.MEIER,J.G.DELCROS,D.NIKODEMUS,R.REUTEN, JRNL AUTH 2 T.R.PATEL,D.GOLDSCHNEIDER,G.ORRISS,N.KRAHN,A.BOUSSOUAR, JRNL AUTH 3 R.ABES,Y.DEAN,D.NEVES,A.BERNET,S.DEPIL,F.SCHNEIDERS,K.POOLE, JRNL AUTH 4 R.DANTE,M.KOCH,P.MEHLEN,J.STETEFELD JRNL TITL STRUCTURAL DECODING OF THE NETRIN-1/UNC5 INTERACTION AND ITS JRNL TITL 2 THERAPEUTICAL IMPLICATIONS IN CANCERS. JRNL REF CANCER CELL V. 29 173 2016 JRNL REFN ISSN 1535-6108 JRNL PMID 26859457 JRNL DOI 10.1016/J.CCELL.2016.01.001 REMARK 2 REMARK 2 RESOLUTION. 2.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 2.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 89.5 REMARK 3 NUMBER OF REFLECTIONS : 24458 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) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1308 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 REFLECTION IN BIN (WORKING SET) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3309 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 105 REMARK 3 SOLVENT ATOMS : 97 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 60.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 64.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.84000 REMARK 3 B22 (A**2) : -0.84000 REMARK 3 B33 (A**2) : 2.72000 REMARK 3 B12 (A**2) : -0.42000 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): 0.362 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.299 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.267 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 29.397 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.926 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.862 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3662 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3265 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4985 ; 1.806 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7484 ; 0.857 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 440 ;13.261 ; 5.148 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 176 ;36.259 ;22.443 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 557 ;18.164 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;15.243 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 537 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4161 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 897 ; 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): 1726 ; 3.621 ; 4.680 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1724 ; 3.622 ; 4.679 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2163 ; 5.951 ; 7.013 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1936 ; 3.878 ; 5.257 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 7 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 35 A 456 REMARK 3 RESIDUE RANGE : A 509 A 509 REMARK 3 RESIDUE RANGE : A 501 A 505 REMARK 3 RESIDUE RANGE : A 506 A 507 REMARK 3 RESIDUE RANGE : A 508 A 508 REMARK 3 RESIDUE RANGE : A 510 A 510 REMARK 3 RESIDUE RANGE : A 601 A 697 REMARK 3 ORIGIN FOR THE GROUP (A): 29.0771 15.8929 3.8209 REMARK 3 T TENSOR REMARK 3 T11: 0.0711 T22: 0.0822 REMARK 3 T33: 0.0237 T12: 0.0258 REMARK 3 T13: 0.0085 T23: 0.0231 REMARK 3 L TENSOR REMARK 3 L11: 0.5237 L22: 0.3894 REMARK 3 L33: 4.0219 L12: 0.3001 REMARK 3 L13: -0.9402 L23: -0.9701 REMARK 3 S TENSOR REMARK 3 S11: -0.0510 S12: 0.1256 S13: 0.0392 REMARK 3 S21: -0.0033 S22: 0.0180 S23: -0.0184 REMARK 3 S31: -0.0270 S32: -0.2278 S33: 0.0331 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: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REMARK 3 REMARK 3 THE DIFFRACTION PATTERN OF NETRIN-1 CRYSTALS SHOWS STRONG REMARK 3 ANISOTROPY. THE RESOLUTION LIMITS IN DIRECTION A*/B* ARE 44.85 - REMARK 3 2.80 A AND IN DIRECTION C* 44.85 - 2.64 A. COMPLETENESS OF THE REMARK 3 DATASET IN THE RESOLUTION RANGE OF INF - 2.80 A IS 0.999, IN THE REMARK 3 RANGE OF INF - 2.64 A IT IS 0.896. THE WILSON B-FACTOR CALCULATED REMARK 3 FROM THE LINEAR RANGE OF THE DATA IS 68.0 A**2. REMARK 3 REMARK 3 THE ELLIPSOIDAL OUTER SHELL IN THE RANGE OF 2.90 - 2.80 A (A*/B*) REMARK 3 AND 2.74 - 2.64 A (C*) CONTAINS 2564 REFLECTIONS, HAS A REMARK 3 COMPLETENESS OF 1.0, A REDUNDANCY OF 10.8, I/SIGMAI OF 2.0, RMEAS REMARK 3 OF 1.344, RMERGE OF 1.280 AND RPIM OF 0.406. REMARK 3 REMARK 3 FOR REFINEMENT, AN ELLIPSOIDAL TRUNCTION (LIMIT OF 2.80 A IN A*/B*, REMARK 3 LIMIT OF 2.50 A IN C*), ANISOTROPIC SCALING AND A NEGATIVE REMARK 3 ISOTROPIC B-FACTOR CORRECTION OF 50% OF THE B-FACTOR IN DIRECTION REMARK 3 OF THE LOWEST FALL-OFF (C*) WAS APPLIED ACCORDING TO THE PROCEDURE REMARK 3 DESCRIBED BY M. STRONG, M.R. SAWAYA, S. WANG, M. PHILLIPS, D. REMARK 3 CASCIO, D. EISENBERG, PROC NATL ACAD SCI USA. 103, 8060-8-65, 2006. REMARK 3 REMARK 3 AFTER ABOVE ANISOTROPY CORRECTION AND CONVERSION TO AMPLITUDES, REMARK 3 THE COMPLETENESS OF THE REFINEMENT DATASET IS AS FOLLOWS: INF - REMARK 3 2.80 A: 0.996, INF - 2.50 A: 0.807. THE WILSON B-FACTOR CALCULATED REMARK 3 FROM THE LINEAR RANGE OF DATA IS 60.1 A**2. REMARK 4 REMARK 4 4OVE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1000084996. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-OCT-11; 12-OCT-05 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 7.7 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : CLSI; SLS REMARK 200 BEAMLINE : 08B1-1; X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.25440; 1.25470, 1.25520, REMARK 200 1.24210 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 (DCM) WITH WATER-COOLED FIRST REMARK 200 CRYSTAL; LIQUID NITROGEN COOLED REMARK 200 FIXED-EXIT SI(111) MONOCHROMATOR REMARK 200 OPTICS : VERTICAL COLLIMATING MIRROR, REMARK 200 TOROIDAL FOCUSING MIRROR; REMARK 200 DYNAMICALLY BENDABLE MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300; RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27279 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 80.9 REMARK 200 DATA REDUNDANCY : 10.50 REMARK 200 R MERGE (I) : 0.12900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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; SIRAS REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 74.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, 2.7-2.8 M NACL, 0.02-0.2 REMARK 280 M GLYCINE, PH 7.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -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 223.20133 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 111.60067 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 111.60067 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 223.20133 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 300 REMARK: NETRIN-1 WITHOUT C-TERMINAL DOMAIN FORMS MONOMERS, DIMERS, REMARK 300 AND HIGHER ORDER OLIGOMERS IN SOLUTION, AS EVIDENCED BY DYNAMIC REMARK 300 LIGHT SCATTERING (DLS), SIZE EXCLUSION CHROMATOGRAPHY (SEC), AND REMARK 300 SMALL ANGLE X-RAY SCATTERING (SAXS). IN THE PRESENCE OF GLYCINE AND REMARK 300 HIGH CONCENTRATIONS OF SODIUM CHLORIDE, THE DIMERIC FORM CAN BE REMARK 300 STABILIZED. THE ASYMMETRIC UNIT CONTAINS ONE MONOMER. A DIMER THAT REMARK 300 RESEMBLES THE SHAPE MODEL OBTAINED FROM SAXS CAN BE OBTAINED BY REMARK 300 APPLYING THE FOLLOWING CRYSTALLOGRAPHIC SYMMETRY OPERATION: X-Y, -Y, REMARK 300 -Z+1/3. 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: 6770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 46900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 111.60067 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 ARG A 23 REMARK 465 GLY A 24 REMARK 465 GLY A 25 REMARK 465 PRO A 26 REMARK 465 GLY A 27 REMARK 465 LEU A 28 REMARK 465 SER A 29 REMARK 465 MET A 30 REMARK 465 PHE A 31 REMARK 465 ALA A 32 REMARK 465 GLY A 33 REMARK 465 GLN A 34 REMARK 465 ALA A 457 REMARK 465 LEU A 458 REMARK 465 GLU A 459 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 N HIS A 373 O HOH A 691 2.05 REMARK 500 OD1 ASN A 131 OG SER A 252 2.06 REMARK 500 OG1 THR A 375 O HOH A 691 2.17 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 PRO A 74 151.32 -47.50 REMARK 500 HIS A 115 -4.47 74.80 REMARK 500 ASN A 116 47.17 -163.39 REMARK 500 SER A 178 155.12 178.98 REMARK 500 ASP A 259 -60.78 77.66 REMARK 500 SER A 265 91.28 -66.09 REMARK 500 ASP A 299 6.51 84.25 REMARK 500 HIS A 373 56.23 -119.90 REMARK 500 CYS A 380 55.20 37.72 REMARK 500 ASP A 390 93.50 -67.16 REMARK 500 LYS A 399 44.29 73.50 REMARK 500 ASP A 405 56.08 -113.69 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 509 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 107 O REMARK 620 2 ASP A 110 OD1 69.6 REMARK 620 3 ASN A 112 OD1 159.0 120.6 REMARK 620 4 THR A 118 OG1 90.7 77.2 109.1 REMARK 620 5 THR A 118 O 85.4 139.4 94.1 71.4 REMARK 620 6 SER A 277 O 81.2 127.8 78.3 147.1 76.1 REMARK 620 7 HOH A 604 O 89.5 68.5 78.9 143.3 145.0 68.9 REMARK 620 N 1 2 3 4 5 6 DBREF 4OVE A 23 457 UNP O09118 NET1_MOUSE 23 457 SEQADV 4OVE LEU A 458 UNP O09118 EXPRESSION TAG SEQADV 4OVE GLU A 459 UNP O09118 EXPRESSION TAG SEQRES 1 A 437 ARG GLY GLY PRO GLY LEU SER MET PHE ALA GLY GLN ALA SEQRES 2 A 437 ALA GLN PRO ASP PRO CYS SER ASP GLU ASN GLY HIS PRO SEQRES 3 A 437 ARG ARG CYS ILE PRO ASP PHE VAL ASN ALA ALA PHE GLY SEQRES 4 A 437 LYS ASP VAL ARG VAL SER SER THR CYS GLY ARG PRO PRO SEQRES 5 A 437 ALA ARG TYR CYS VAL VAL SER GLU ARG GLY GLU GLU ARG SEQRES 6 A 437 LEU ARG SER CYS HIS LEU CYS ASN SER SER ASP PRO LYS SEQRES 7 A 437 LYS ALA HIS PRO PRO ALA PHE LEU THR ASP LEU ASN ASN SEQRES 8 A 437 PRO HIS ASN LEU THR CYS TRP GLN SER GLU ASN TYR LEU SEQRES 9 A 437 GLN PHE PRO HIS ASN VAL THR LEU THR LEU SER LEU GLY SEQRES 10 A 437 LYS LYS PHE GLU VAL THR TYR VAL SER LEU GLN PHE CYS SEQRES 11 A 437 SER PRO ARG PRO GLU SER MET ALA ILE TYR LYS SER MET SEQRES 12 A 437 ASP TYR GLY ARG THR TRP VAL PRO PHE GLN PHE TYR SER SEQRES 13 A 437 THR GLN CYS ARG LYS MET TYR ASN ARG PRO HIS ARG ALA SEQRES 14 A 437 PRO ILE THR LYS GLN ASN GLU GLN GLU ALA VAL CYS THR SEQRES 15 A 437 ASP SER HIS THR ASP MET ARG PRO LEU SER GLY GLY LEU SEQRES 16 A 437 ILE ALA PHE SER THR LEU ASP GLY ARG PRO SER ALA HIS SEQRES 17 A 437 ASP PHE ASP ASN SER PRO VAL LEU GLN ASP TRP VAL THR SEQRES 18 A 437 ALA THR ASP ILE ARG VAL ALA PHE SER ARG LEU HIS THR SEQRES 19 A 437 PHE GLY ASP GLU ASN GLU ASP ASP SER GLU LEU ALA ARG SEQRES 20 A 437 ASP SER TYR TYR TYR ALA VAL SER ASP LEU GLN VAL GLY SEQRES 21 A 437 GLY ARG CYS LYS CYS ASN GLY HIS ALA ALA ARG CYS VAL SEQRES 22 A 437 ARG ASP ARG ASP ASP SER LEU VAL CYS ASP CYS ARG HIS SEQRES 23 A 437 ASN THR ALA GLY PRO GLU CYS ASP ARG CYS LYS PRO PHE SEQRES 24 A 437 HIS TYR ASP ARG PRO TRP GLN ARG ALA THR ALA ARG GLU SEQRES 25 A 437 ALA ASN GLU CYS VAL ALA CYS ASN CYS ASN LEU HIS ALA SEQRES 26 A 437 ARG ARG CYS ARG PHE ASN MET GLU LEU TYR LYS LEU SER SEQRES 27 A 437 GLY ARG LYS SER GLY GLY VAL CYS LEU ASN CYS ARG HIS SEQRES 28 A 437 ASN THR ALA GLY ARG HIS CYS HIS TYR CYS LYS GLU GLY SEQRES 29 A 437 PHE TYR ARG ASP MET GLY LYS PRO ILE THR HIS ARG LYS SEQRES 30 A 437 ALA CYS LYS ALA CYS ASP CYS HIS PRO VAL GLY ALA ALA SEQRES 31 A 437 GLY LYS THR CYS ASN GLN THR THR GLY GLN CYS PRO CYS SEQRES 32 A 437 LYS ASP GLY VAL THR GLY ILE THR CYS ASN ARG CYS ALA SEQRES 33 A 437 LYS GLY TYR GLN GLN SER ARG SER PRO ILE ALA PRO CYS SEQRES 34 A 437 ILE LYS ILE PRO VAL ALA LEU GLU MODRES 4OVE ASN A 116 ASN GLYCOSYLATION SITE MODRES 4OVE ASN A 131 ASN GLYCOSYLATION SITE MODRES 4OVE ASN A 95 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET BMA B 3 11 HET MAN B 4 11 HET MAN B 5 11 HET NAG C 1 42 HET NAG C 2 42 HET NAG A 508 14 HET CA A 509 1 HET CL A 510 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM CA CALCIUM ION HETNAM CL CHLORIDE ION FORMUL 2 NAG 5(C8 H15 N O6) FORMUL 2 BMA C6 H12 O6 FORMUL 2 MAN 2(C6 H12 O6) FORMUL 5 CA CA 2+ FORMUL 6 CL CL 1- FORMUL 7 HOH *97(H2 O) HELIX 1 1 PRO A 104 THR A 109 5 6 HELIX 2 2 GLN A 180 ASN A 186 1 7 HELIX 3 3 THR A 194 GLU A 198 5 5 HELIX 4 4 ASP A 205 ASP A 209 5 5 HELIX 5 5 ARG A 226 ASN A 234 5 9 HELIX 6 6 SER A 235 VAL A 242 1 8 HELIX 7 7 ASN A 353 SER A 360 1 8 SHEET 1 A 2 VAL A 56 ASN A 57 0 SHEET 2 A 2 ALA A 275 CYS A 285 -1 O GLY A 283 N VAL A 56 SHEET 1 B 7 TRP A 120 GLN A 121 0 SHEET 2 B 7 ALA A 275 CYS A 285 -1 O VAL A 276 N TRP A 120 SHEET 3 B 7 VAL A 132 PHE A 151 -1 N GLU A 143 O ARG A 284 SHEET 4 B 7 THR A 243 ARG A 253 -1 O ILE A 247 N LEU A 136 SHEET 5 B 7 SER A 158 SER A 164 -1 N TYR A 162 O ARG A 248 SHEET 6 B 7 VAL A 172 TYR A 177 -1 O PHE A 174 N ILE A 161 SHEET 7 B 7 CYS A 203 THR A 204 1 O THR A 204 N PHE A 176 SHEET 1 C 3 ARG A 65 VAL A 66 0 SHEET 2 C 3 VAL A 132 PHE A 151 -1 O THR A 135 N ARG A 65 SHEET 3 C 3 LEU A 217 SER A 221 -1 O PHE A 220 N VAL A 147 SHEET 1 D 2 ALA A 75 SER A 81 0 SHEET 2 D 2 LEU A 88 CYS A 94 -1 O HIS A 92 N TYR A 77 SHEET 1 E 2 CYS A 294 ARG A 296 0 SHEET 2 E 2 LEU A 302 CYS A 304 -1 O VAL A 303 N VAL A 295 SHEET 1 F 2 THR A 310 ALA A 311 0 SHEET 2 F 2 ARG A 317 CYS A 318 -1 O ARG A 317 N ALA A 311 SHEET 1 G 2 ARG A 349 PHE A 352 0 SHEET 2 G 2 GLY A 366 LEU A 369 -1 O VAL A 367 N ARG A 351 SHEET 1 H 2 THR A 375 ALA A 376 0 SHEET 2 H 2 TYR A 382 CYS A 383 -1 O TYR A 382 N ALA A 376 SHEET 1 I 2 PHE A 387 ARG A 389 0 SHEET 2 I 2 CYS A 401 ALA A 403 -1 O LYS A 402 N TYR A 388 SHEET 1 J 2 VAL A 429 THR A 430 0 SHEET 2 J 2 ARG A 436 CYS A 437 -1 O ARG A 436 N THR A 430 SHEET 1 K 2 TYR A 441 GLN A 443 0 SHEET 2 K 2 CYS A 451 LYS A 453 -1 O ILE A 452 N GLN A 442 SSBOND 1 CYS A 41 CYS A 51 1555 1555 2.05 SSBOND 2 CYS A 70 CYS A 94 1555 1555 2.07 SSBOND 3 CYS A 78 CYS A 91 1555 1555 2.06 SSBOND 4 CYS A 119 CYS A 152 1555 1555 2.08 SSBOND 5 CYS A 181 CYS A 203 1555 1555 2.08 SSBOND 6 CYS A 285 CYS A 294 1555 1555 2.09 SSBOND 7 CYS A 287 CYS A 304 1555 1555 2.06 SSBOND 8 CYS A 306 CYS A 315 1555 1555 2.06 SSBOND 9 CYS A 318 CYS A 338 1555 1555 2.08 SSBOND 10 CYS A 341 CYS A 350 1555 1555 1.97 SSBOND 11 CYS A 343 CYS A 368 1555 1555 2.02 SSBOND 12 CYS A 371 CYS A 380 1555 1555 2.05 SSBOND 13 CYS A 383 CYS A 401 1555 1555 2.06 SSBOND 14 CYS A 404 CYS A 416 1555 1555 2.08 SSBOND 15 CYS A 406 CYS A 423 1555 1555 2.07 SSBOND 16 CYS A 425 CYS A 434 1555 1555 2.06 SSBOND 17 CYS A 437 CYS A 451 1555 1555 2.03 LINK ND2 ASN A 95 C1 NAG B 1 1555 1555 1.46 LINK ND2 ASN A 116 C1 NAG A 508 1555 1555 1.44 LINK ND2AASN A 131 C1 ANAG C 1 1555 1555 1.46 LINK ND2CASN A 131 C1 CNAG C 1 1555 1555 1.46 LINK ND2BASN A 131 C1 BNAG C 1 1555 1555 1.47 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.45 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.46 LINK O3 BMA B 3 C1 MAN B 4 1555 1555 1.45 LINK O6 BMA B 3 C1 MAN B 5 1555 1555 1.47 LINK O4 CNAG C 1 C1 CNAG C 2 1555 1555 1.44 LINK O4 ANAG C 1 C1 ANAG C 2 1555 1555 1.44 LINK O4 BNAG C 1 C1 BNAG C 2 1555 1555 1.44 LINK O PHE A 107 CA CA A 509 1555 1555 2.44 LINK OD1 ASP A 110 CA CA A 509 1555 1555 2.35 LINK OD1 ASN A 112 CA CA A 509 1555 1555 2.89 LINK OG1 THR A 118 CA CA A 509 1555 1555 2.33 LINK O THR A 118 CA CA A 509 1555 1555 2.54 LINK O SER A 277 CA CA A 509 1555 1555 2.19 LINK CA CA A 509 O HOH A 604 1555 1555 2.22 CISPEP 1 ARG A 72 PRO A 73 0 -0.75 CISPEP 2 PHE A 128 PRO A 129 0 6.44 CRYST1 69.754 69.754 334.802 90.00 90.00 120.00 P 32 2 1 6 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 0.014336 0.008277 0.000000 0.00000 SCALE2 0.000000 0.016554 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002987 0.00000