HEADER CELL ADHESION 30-JUN-16 5LF5 TITLE MYELIN-ASSOCIATED GLYCOPROTEIN (MAG) DEGLYCOSYLATED FULL EXTRACELLULAR TITLE 2 DOMAIN WITH CO-PURIFIED LIGAND CAVEAT 5LF5 NAG B 1 HAS WRONG CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYELIN-ASSOCIATED GLYCOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SIGLEC-4A; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: THE TWO C-TERMINAL RESIDUES OF THE CONSTRUCT AND THE COMPND 7 CLONING SITES AND PURIFICATION TAG ARE NOT OBSERVED IN THE ELECTRON COMPND 8 DENSITY, PROBABLY BECAUSE OF DISORDER SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: MAG; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: GNTI-/- AND EBNA1-EXPRESSING; SOURCE 10 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 11 EXPRESSION_SYSTEM_ORGAN: KIDNEY; SOURCE 12 EXPRESSION_SYSTEM_CELL: HEK293ES; SOURCE 13 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 14 EXPRESSION_SYSTEM_VECTOR: PUPE; SOURCE 15 EXPRESSION_SYSTEM_PLASMID: PUPE107.03 KEYWDS MYELIN, CELL ADHESION, SIGNALING EXPDTA X-RAY DIFFRACTION AUTHOR M.F.PRONKER,B.J.C.JANSSEN REVDAT 4 10-JAN-24 5LF5 1 HETSYN LINK REVDAT 3 29-JUL-20 5LF5 1 CAVEAT COMPND REMARK HETNAM REVDAT 3 2 1 LINK SITE ATOM REVDAT 2 13-SEP-17 5LF5 1 REMARK REVDAT 1 14-DEC-16 5LF5 0 JRNL AUTH M.F.PRONKER,S.LEMSTRA,J.SNIJDER,A.J.HECK,D.M.THIES-WEESIE, JRNL AUTH 2 R.J.PASTERKAMP,B.J.JANSSEN JRNL TITL STRUCTURAL BASIS OF MYELIN-ASSOCIATED GLYCOPROTEIN ADHESION JRNL TITL 2 AND SIGNALLING. JRNL REF NAT COMMUN V. 7 13584 2016 JRNL REFN ESSN 2041-1723 JRNL PMID 27922006 JRNL DOI 10.1038/NCOMMS13584 REMARK 2 REMARK 2 RESOLUTION. 3.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 27582 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1407 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 52.7061 - 8.1779 1.00 2708 140 0.1726 0.2024 REMARK 3 2 8.1779 - 6.4948 1.00 2643 139 0.1874 0.2089 REMARK 3 3 6.4948 - 5.6749 1.00 2612 126 0.1920 0.2576 REMARK 3 4 5.6749 - 5.1565 1.00 2628 152 0.1641 0.1996 REMARK 3 5 5.1565 - 4.7872 1.00 2587 148 0.1679 0.1856 REMARK 3 6 4.7872 - 4.5051 1.00 2597 153 0.1713 0.2068 REMARK 3 7 4.5051 - 4.2796 1.00 2632 134 0.1913 0.2099 REMARK 3 8 4.2796 - 4.0934 1.00 2581 135 0.2288 0.2675 REMARK 3 9 4.0934 - 3.9359 1.00 2599 144 0.2888 0.3051 REMARK 3 10 3.9359 - 3.8001 0.99 2588 136 0.4250 0.4192 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.510 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.300 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 3998 REMARK 3 ANGLE : 1.397 5474 REMARK 3 CHIRALITY : 0.192 644 REMARK 3 PLANARITY : 0.013 703 REMARK 3 DIHEDRAL : 14.034 1453 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 20 THROUGH 138 ) REMARK 3 ORIGIN FOR THE GROUP (A): 72.6668 131.7701 16.8174 REMARK 3 T TENSOR REMARK 3 T11: 0.6117 T22: 0.8528 REMARK 3 T33: 1.0315 T12: 0.2995 REMARK 3 T13: -0.0492 T23: 0.0254 REMARK 3 L TENSOR REMARK 3 L11: 3.0707 L22: 5.6240 REMARK 3 L33: 7.6483 L12: 2.8206 REMARK 3 L13: -0.0096 L23: -0.1956 REMARK 3 S TENSOR REMARK 3 S11: 0.1533 S12: 0.3321 S13: -0.2428 REMARK 3 S21: -0.2551 S22: -0.1452 S23: -0.0764 REMARK 3 S31: 0.1020 S32: 0.6495 S33: 0.0387 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 139 THROUGH 238 ) REMARK 3 ORIGIN FOR THE GROUP (A): 46.0950 151.0999 13.5661 REMARK 3 T TENSOR REMARK 3 T11: 1.6188 T22: 1.2655 REMARK 3 T33: 1.7507 T12: 0.6964 REMARK 3 T13: -0.1611 T23: -0.1534 REMARK 3 L TENSOR REMARK 3 L11: 7.0678 L22: 6.6158 REMARK 3 L33: 1.3226 L12: -6.4501 REMARK 3 L13: 1.0739 L23: 0.6232 REMARK 3 S TENSOR REMARK 3 S11: -0.2173 S12: 0.0571 S13: 0.3476 REMARK 3 S21: -0.3686 S22: -0.0933 S23: 0.9175 REMARK 3 S31: -1.0455 S32: -0.9221 S33: 0.2237 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 239 THROUGH 323 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.2755 192.7792 20.7303 REMARK 3 T TENSOR REMARK 3 T11: 2.2549 T22: 1.1201 REMARK 3 T33: 2.2498 T12: 0.7287 REMARK 3 T13: 0.0107 T23: 0.0502 REMARK 3 L TENSOR REMARK 3 L11: 7.7350 L22: 5.1713 REMARK 3 L33: 2.1982 L12: -3.4710 REMARK 3 L13: -4.3071 L23: 7.0568 REMARK 3 S TENSOR REMARK 3 S11: 0.5513 S12: 0.1822 S13: -0.0957 REMARK 3 S21: -0.6329 S22: -0.5511 S23: 0.2605 REMARK 3 S31: -0.4804 S32: 0.0981 S33: 0.0127 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 324 THROUGH 409 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.0655 226.7843 27.6531 REMARK 3 T TENSOR REMARK 3 T11: 1.4787 T22: 0.6951 REMARK 3 T33: 1.2284 T12: 0.2054 REMARK 3 T13: 0.2826 T23: -0.1127 REMARK 3 L TENSOR REMARK 3 L11: 9.0603 L22: 7.7618 REMARK 3 L33: 4.2039 L12: 1.6493 REMARK 3 L13: 2.7429 L23: -3.9637 REMARK 3 S TENSOR REMARK 3 S11: -0.0739 S12: 0.1602 S13: -0.4965 REMARK 3 S21: -1.4082 S22: 0.1647 S23: -0.4576 REMARK 3 S31: 1.2517 S32: 1.1894 S33: -0.0609 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 410 THROUGH 506 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.7747 263.6319 39.6996 REMARK 3 T TENSOR REMARK 3 T11: 1.5225 T22: 0.5910 REMARK 3 T33: 1.3581 T12: 0.0404 REMARK 3 T13: 0.0117 T23: -0.0137 REMARK 3 L TENSOR REMARK 3 L11: 7.3045 L22: 7.3137 REMARK 3 L33: 6.2890 L12: 1.1425 REMARK 3 L13: 0.3953 L23: -2.5672 REMARK 3 S TENSOR REMARK 3 S11: 0.1201 S12: -0.6036 S13: 1.4817 REMARK 3 S21: -0.4675 S22: -0.1667 S23: -0.1823 REMARK 3 S31: -1.8414 S32: 0.0250 S33: -0.0419 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5LF5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1200000630. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-AUG-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99998 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 : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27623 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.800 REMARK 200 RESOLUTION RANGE LOW (A) : 52.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : 0.23300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.70 REMARK 200 R MERGE FOR SHELL (I) : 1.68500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 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: 1URL, 4FRW, 1CS6, 3P3Y, 2YD6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 90.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 12.7 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM NACL, 20 MM TRIS/HCL PH 7.0, REMARK 280 7.7 % PEG 4000 (W/V), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 291K 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 41.68000 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 20.84000 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 20.84000 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 41.68000 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: 9360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 53000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 31.0 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 483.01354 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 83.36000 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 GLY A 18 REMARK 465 SER A 19 REMARK 465 ARG A 449 REMARK 465 ASN A 450 REMARK 465 VAL A 451 REMARK 465 HIS A 507 REMARK 465 ARG A 508 REMARK 465 ALA A 509 REMARK 465 ALA A 510 REMARK 465 ALA A 511 REMARK 465 HIS A 512 REMARK 465 HIS A 513 REMARK 465 HIS A 514 REMARK 465 HIS A 515 REMARK 465 HIS A 516 REMARK 465 HIS A 517 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 O3 GAL C 2 O6 SIA C 3 1.97 REMARK 500 OE1 GLU A 410 OH TYR A 494 2.19 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 PRO A 267 C - N - CA ANGL. DEV. = -9.9 DEGREES REMARK 500 PRO A 269 C - N - CA ANGL. DEV. = -11.3 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 ARG A 43 142.57 -172.33 REMARK 500 VAL A 54 62.60 37.28 REMARK 500 ASN A 62 -62.82 65.96 REMARK 500 TYR A 124 -12.58 70.90 REMARK 500 ASN A 125 58.55 -90.95 REMARK 500 PRO A 162 99.84 -62.27 REMARK 500 GLU A 178 -114.33 50.60 REMARK 500 ASP A 192 -119.88 52.29 REMARK 500 LEU A 280 -120.69 56.58 REMARK 500 PHE A 360 140.50 -172.28 REMARK 500 REMARK 500 REMARK: NULL DBREF 5LF5 A 20 508 UNP P20917 MAG_MOUSE 20 508 SEQADV 5LF5 GLY A 18 UNP P20917 EXPRESSION TAG SEQADV 5LF5 SER A 19 UNP P20917 EXPRESSION TAG SEQADV 5LF5 ALA A 509 UNP P20917 EXPRESSION TAG SEQADV 5LF5 ALA A 510 UNP P20917 EXPRESSION TAG SEQADV 5LF5 ALA A 511 UNP P20917 EXPRESSION TAG SEQADV 5LF5 HIS A 512 UNP P20917 EXPRESSION TAG SEQADV 5LF5 HIS A 513 UNP P20917 EXPRESSION TAG SEQADV 5LF5 HIS A 514 UNP P20917 EXPRESSION TAG SEQADV 5LF5 HIS A 515 UNP P20917 EXPRESSION TAG SEQADV 5LF5 HIS A 516 UNP P20917 EXPRESSION TAG SEQADV 5LF5 HIS A 517 UNP P20917 EXPRESSION TAG SEQRES 1 A 500 GLY SER GLY HIS TRP GLY ALA TRP MET PRO SER THR ILE SEQRES 2 A 500 SER ALA PHE GLU GLY THR CYS VAL SER ILE PRO CYS ARG SEQRES 3 A 500 PHE ASP PHE PRO ASP GLU LEU ARG PRO ALA VAL VAL HIS SEQRES 4 A 500 GLY VAL TRP TYR PHE ASN SER PRO TYR PRO LYS ASN TYR SEQRES 5 A 500 PRO PRO VAL VAL PHE LYS SER ARG THR GLN VAL VAL HIS SEQRES 6 A 500 GLU SER PHE GLN GLY ARG SER ARG LEU LEU GLY ASP LEU SEQRES 7 A 500 GLY LEU ARG ASN CYS THR LEU LEU LEU SER THR LEU SER SEQRES 8 A 500 PRO GLU LEU GLY GLY LYS TYR TYR PHE ARG GLY ASP LEU SEQRES 9 A 500 GLY GLY TYR ASN GLN TYR THR PHE SER GLU HIS SER VAL SEQRES 10 A 500 LEU ASP ILE VAL ASN THR PRO ASN ILE VAL VAL PRO PRO SEQRES 11 A 500 GLU VAL VAL ALA GLY THR GLU VAL GLU VAL SER CYS MET SEQRES 12 A 500 VAL PRO ASP ASN CYS PRO GLU LEU ARG PRO GLU LEU SER SEQRES 13 A 500 TRP LEU GLY HIS GLU GLY LEU GLY GLU PRO THR VAL LEU SEQRES 14 A 500 GLY ARG LEU ARG GLU ASP GLU GLY THR TRP VAL GLN VAL SEQRES 15 A 500 SER LEU LEU HIS PHE VAL PRO THR ARG GLU ALA ASN GLY SEQRES 16 A 500 HIS ARG LEU GLY CYS GLN ALA ALA PHE PRO ASN THR THR SEQRES 17 A 500 LEU GLN PHE GLU GLY TYR ALA SER LEU ASP VAL LYS TYR SEQRES 18 A 500 PRO PRO VAL ILE VAL GLU MET ASN SER SER VAL GLU ALA SEQRES 19 A 500 ILE GLU GLY SER HIS VAL SER LEU LEU CYS GLY ALA ASP SEQRES 20 A 500 SER ASN PRO PRO PRO LEU LEU THR TRP MET ARG ASP GLY SEQRES 21 A 500 MET VAL LEU ARG GLU ALA VAL ALA LYS SER LEU TYR LEU SEQRES 22 A 500 ASP LEU GLU GLU VAL THR PRO GLY GLU ASP GLY VAL TYR SEQRES 23 A 500 ALA CYS LEU ALA GLU ASN ALA TYR GLY GLN ASP ASN ARG SEQRES 24 A 500 THR VAL GLU LEU SER VAL MET TYR ALA PRO TRP LYS PRO SEQRES 25 A 500 THR VAL ASN GLY THR VAL VAL ALA VAL GLU GLY GLU THR SEQRES 26 A 500 VAL SER ILE LEU CYS SER THR GLN SER ASN PRO ASP PRO SEQRES 27 A 500 ILE LEU THR ILE PHE LYS GLU LYS GLN ILE LEU ALA THR SEQRES 28 A 500 VAL ILE TYR GLU SER GLN LEU GLN LEU GLU LEU PRO ALA SEQRES 29 A 500 VAL THR PRO GLU ASP ASP GLY GLU TYR TRP CYS VAL ALA SEQRES 30 A 500 GLU ASN GLN TYR GLY GLN ARG ALA THR ALA PHE ASN LEU SEQRES 31 A 500 SER VAL GLU PHE ALA PRO ILE ILE LEU LEU GLU SER HIS SEQRES 32 A 500 CYS ALA ALA ALA ARG ASP THR VAL GLN CYS LEU CYS VAL SEQRES 33 A 500 VAL LYS SER ASN PRO GLU PRO SER VAL ALA PHE GLU LEU SEQRES 34 A 500 PRO SER ARG ASN VAL THR VAL ASN GLU THR GLU ARG GLU SEQRES 35 A 500 PHE VAL TYR SER GLU ARG SER GLY LEU LEU LEU THR SER SEQRES 36 A 500 ILE LEU THR ILE ARG GLY GLN ALA GLN ALA PRO PRO ARG SEQRES 37 A 500 VAL ILE CYS THR SER ARG ASN LEU TYR GLY THR GLN SER SEQRES 38 A 500 LEU GLU LEU PRO PHE GLN GLY ALA HIS ARG ALA ALA ALA SEQRES 39 A 500 HIS HIS HIS HIS HIS HIS HET NAG B 1 14 HET FUC B 2 10 HET NGA C 1 15 HET GAL C 2 11 HET SIA C 3 20 HET MAN A 601 11 HET NAG A 602 14 HET NAG A 603 14 HET NAG A 604 14 HET NAG A 607 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM NGA 2-ACETAMIDO-2-DEOXY-BETA-D-GALACTOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM SIA N-ACETYL-ALPHA-NEURAMINIC ACID HETNAM MAN ALPHA-D-MANNOPYRANOSE 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 FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN NGA N-ACETYL-BETA-D-GALACTOSAMINE; 2-ACETAMIDO-2-DEOXY- HETSYN 2 NGA BETA-D-GALACTOSE; 2-ACETAMIDO-2-DEOXY-D-GALACTOSE; 2- HETSYN 3 NGA ACETAMIDO-2-DEOXY-GALACTOSE; N-ACETYL-D-GALACTOSAMINE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE HETSYN SIA N-ACETYLNEURAMINIC ACID; SIALIC ACID; ALPHA-SIALIC HETSYN 2 SIA ACID; O-SIALIC ACID HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 2 NAG 5(C8 H15 N O6) FORMUL 2 FUC C6 H12 O5 FORMUL 3 NGA C8 H15 N O6 FORMUL 3 GAL C6 H12 O6 FORMUL 3 SIA C11 H19 N O9 FORMUL 4 MAN C6 H12 O6 HELIX 1 AA1 ASP A 94 ARG A 98 5 5 HELIX 2 AA2 SER A 108 GLY A 112 5 5 HELIX 3 AA3 THR A 207 ASN A 211 5 5 HELIX 4 AA4 THR A 383 ASP A 387 5 5 SHEET 1 AA1 2 GLY A 23 TRP A 25 0 SHEET 2 AA1 2 ARG A 43 ASP A 45 -1 O ARG A 43 N TRP A 25 SHEET 1 AA2 5 THR A 29 PHE A 33 0 SHEET 2 AA2 5 SER A 133 VAL A 138 1 O ASP A 136 N ILE A 30 SHEET 3 AA2 5 GLY A 113 ASP A 120 -1 N GLY A 113 O LEU A 135 SHEET 4 AA2 5 HIS A 56 PHE A 61 -1 N HIS A 56 O ASP A 120 SHEET 5 AA2 5 VAL A 72 LYS A 75 -1 O PHE A 74 N TRP A 59 SHEET 1 AA3 4 THR A 29 PHE A 33 0 SHEET 2 AA3 4 SER A 133 VAL A 138 1 O ASP A 136 N ILE A 30 SHEET 3 AA3 4 GLY A 113 ASP A 120 -1 N GLY A 113 O LEU A 135 SHEET 4 AA3 4 GLN A 126 THR A 128 -1 O TYR A 127 N GLY A 119 SHEET 1 AA4 3 VAL A 38 ILE A 40 0 SHEET 2 AA4 3 LEU A 102 LEU A 104 -1 O LEU A 102 N ILE A 40 SHEET 3 AA4 3 SER A 89 LEU A 91 -1 N ARG A 90 O LEU A 103 SHEET 1 AA5 4 ASN A 142 VAL A 144 0 SHEET 2 AA5 4 VAL A 155 PRO A 162 -1 O MET A 160 N ASN A 142 SHEET 3 AA5 4 THR A 195 PHE A 204 -1 O GLN A 198 N VAL A 161 SHEET 4 AA5 4 PRO A 183 GLU A 191 -1 N GLU A 191 O THR A 195 SHEET 1 AA6 2 VAL A 149 VAL A 150 0 SHEET 2 AA6 2 VAL A 236 LYS A 237 1 O LYS A 237 N VAL A 149 SHEET 1 AA7 3 GLU A 171 LEU A 175 0 SHEET 2 AA7 3 ARG A 214 ALA A 220 -1 O GLN A 218 N SER A 173 SHEET 3 AA7 3 GLN A 227 SER A 233 -1 O ALA A 232 N LEU A 215 SHEET 1 AA8 3 VAL A 241 MET A 245 0 SHEET 2 AA8 3 HIS A 256 ASP A 264 -1 O GLY A 262 N GLU A 244 SHEET 3 AA8 3 SER A 287 GLU A 293 -1 O LEU A 292 N VAL A 257 SHEET 1 AA9 5 VAL A 249 ILE A 252 0 SHEET 2 AA9 5 GLY A 312 MET A 323 1 O MET A 323 N ALA A 251 SHEET 3 AA9 5 GLY A 301 ASN A 309 -1 N ASN A 309 O GLY A 312 SHEET 4 AA9 5 LEU A 270 MET A 274 -1 N MET A 274 O ALA A 304 SHEET 5 AA9 5 GLU A 282 ALA A 283 -1 O ALA A 283 N LEU A 271 SHEET 1 AB1 3 THR A 330 GLY A 333 0 SHEET 2 AB1 3 VAL A 343 SER A 348 -1 O SER A 348 N THR A 330 SHEET 3 AB1 3 GLN A 374 LEU A 379 -1 O LEU A 377 N ILE A 345 SHEET 1 AB2 5 VAL A 336 VAL A 338 0 SHEET 2 AB2 5 ARG A 401 GLU A 410 1 O SER A 408 N ALA A 337 SHEET 3 AB2 5 GLY A 388 ALA A 394 -1 N ALA A 394 O ARG A 401 SHEET 4 AB2 5 LEU A 357 LYS A 361 -1 N THR A 358 O VAL A 393 SHEET 5 AB2 5 GLN A 364 VAL A 369 -1 O VAL A 369 N LEU A 357 SHEET 1 AB3 3 ILE A 414 ILE A 415 0 SHEET 2 AB3 3 VAL A 428 LYS A 435 -1 O LYS A 435 N ILE A 414 SHEET 3 AB3 3 HIS A 420 ALA A 423 -1 N HIS A 420 O LEU A 431 SHEET 1 AB4 4 ILE A 414 ILE A 415 0 SHEET 2 AB4 4 VAL A 428 LYS A 435 -1 O LYS A 435 N ILE A 414 SHEET 3 AB4 4 LEU A 469 ILE A 476 -1 O LEU A 474 N CYS A 430 SHEET 4 AB4 4 PHE A 460 SER A 466 -1 N TYR A 462 O ILE A 473 SHEET 1 AB5 3 SER A 441 GLU A 445 0 SHEET 2 AB5 3 ILE A 487 ARG A 491 -1 O ILE A 487 N GLU A 445 SHEET 3 AB5 3 THR A 496 GLU A 500 -1 O GLN A 497 N SER A 490 SSBOND 1 CYS A 37 CYS A 165 1555 1555 2.03 SSBOND 2 CYS A 42 CYS A 100 1555 1555 2.03 SSBOND 3 CYS A 159 CYS A 217 1555 1555 2.03 SSBOND 4 CYS A 261 CYS A 305 1555 1555 2.03 SSBOND 5 CYS A 347 CYS A 392 1555 1555 2.03 SSBOND 6 CYS A 421 CYS A 430 1555 1555 2.03 SSBOND 7 CYS A 432 CYS A 488 1555 1555 2.03 LINK CD1 TRP A 22 C1 MAN A 601 1555 1555 1.48 LINK ND2 ASN A 99 C1 NAG A 602 1555 1555 1.44 LINK ND2 ASN A 246 C1 NAG A 603 1555 1555 1.43 LINK ND2 ASN A 315 C1 NAG A 604 1555 1555 1.43 LINK ND2 ASN A 332 C1 NAG B 1 1555 1555 1.55 LINK ND2 ASN A 406 C1 NAG A 607 1555 1555 1.44 LINK O6 NAG B 1 C1 FUC B 2 1555 1555 1.43 LINK O3 NGA C 1 C1 GAL C 2 1555 1555 1.45 LINK O3 GAL C 2 C2 SIA C 3 1555 1555 1.47 CISPEP 1 THR A 456 GLU A 457 0 -0.10 CRYST1 278.868 278.868 62.520 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 0.003586 0.002070 0.000000 0.00000 SCALE2 0.000000 0.004141 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015995 0.00000