PDB Short entry for 3ZYG HEADER CELL ADHESION 22-AUG-11 3ZYG TITLE NETRING2 LAM AND EGF1 DOMAINS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NETRIN-G2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: LAM AND EGF1 DOMAINS, RESIDUES 423-767; COMPND 5 SYNONYM: LAMINET-2, NETRING; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK 293 GNTI(-); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PHLSEC KEYWDS CELL ADHESION, SYNAPSE 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 5 20-DEC-23 3ZYG 1 HETSYN REVDAT 4 29-JUL-20 3ZYG 1 COMPND REMARK HETNAM SSBOND REVDAT 4 2 1 LINK SITE REVDAT 3 16-NOV-11 3ZYG 1 JRNL REVDAT 2 26-OCT-11 3ZYG 1 JRNL REVDAT 1 05-OCT-11 3ZYG 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. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0077 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 40042 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) : 0.251 REMARK 3 R VALUE (WORKING SET) : 0.248 REMARK 3 FREE R VALUE : 0.297 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2125 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2801 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.3050 REMARK 3 BIN FREE R VALUE SET COUNT : 153 REMARK 3 BIN FREE R VALUE : 0.3700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5117 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 208 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.64000 REMARK 3 B22 (A**2) : -0.55000 REMARK 3 B33 (A**2) : 2.24000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.10000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.301 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.245 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.181 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.952 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.932 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.893 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5330 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7237 ; 1.862 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 634 ; 3.581 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 254 ;34.555 ;22.756 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 859 ;15.178 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 48 ;18.274 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 756 ; 0.135 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4122 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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 : 2 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 19 A 345 REMARK 3 ORIGIN FOR THE GROUP (A): -13.7241 -19.1720 10.5690 REMARK 3 T TENSOR REMARK 3 T11: 0.0186 T22: 0.0094 REMARK 3 T33: 0.0247 T12: -0.0017 REMARK 3 T13: -0.0045 T23: 0.0040 REMARK 3 L TENSOR REMARK 3 L11: 0.4976 L22: 0.2593 REMARK 3 L33: 0.2947 L12: 0.2146 REMARK 3 L13: 0.1539 L23: 0.2388 REMARK 3 S TENSOR REMARK 3 S11: 0.0094 S12: -0.0417 S13: -0.0001 REMARK 3 S21: 0.0017 S22: -0.0118 S23: 0.0291 REMARK 3 S31: 0.0067 S32: 0.0026 S33: 0.0024 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 : B 19 B 345 REMARK 3 ORIGIN FOR THE GROUP (A): 0.5251 5.1947 48.1741 REMARK 3 T TENSOR REMARK 3 T11: 0.0127 T22: 0.0066 REMARK 3 T33: 0.0281 T12: 0.0035 REMARK 3 T13: -0.0040 T23: -0.0077 REMARK 3 L TENSOR REMARK 3 L11: 0.4077 L22: 0.3247 REMARK 3 L33: 0.2536 L12: -0.2443 REMARK 3 L13: 0.1323 L23: -0.2231 REMARK 3 S TENSOR REMARK 3 S11: 0.0175 S12: 0.0399 S13: -0.0206 REMARK 3 S21: -0.0021 S22: -0.0257 S23: -0.0017 REMARK 3 S31: -0.0019 S32: 0.0062 S33: 0.0083 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 USED IF PRESENT REMARK 3 PRESENT IN THE INPUT. REMARK 4 REMARK 4 3ZYG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1290049426. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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) : 1.0, 0.979400 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42208 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 29.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.32000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.84000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.350 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 1TVG REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% MME550, 0.1M NACL, 0.1M BICINE PH9 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 55.75000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.44000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 55.75000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 32.44000 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 MET A 1 REMARK 465 LEU A 2 REMARK 465 HIS A 3 REMARK 465 LEU A 4 REMARK 465 LEU A 5 REMARK 465 ALA A 6 REMARK 465 LEU A 7 REMARK 465 PHE A 8 REMARK 465 LEU A 9 REMARK 465 HIS A 10 REMARK 465 CYS A 11 REMARK 465 LEU A 12 REMARK 465 PRO A 13 REMARK 465 LEU A 14 REMARK 465 ALA A 15 REMARK 465 SER A 16 REMARK 465 GLY A 17 REMARK 465 ASP A 18 REMARK 465 ALA A 203 REMARK 465 GLY A 204 REMARK 465 SER A 205 REMARK 465 LYS A 206 REMARK 465 LYS A 207 REMARK 465 GLY A 346 REMARK 465 THR A 347 REMARK 465 HIS A 348 REMARK 465 HIS A 349 REMARK 465 HIS A 350 REMARK 465 HIS A 351 REMARK 465 HIS A 352 REMARK 465 HIS A 353 REMARK 465 MET B 1 REMARK 465 LEU B 2 REMARK 465 HIS B 3 REMARK 465 LEU B 4 REMARK 465 LEU B 5 REMARK 465 ALA B 6 REMARK 465 LEU B 7 REMARK 465 PHE B 8 REMARK 465 LEU B 9 REMARK 465 HIS B 10 REMARK 465 CYS B 11 REMARK 465 LEU B 12 REMARK 465 PRO B 13 REMARK 465 LEU B 14 REMARK 465 ALA B 15 REMARK 465 SER B 16 REMARK 465 GLY B 17 REMARK 465 ASP B 18 REMARK 465 VAL B 26 REMARK 465 THR B 27 REMARK 465 THR B 28 REMARK 465 ASP B 29 REMARK 465 GLU B 30 REMARK 465 ALA B 203 REMARK 465 GLY B 204 REMARK 465 SER B 205 REMARK 465 LYS B 206 REMARK 465 LYS B 207 REMARK 465 GLY B 346 REMARK 465 THR B 347 REMARK 465 HIS B 348 REMARK 465 HIS B 349 REMARK 465 HIS B 350 REMARK 465 HIS B 351 REMARK 465 HIS B 352 REMARK 465 HIS B 353 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP A 29 CG OD1 OD2 REMARK 470 GLU A 30 CG CD OE1 OE2 REMARK 470 GLU A 72 CG CD OE1 OE2 REMARK 470 GLU A 208 CG CD OE1 OE2 REMARK 470 ARG A 228 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 241 CG CD CE NZ REMARK 470 GLU A 245 CG CD OE1 OE2 REMARK 470 LYS A 321 CG CD CE NZ REMARK 470 GLU B 35 CG CD OE1 OE2 REMARK 470 ARG B 192 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 208 CG CD OE1 OE2 REMARK 470 LYS B 241 CG CD CE NZ REMARK 470 GLU B 245 CG CD OE1 OE2 REMARK 470 LYS B 321 CG CD CE NZ 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 THR A 28 -169.43 -104.34 REMARK 500 ASN A 73 75.25 -119.38 REMARK 500 CYS A 77 51.45 39.45 REMARK 500 TRP A 112 40.45 -83.17 REMARK 500 GLU A 214 99.75 -69.19 REMARK 500 ASN A 229 59.24 -100.51 REMARK 500 ASN B 73 74.58 -119.82 REMARK 500 TYR B 75 -54.91 -124.39 REMARK 500 CYS B 77 48.90 37.79 REMARK 500 TRP B 112 43.48 -84.22 REMARK 500 TYR B 143 53.46 -117.95 REMARK 500 GLU B 214 99.68 -67.65 REMARK 500 ASN B 229 61.11 -101.73 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 403 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 94 O REMARK 620 2 ASP A 97 OD1 76.0 REMARK 620 3 GLU A 99 OE2 165.5 117.1 REMARK 620 4 THR A 105 O 86.0 133.0 80.3 REMARK 620 5 THR A 105 OG1 92.7 69.7 86.6 68.2 REMARK 620 6 SER A 279 O 82.8 134.2 91.1 84.3 152.3 REMARK 620 7 HOH A 538 O 106.3 66.7 85.7 159.8 125.6 81.6 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 403 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU B 94 O REMARK 620 2 ASP B 97 OD1 78.3 REMARK 620 3 GLU B 99 OE2 167.6 113.4 REMARK 620 4 THR B 105 O 87.9 133.3 81.0 REMARK 620 5 THR B 105 OG1 99.4 69.8 81.7 68.9 REMARK 620 6 SER B 279 O 82.7 138.0 90.3 82.4 151.0 REMARK 620 7 HOH B 529 O 100.6 67.6 88.2 159.0 127.4 79.8 REMARK 620 N 1 2 3 4 5 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZYJ RELATED DB: PDB REMARK 900 NETRING1 IN COMPLEX WITH NGL1 REMARK 900 RELATED ID: 3ZYI RELATED DB: PDB REMARK 900 NETRING2 IN COMPLEX WITH NGL2 REMARK 999 REMARK 999 SEQUENCE REMARK 999 N-TERMINAL SECRETION SIGNAL IS CLEAVED DURING PROTEIN REMARK 999 PRODUCTION. C-TERMINUS CONTAINS 6X HISTIDINE TAG. DBREF 3ZYG A 1 345 UNP Q96CW9 NTNG2_HUMAN 423 767 DBREF 3ZYG B 1 345 UNP Q96CW9 NTNG2_HUMAN 423 767 SEQADV 3ZYG GLY A 346 UNP Q96CW9 EXPRESSION TAG SEQADV 3ZYG THR A 347 UNP Q96CW9 EXPRESSION TAG SEQADV 3ZYG HIS A 348 UNP Q96CW9 EXPRESSION TAG SEQADV 3ZYG HIS A 349 UNP Q96CW9 EXPRESSION TAG SEQADV 3ZYG HIS A 350 UNP Q96CW9 EXPRESSION TAG SEQADV 3ZYG HIS A 351 UNP Q96CW9 EXPRESSION TAG SEQADV 3ZYG HIS A 352 UNP Q96CW9 EXPRESSION TAG SEQADV 3ZYG HIS A 353 UNP Q96CW9 EXPRESSION TAG SEQADV 3ZYG GLY B 346 UNP Q96CW9 EXPRESSION TAG SEQADV 3ZYG THR B 347 UNP Q96CW9 EXPRESSION TAG SEQADV 3ZYG HIS B 348 UNP Q96CW9 EXPRESSION TAG SEQADV 3ZYG HIS B 349 UNP Q96CW9 EXPRESSION TAG SEQADV 3ZYG HIS B 350 UNP Q96CW9 EXPRESSION TAG SEQADV 3ZYG HIS B 351 UNP Q96CW9 EXPRESSION TAG SEQADV 3ZYG HIS B 352 UNP Q96CW9 EXPRESSION TAG SEQADV 3ZYG HIS B 353 UNP Q96CW9 EXPRESSION TAG SEQRES 1 A 353 MET LEU HIS LEU LEU ALA LEU PHE LEU HIS CYS LEU PRO SEQRES 2 A 353 LEU ALA SER GLY ASP TYR ASP ILE CYS LYS SER TRP VAL SEQRES 3 A 353 THR THR ASP GLU GLY PRO THR TRP GLU PHE TYR ALA CYS SEQRES 4 A 353 GLN PRO LYS VAL MET ARG LEU LYS ASP TYR VAL LYS VAL SEQRES 5 A 353 LYS VAL GLU PRO SER GLY ILE THR CYS GLY ASP PRO PRO SEQRES 6 A 353 GLU ARG PHE CYS SER HIS GLU ASN PRO TYR LEU CYS SER SEQRES 7 A 353 ASN GLU CYS ASP ALA SER ASN PRO ASP LEU ALA HIS PRO SEQRES 8 A 353 PRO ARG LEU MET PHE ASP LYS GLU GLU GLU GLY LEU ALA SEQRES 9 A 353 THR TYR TRP GLN SER ILE THR TRP SER ARG TYR PRO SER SEQRES 10 A 353 PRO LEU GLU ALA ASN ILE THR LEU SER TRP ASN LYS THR SEQRES 11 A 353 VAL GLU LEU THR ASP ASP VAL VAL MET THR PHE GLU TYR SEQRES 12 A 353 GLY ARG PRO THR VAL MET VAL LEU GLU LYS SER LEU ASP SEQRES 13 A 353 ASN GLY ARG THR TRP GLN PRO TYR GLN PHE TYR ALA GLU SEQRES 14 A 353 ASP CYS MET GLU ALA PHE GLY MET SER ALA ARG ARG ALA SEQRES 15 A 353 ARG ASP MET SER SER SER SER ALA HIS ARG VAL LEU CYS SEQRES 16 A 353 THR GLU GLU TYR SER ARG TRP ALA GLY SER LYS LYS GLU SEQRES 17 A 353 LYS HIS VAL ARG PHE GLU VAL ARG ASP ARG PHE ALA ILE SEQRES 18 A 353 PHE ALA GLY PRO ASP LEU ARG ASN MET ASP ASN LEU TYR SEQRES 19 A 353 THR ARG LEU GLU SER ALA LYS GLY LEU LYS GLU PHE PHE SEQRES 20 A 353 THR LEU THR ASP LEU ARG MET ARG LEU LEU ARG PRO ALA SEQRES 21 A 353 LEU GLY GLY THR TYR VAL GLN ARG GLU ASN LEU TYR LYS SEQRES 22 A 353 TYR PHE TYR ALA ILE SER ASN ILE GLU VAL ILE GLY ARG SEQRES 23 A 353 CYS LYS CYS ASN LEU HIS ALA ASN LEU CYS SER MET ARG SEQRES 24 A 353 GLU GLY SER LEU GLN CYS GLU CYS GLU HIS ASN THR THR SEQRES 25 A 353 GLY PRO ASP CYS GLY LYS CYS LYS LYS ASN PHE ARG THR SEQRES 26 A 353 ARG SER TRP ARG ALA GLY SER TYR LEU PRO LEU PRO HIS SEQRES 27 A 353 GLY SER PRO ASN ALA CYS ALA GLY THR HIS HIS HIS HIS SEQRES 28 A 353 HIS HIS SEQRES 1 B 353 MET LEU HIS LEU LEU ALA LEU PHE LEU HIS CYS LEU PRO SEQRES 2 B 353 LEU ALA SER GLY ASP TYR ASP ILE CYS LYS SER TRP VAL SEQRES 3 B 353 THR THR ASP GLU GLY PRO THR TRP GLU PHE TYR ALA CYS SEQRES 4 B 353 GLN PRO LYS VAL MET ARG LEU LYS ASP TYR VAL LYS VAL SEQRES 5 B 353 LYS VAL GLU PRO SER GLY ILE THR CYS GLY ASP PRO PRO SEQRES 6 B 353 GLU ARG PHE CYS SER HIS GLU ASN PRO TYR LEU CYS SER SEQRES 7 B 353 ASN GLU CYS ASP ALA SER ASN PRO ASP LEU ALA HIS PRO SEQRES 8 B 353 PRO ARG LEU MET PHE ASP LYS GLU GLU GLU GLY LEU ALA SEQRES 9 B 353 THR TYR TRP GLN SER ILE THR TRP SER ARG TYR PRO SER SEQRES 10 B 353 PRO LEU GLU ALA ASN ILE THR LEU SER TRP ASN LYS THR SEQRES 11 B 353 VAL GLU LEU THR ASP ASP VAL VAL MET THR PHE GLU TYR SEQRES 12 B 353 GLY ARG PRO THR VAL MET VAL LEU GLU LYS SER LEU ASP SEQRES 13 B 353 ASN GLY ARG THR TRP GLN PRO TYR GLN PHE TYR ALA GLU SEQRES 14 B 353 ASP CYS MET GLU ALA PHE GLY MET SER ALA ARG ARG ALA SEQRES 15 B 353 ARG ASP MET SER SER SER SER ALA HIS ARG VAL LEU CYS SEQRES 16 B 353 THR GLU GLU TYR SER ARG TRP ALA GLY SER LYS LYS GLU SEQRES 17 B 353 LYS HIS VAL ARG PHE GLU VAL ARG ASP ARG PHE ALA ILE SEQRES 18 B 353 PHE ALA GLY PRO ASP LEU ARG ASN MET ASP ASN LEU TYR SEQRES 19 B 353 THR ARG LEU GLU SER ALA LYS GLY LEU LYS GLU PHE PHE SEQRES 20 B 353 THR LEU THR ASP LEU ARG MET ARG LEU LEU ARG PRO ALA SEQRES 21 B 353 LEU GLY GLY THR TYR VAL GLN ARG GLU ASN LEU TYR LYS SEQRES 22 B 353 TYR PHE TYR ALA ILE SER ASN ILE GLU VAL ILE GLY ARG SEQRES 23 B 353 CYS LYS CYS ASN LEU HIS ALA ASN LEU CYS SER MET ARG SEQRES 24 B 353 GLU GLY SER LEU GLN CYS GLU CYS GLU HIS ASN THR THR SEQRES 25 B 353 GLY PRO ASP CYS GLY LYS CYS LYS LYS ASN PHE ARG THR SEQRES 26 B 353 ARG SER TRP ARG ALA GLY SER TYR LEU PRO LEU PRO HIS SEQRES 27 B 353 GLY SER PRO ASN ALA CYS ALA GLY THR HIS HIS HIS HIS SEQRES 28 B 353 HIS HIS MODRES 3ZYG ASN A 122 ASN GLYCOSYLATION SITE MODRES 3ZYG ASN A 128 ASN GLYCOSYLATION SITE MODRES 3ZYG ASN B 122 ASN GLYCOSYLATION SITE MODRES 3ZYG ASN B 128 ASN GLYCOSYLATION SITE HET NAG A 401 14 HET NAG A 402 14 HET CA A 403 1 HET NAG B 401 14 HET NAG B 402 14 HET CA B 403 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM CA CALCIUM ION 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 4(C8 H15 N O6) FORMUL 5 CA 2(CA 2+) FORMUL 9 HOH *208(H2 O) HELIX 1 AA1 LYS A 47 VAL A 50 5 4 HELIX 2 AA2 ASN A 85 ALA A 89 5 5 HELIX 3 AA3 PRO A 91 PHE A 96 5 6 HELIX 4 AA4 ASP A 170 GLY A 176 1 7 HELIX 5 AA5 ARG A 181 MET A 185 5 5 HELIX 6 AA6 VAL A 215 GLY A 224 1 10 HELIX 7 AA7 ASN A 229 ALA A 240 1 12 HELIX 8 AA8 GLY A 242 PHE A 247 1 6 HELIX 9 AA9 ASN A 270 TYR A 274 5 5 HELIX 10 AB1 LYS B 47 VAL B 50 5 4 HELIX 11 AB2 PRO B 91 PHE B 96 5 6 HELIX 12 AB3 ASP B 170 GLY B 176 1 7 HELIX 13 AB4 ARG B 181 MET B 185 5 5 HELIX 14 AB5 VAL B 215 GLY B 224 1 10 HELIX 15 AB6 ASN B 229 ALA B 240 1 12 HELIX 16 AB7 GLY B 242 PHE B 247 1 6 HELIX 17 AB8 ASN B 270 TYR B 274 5 5 SHEET 1 AA1 2 LYS A 23 THR A 27 0 SHEET 2 AA1 2 PRO A 32 PHE A 36 -1 O THR A 33 N VAL A 26 SHEET 1 AA2 4 MET A 44 ARG A 45 0 SHEET 2 AA2 4 ILE A 284 CYS A 287 -1 O GLY A 285 N MET A 44 SHEET 3 AA2 4 ALA A 121 LEU A 133 -1 N GLU A 132 O ARG A 286 SHEET 4 AA2 4 LYS A 51 GLU A 55 -1 N GLU A 55 O ASN A 122 SHEET 1 AA3 7 MET A 44 ARG A 45 0 SHEET 2 AA3 7 ILE A 284 CYS A 287 -1 O GLY A 285 N MET A 44 SHEET 3 AA3 7 ALA A 121 LEU A 133 -1 N GLU A 132 O ARG A 286 SHEET 4 AA3 7 THR A 248 ARG A 258 -1 O LEU A 256 N ALA A 121 SHEET 5 AA3 7 VAL A 148 SER A 154 -1 N VAL A 150 O ARG A 255 SHEET 6 AA3 7 GLN A 162 ALA A 168 -1 O GLN A 165 N LEU A 151 SHEET 7 AA3 7 CYS A 195 THR A 196 1 O THR A 196 N PHE A 166 SHEET 1 AA4 2 GLU A 66 PHE A 68 0 SHEET 2 AA4 2 ASN A 79 CYS A 81 -1 O CYS A 81 N GLU A 66 SHEET 1 AA5 4 TRP A 107 GLN A 108 0 SHEET 2 AA5 4 ALA A 277 GLU A 282 -1 O ILE A 278 N TRP A 107 SHEET 3 AA5 4 VAL A 137 PHE A 141 -1 N THR A 140 O ASN A 280 SHEET 4 AA5 4 HIS A 210 PHE A 213 -1 O VAL A 211 N MET A 139 SHEET 1 AA6 2 CYS A 296 ARG A 299 0 SHEET 2 AA6 2 SER A 302 CYS A 305 -1 O SER A 302 N ARG A 299 SHEET 1 AA7 2 THR A 311 THR A 312 0 SHEET 2 AA7 2 LYS A 318 CYS A 319 -1 O LYS A 318 N THR A 312 SHEET 1 AA8 2 LYS B 23 SER B 24 0 SHEET 2 AA8 2 GLU B 35 PHE B 36 -1 O GLU B 35 N SER B 24 SHEET 1 AA9 4 MET B 44 ARG B 45 0 SHEET 2 AA9 4 ILE B 284 CYS B 287 -1 O GLY B 285 N MET B 44 SHEET 3 AA9 4 ALA B 121 LEU B 133 -1 N GLU B 132 O ARG B 286 SHEET 4 AA9 4 LYS B 51 GLU B 55 -1 N GLU B 55 O ASN B 122 SHEET 1 AB1 7 MET B 44 ARG B 45 0 SHEET 2 AB1 7 ILE B 284 CYS B 287 -1 O GLY B 285 N MET B 44 SHEET 3 AB1 7 ALA B 121 LEU B 133 -1 N GLU B 132 O ARG B 286 SHEET 4 AB1 7 THR B 248 ARG B 258 -1 O LEU B 252 N LEU B 125 SHEET 5 AB1 7 VAL B 148 SER B 154 -1 N VAL B 150 O ARG B 255 SHEET 6 AB1 7 GLN B 162 ALA B 168 -1 O GLN B 165 N LEU B 151 SHEET 7 AB1 7 CYS B 195 THR B 196 1 O THR B 196 N PHE B 166 SHEET 1 AB2 2 GLU B 66 PHE B 68 0 SHEET 2 AB2 2 ASN B 79 CYS B 81 -1 O CYS B 81 N GLU B 66 SHEET 1 AB3 4 TRP B 107 GLN B 108 0 SHEET 2 AB3 4 ALA B 277 GLU B 282 -1 O ILE B 278 N TRP B 107 SHEET 3 AB3 4 VAL B 137 PHE B 141 -1 N THR B 140 O ASN B 280 SHEET 4 AB3 4 HIS B 210 PHE B 213 -1 O VAL B 211 N MET B 139 SHEET 1 AB4 2 CYS B 296 ARG B 299 0 SHEET 2 AB4 2 SER B 302 CYS B 305 -1 O SER B 302 N ARG B 299 SHEET 1 AB5 2 THR B 311 THR B 312 0 SHEET 2 AB5 2 LYS B 318 CYS B 319 -1 O LYS B 318 N THR B 312 SSBOND 1 CYS A 22 CYS A 39 1555 1555 2.04 SSBOND 2 CYS A 61 CYS A 81 1555 1555 2.04 SSBOND 3 CYS A 69 CYS A 77 1555 1555 2.04 SSBOND 4 CYS A 171 CYS A 195 1555 1555 2.04 SSBOND 5 CYS A 287 CYS A 296 1555 1555 2.05 SSBOND 6 CYS A 289 CYS A 305 1555 1555 2.01 SSBOND 7 CYS A 307 CYS A 316 1555 1555 2.05 SSBOND 8 CYS A 319 CYS A 344 1555 1555 2.05 SSBOND 9 CYS B 22 CYS B 39 1555 1555 2.05 SSBOND 10 CYS B 61 CYS B 81 1555 1555 2.04 SSBOND 11 CYS B 69 CYS B 77 1555 1555 2.04 SSBOND 12 CYS B 171 CYS B 195 1555 1555 2.05 SSBOND 13 CYS B 287 CYS B 296 1555 1555 2.05 SSBOND 14 CYS B 289 CYS B 305 1555 1555 2.02 SSBOND 15 CYS B 307 CYS B 316 1555 1555 2.06 SSBOND 16 CYS B 319 CYS B 344 1555 1555 2.05 LINK ND2 ASN A 122 C1 NAG A 402 1555 1555 1.49 LINK ND2 ASN A 128 C1 NAG A 401 1555 1555 1.44 LINK ND2 ASN B 122 C1 NAG B 402 1555 1555 1.48 LINK ND2 ASN B 128 C1 NAG B 401 1555 1555 1.45 LINK O LEU A 94 CA CA A 403 1555 1555 2.18 LINK OD1 ASP A 97 CA CA A 403 1555 1555 2.42 LINK OE2 GLU A 99 CA CA A 403 1555 1555 2.35 LINK O THR A 105 CA CA A 403 1555 1555 2.43 LINK OG1 THR A 105 CA CA A 403 1555 1555 2.65 LINK O SER A 279 CA CA A 403 1555 1555 2.29 LINK CA CA A 403 O HOH A 538 1555 1555 2.54 LINK O LEU B 94 CA CA B 403 1555 1555 2.16 LINK OD1 ASP B 97 CA CA B 403 1555 1555 2.38 LINK OE2 GLU B 99 CA CA B 403 1555 1555 2.35 LINK O THR B 105 CA CA B 403 1555 1555 2.37 LINK OG1 THR B 105 CA CA B 403 1555 1555 2.87 LINK O SER B 279 CA CA B 403 1555 1555 2.29 LINK CA CA B 403 O HOH B 529 1555 1555 2.49 CISPEP 1 GLU A 55 PRO A 56 0 -0.04 CISPEP 2 ASP A 63 PRO A 64 0 3.98 CISPEP 3 TYR A 115 PRO A 116 0 7.96 CISPEP 4 LEU A 334 PRO A 335 0 0.56 CISPEP 5 LEU A 336 PRO A 337 0 7.91 CISPEP 6 GLU B 55 PRO B 56 0 -1.40 CISPEP 7 ASP B 63 PRO B 64 0 5.66 CISPEP 8 TYR B 115 PRO B 116 0 3.75 CISPEP 9 LEU B 334 PRO B 335 0 2.64 CISPEP 10 LEU B 336 PRO B 337 0 5.97 CRYST1 111.500 64.880 120.080 90.00 103.06 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 0.008969 0.000000 0.002080 0.00000 SCALE2 0.000000 0.015413 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008549 0.00000