PDB Short entry for 3TBD HEADER CELL ADHESION 05-AUG-11 3TBD TITLE CRYSTAL STRUCTURE OF DOMAIN VI AND LE1 OF HUMAN NETRIN-G2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NETRIN-G2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DOMAIN VI AND LE1, UNP RESIDUES 18-349; COMPND 5 SYNONYM: LAMINET-2; 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 GENE: NTNG2, KIAA1857, LMNT2, UNQ9381/PRO34206; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK 293 GNTI(-); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: EPISOMAL; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PCEP4 KEYWDS LAMININ N-TERMINAL DOMAIN, DOMAIN VI, LE-DOMAIN, NETRIN-G, NETRIN, KEYWDS 2 NEURONAL CELL ADHESION MOLECULE, NETRIN G LIGAND 2, NGL-2, LRRC4, KEYWDS 3 NERVOUS SYSTEM, NEURONAL SYNAPSES, AXONAL, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR J.BRASCH,Q.LIU,L.SHAPIRO REVDAT 4 21-DEC-22 3TBD 1 SEQADV HETSYN REVDAT 3 29-JUL-20 3TBD 1 COMPND REMARK SEQADV HETNAM REVDAT 3 2 1 LINK SITE ATOM REVDAT 2 11-JAN-12 3TBD 1 JRNL REVDAT 1 02-NOV-11 3TBD 0 JRNL AUTH J.BRASCH,O.J.HARRISON,G.AHLSEN,Q.LIU,L.SHAPIRO JRNL TITL CRYSTAL STRUCTURE OF THE LIGAND BINDING DOMAIN OF NETRIN G2. JRNL REF J.MOL.BIOL. V. 414 723 2011 JRNL REFN ISSN 0022-2836 JRNL PMID 22041449 JRNL DOI 10.1016/J.JMB.2011.10.030 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 38026 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) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2020 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2079 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 74.72 REMARK 3 BIN R VALUE (WORKING SET) : 0.2590 REMARK 3 BIN FREE R VALUE SET COUNT : 141 REMARK 3 BIN FREE R VALUE : 0.3480 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2662 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 69 REMARK 3 SOLVENT ATOMS : 412 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.83000 REMARK 3 B22 (A**2) : 0.83000 REMARK 3 B33 (A**2) : -1.24000 REMARK 3 B12 (A**2) : 0.41000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.124 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.073 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.318 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2950 ; 0.028 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4033 ; 2.272 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 368 ; 7.163 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 147 ;33.289 ;22.857 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 500 ;14.662 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;18.592 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 420 ; 0.184 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2299 ; 0.012 ; 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): 1717 ; 1.578 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2792 ; 2.571 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1233 ; 3.752 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1222 ; 5.774 ; 4.500 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3TBD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1000067271. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.071 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40558 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.8 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.2M CALCIUM ACETATE, REMARK 280 0.1M SODIUM CACODYLATE PH6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293.15K 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 127.09333 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 63.54667 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 63.54667 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 127.09333 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 SER A 332 REMARK 465 HIS A 333 REMARK 465 HIS A 334 REMARK 465 HIS A 335 REMARK 465 HIS A 336 REMARK 465 HIS A 337 REMARK 465 HIS A 338 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 O HOH A 517 O HOH A 714 2.04 REMARK 500 O HOH A 566 O HOH A 678 2.06 REMARK 500 O HOH A 394 O HOH A 685 2.06 REMARK 500 O HOH A 460 O HOH A 650 2.06 REMARK 500 O HOH A 397 O HOH A 685 2.08 REMARK 500 O THR A 11 N GLY A 14 2.09 REMARK 500 O HOH A 533 O HOH A 739 2.10 REMARK 500 OE2 GLU A 181 O HOH A 501 2.12 REMARK 500 NZ LYS A 81 O HOH A 729 2.14 REMARK 500 O HOH A 387 O HOH A 437 2.15 REMARK 500 OH TYR A 316 O HOH A 591 2.15 REMARK 500 O HOH A 354 O HOH A 601 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OG SER A 61 O HOH A 343 4565 1.62 REMARK 500 O HOH A 416 O HOH A 605 4565 1.91 REMARK 500 CG2 THR A 10 NH2 ARG A 238 5565 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 TYR A 126 CD1 TYR A 126 CE1 0.092 REMARK 500 VAL A 249 CB VAL A 249 CG2 0.127 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 GLU A 13 N - CA - C ANGL. DEV. = 22.6 DEGREES REMARK 500 MET A 27 CG - SD - CE ANGL. DEV. = -11.7 DEGREES REMARK 500 HIS A 54 N - CA - CB ANGL. DEV. = 12.5 DEGREES REMARK 500 TYR A 126 C - N - CA ANGL. DEV. = -18.4 DEGREES REMARK 500 ASP A 139 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 195 CG - CD - NE ANGL. DEV. = -15.8 DEGREES REMARK 500 ARG A 195 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 195 NE - CZ - NH2 ANGL. DEV. = -8.1 DEGREES REMARK 500 ARG A 251 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG A 269 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 269 NE - CZ - NH2 ANGL. DEV. = -3.3 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 SER A 53 32.29 -92.15 REMARK 500 GLU A 55 -25.62 -151.27 REMARK 500 PRO A 57 57.19 -100.37 REMARK 500 TYR A 58 -40.88 79.07 REMARK 500 CYS A 60 56.44 75.23 REMARK 500 TRP A 95 42.31 -80.80 REMARK 500 LYS A 112 133.48 -171.78 REMARK 500 SER A 183 -35.29 -134.94 REMARK 500 TRP A 185 -11.42 90.96 REMARK 500 TRP A 185 -7.66 87.35 REMARK 500 ALA A 186 125.41 -39.68 REMARK 500 LYS A 192 -40.59 71.03 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 401 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 77 O REMARK 620 2 ASP A 80 OD1 81.7 REMARK 620 3 GLU A 82 OE2 161.1 116.0 REMARK 620 4 THR A 88 O 84.2 136.7 78.2 REMARK 620 5 THR A 88 OG1 93.6 69.5 87.1 70.8 REMARK 620 6 SER A 262 O 84.8 138.0 85.6 80.5 151.2 REMARK 620 7 HOH A 433 O 102.8 70.7 90.1 152.6 133.9 73.9 REMARK 620 N 1 2 3 4 5 6 DBREF 3TBD A 1 332 UNP Q96CW9 NTNG2_HUMAN 18 349 SEQADV 3TBD ALA A 329 UNP Q96CW9 THR 346 VARIANT SEQADV 3TBD HIS A 333 UNP Q96CW9 EXPRESSION TAG SEQADV 3TBD HIS A 334 UNP Q96CW9 EXPRESSION TAG SEQADV 3TBD HIS A 335 UNP Q96CW9 EXPRESSION TAG SEQADV 3TBD HIS A 336 UNP Q96CW9 EXPRESSION TAG SEQADV 3TBD HIS A 337 UNP Q96CW9 EXPRESSION TAG SEQADV 3TBD HIS A 338 UNP Q96CW9 EXPRESSION TAG SEQRES 1 A 338 ASP TYR ASP ILE CYS LYS SER TRP VAL THR THR ASP GLU SEQRES 2 A 338 GLY PRO THR TRP GLU PHE TYR ALA CYS GLN PRO LYS VAL SEQRES 3 A 338 MET ARG LEU LYS ASP TYR VAL LYS VAL LYS VAL GLU PRO SEQRES 4 A 338 SER GLY ILE THR CYS GLY ASP PRO PRO GLU ARG PHE CYS SEQRES 5 A 338 SER HIS GLU ASN PRO TYR LEU CYS SER ASN GLU CYS ASP SEQRES 6 A 338 ALA SER ASN PRO ASP LEU ALA HIS PRO PRO ARG LEU MET SEQRES 7 A 338 PHE ASP LYS GLU GLU GLU GLY LEU ALA THR TYR TRP GLN SEQRES 8 A 338 SER ILE THR TRP SER ARG TYR PRO SER PRO LEU GLU ALA SEQRES 9 A 338 ASN ILE THR LEU SER TRP ASN LYS THR VAL GLU LEU THR SEQRES 10 A 338 ASP ASP VAL VAL MET THR PHE GLU TYR GLY ARG PRO THR SEQRES 11 A 338 VAL MET VAL LEU GLU LYS SER LEU ASP ASN GLY ARG THR SEQRES 12 A 338 TRP GLN PRO TYR GLN PHE TYR ALA GLU ASP CYS MET GLU SEQRES 13 A 338 ALA PHE GLY MET SER ALA ARG ARG ALA ARG ASP MET SER SEQRES 14 A 338 SER SER SER ALA HIS ARG VAL LEU CYS THR GLU GLU TYR SEQRES 15 A 338 SER ARG TRP ALA GLY SER LYS LYS GLU LYS HIS VAL ARG SEQRES 16 A 338 PHE GLU VAL ARG ASP ARG PHE ALA ILE PHE ALA GLY PRO SEQRES 17 A 338 ASP LEU ARG ASN MET ASP ASN LEU TYR THR ARG LEU GLU SEQRES 18 A 338 SER ALA LYS GLY LEU LYS GLU PHE PHE THR LEU THR ASP SEQRES 19 A 338 LEU ARG MET ARG LEU LEU ARG PRO ALA LEU GLY GLY THR SEQRES 20 A 338 TYR VAL GLN ARG GLU ASN LEU TYR LYS TYR PHE TYR ALA SEQRES 21 A 338 ILE SER ASN ILE GLU VAL ILE GLY ARG CYS LYS CYS ASN SEQRES 22 A 338 LEU HIS ALA ASN LEU CYS SER MET ARG GLU GLY SER LEU SEQRES 23 A 338 GLN CYS GLU CYS GLU HIS ASN THR THR GLY PRO ASP CYS SEQRES 24 A 338 GLY LYS CYS LYS LYS ASN PHE ARG THR ARG SER TRP ARG SEQRES 25 A 338 ALA GLY SER TYR LEU PRO LEU PRO HIS GLY SER PRO ASN SEQRES 26 A 338 ALA CYS ALA ALA ALA GLY SER HIS HIS HIS HIS HIS HIS MODRES 3TBD ASN A 111 ASN GLYCOSYLATION SITE MODRES 3TBD ASN A 105 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET NAG C 1 14 HET NAG C 2 14 HET CA A 401 1 HET PO4 A 339 5 HET PO4 A 340 5 HET CL A 341 1 HET CL A 342 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM CA CALCIUM ION HETNAM PO4 PHOSPHATE ION HETNAM CL CHLORIDE 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 2 NAG 4(C8 H15 N O6) FORMUL 4 CA CA 2+ FORMUL 5 PO4 2(O4 P 3-) FORMUL 7 CL 2(CL 1-) FORMUL 9 HOH *412(H2 O) HELIX 1 1 LYS A 30 VAL A 33 5 4 HELIX 2 2 PRO A 74 PHE A 79 5 6 HELIX 3 3 ASP A 153 GLY A 159 1 7 HELIX 4 4 ARG A 164 MET A 168 5 5 HELIX 5 5 SER A 169 ALA A 173 5 5 HELIX 6 6 VAL A 198 GLY A 207 1 10 HELIX 7 7 ASN A 212 ALA A 223 1 12 HELIX 8 8 GLY A 225 PHE A 230 1 6 HELIX 9 9 ASN A 253 TYR A 257 5 5 SHEET 1 A 2 LYS A 6 THR A 11 0 SHEET 2 A 2 GLY A 14 PHE A 19 -1 O THR A 16 N VAL A 9 SHEET 1 B 4 MET A 27 ARG A 28 0 SHEET 2 B 4 ILE A 267 CYS A 270 -1 O GLY A 268 N MET A 27 SHEET 3 B 4 ALA A 104 LEU A 116 -1 N GLU A 115 O ARG A 269 SHEET 4 B 4 LYS A 34 GLU A 38 -1 N GLU A 38 O ASN A 105 SHEET 1 C 7 MET A 27 ARG A 28 0 SHEET 2 C 7 ILE A 267 CYS A 270 -1 O GLY A 268 N MET A 27 SHEET 3 C 7 ALA A 104 LEU A 116 -1 N GLU A 115 O ARG A 269 SHEET 4 C 7 THR A 231 ARG A 241 -1 O LEU A 235 N LEU A 108 SHEET 5 C 7 VAL A 131 SER A 137 -1 N SER A 137 O THR A 233 SHEET 6 C 7 GLN A 145 ALA A 151 -1 O GLN A 148 N LEU A 134 SHEET 7 C 7 CYS A 178 THR A 179 1 O THR A 179 N PHE A 149 SHEET 1 D 2 GLU A 49 PHE A 51 0 SHEET 2 D 2 ASN A 62 CYS A 64 -1 O CYS A 64 N GLU A 49 SHEET 1 E 4 TRP A 90 GLN A 91 0 SHEET 2 E 4 ALA A 260 GLU A 265 -1 O ILE A 261 N TRP A 90 SHEET 3 E 4 VAL A 120 PHE A 124 -1 N THR A 123 O ASN A 263 SHEET 4 E 4 HIS A 193 PHE A 196 -1 O VAL A 194 N MET A 122 SHEET 1 F 2 CYS A 279 ARG A 282 0 SHEET 2 F 2 SER A 285 CYS A 288 -1 O SER A 285 N ARG A 282 SHEET 1 G 2 THR A 294 THR A 295 0 SHEET 2 G 2 LYS A 301 CYS A 302 -1 O LYS A 301 N THR A 295 SSBOND 1 CYS A 5 CYS A 22 1555 1555 2.04 SSBOND 2 CYS A 44 CYS A 64 1555 1555 2.10 SSBOND 3 CYS A 52 CYS A 60 1555 1555 2.01 SSBOND 4 CYS A 154 CYS A 178 1555 1555 2.06 SSBOND 5 CYS A 270 CYS A 279 1555 1555 2.09 SSBOND 6 CYS A 272 CYS A 288 1555 1555 2.01 SSBOND 7 CYS A 290 CYS A 299 1555 1555 2.05 SSBOND 8 CYS A 302 CYS A 327 1555 1555 2.10 LINK ND2 ASN A 105 C1 NAG B 1 1555 1555 1.47 LINK ND2 ASN A 111 C1 NAG C 1 1555 1555 1.46 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.44 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.44 LINK O LEU A 77 CA CA A 401 1555 1555 2.32 LINK OD1 ASP A 80 CA CA A 401 1555 1555 2.37 LINK OE2 GLU A 82 CA CA A 401 1555 1555 2.31 LINK O THR A 88 CA CA A 401 1555 1555 2.42 LINK OG1 THR A 88 CA CA A 401 1555 1555 2.50 LINK O SER A 262 CA CA A 401 1555 1555 2.39 LINK CA CA A 401 O HOH A 433 1555 1555 2.47 CISPEP 1 ASP A 12 GLU A 13 0 19.29 CISPEP 2 GLU A 38 PRO A 39 0 0.90 CISPEP 3 ASP A 46 PRO A 47 0 5.93 CISPEP 4 GLU A 55 ASN A 56 0 0.09 CISPEP 5 ASN A 56 PRO A 57 0 0.03 CISPEP 6 TYR A 98 PRO A 99 0 14.69 CISPEP 7 LEU A 317 PRO A 318 0 0.19 CISPEP 8 LEU A 319 PRO A 320 0 3.60 CRYST1 63.134 63.134 190.640 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 0.015839 0.009145 0.000000 0.00000 SCALE2 0.000000 0.018290 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005245 0.00000