HEADER IMMUNE SYSTEM 27-JAN-09 3G08 TITLE CRYSTAL STRUCTURE OF THE ALPHA-GALACTOSYLCERAMIDE ANALOG OCH IN TITLE 2 COMPLEX WITH MOUSE CD1D COMPND MOL_ID: 1; COMPND 2 MOLECULE: T-CELL SURFACE GLYCOPROTEIN CD1D1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 19-298; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: BETA-2 MICROGLOBULIN; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: UNP RESIDUES 21-119; COMPND 10 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: CD1.1, CD1D, CD1D1; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS TRANSFER VECTOR; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PBACP10PH; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 13 ORGANISM_COMMON: MOUSE; SOURCE 14 ORGANISM_TAXID: 10090; SOURCE 15 GENE: B2M, BETA 2 MICROGLOBULIN, MCG_11606, RP23-34E24.5-001; SOURCE 16 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: SF9; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS TRANSFER VECTOR; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PBACP10PH KEYWDS ANTIGEN PRESENTATION, GLYCOLIPID, NKT CELLS, CELL MEMBRANE, ENDOSOME, KEYWDS 2 GLYCOPROTEIN, IMMUNE RESPONSE, IMMUNOGLOBULIN DOMAIN, INNATE KEYWDS 3 IMMUNITY, LYSOSOME, MEMBRANE, TRANSMEMBRANE, MHC I, SECRETED, IMMUNE KEYWDS 4 SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR D.M.ZAJONC REVDAT 6 06-SEP-23 3G08 1 HETSYN REVDAT 5 29-JUL-20 3G08 1 COMPND REMARK SEQADV HETNAM REVDAT 5 2 1 LINK SITE ATOM REVDAT 4 13-JUL-11 3G08 1 VERSN REVDAT 3 19-JAN-10 3G08 1 JRNL REVDAT 2 22-DEC-09 3G08 1 JRNL REVDAT 1 08-DEC-09 3G08 0 JRNL AUTH B.A.SULLIVAN,N.A.NAGARAJAN,G.WINGENDER,J.WANG,I.SCOTT, JRNL AUTH 2 M.TSUJI,R.W.FRANCK,S.A.PORCELLI,D.M.ZAJONC,M.KRONENBERG JRNL TITL MECHANISMS FOR GLYCOLIPID ANTIGEN-DRIVEN CYTOKINE JRNL TITL 2 POLARIZATION BY VALPHA14I NKT CELLS. JRNL REF J.IMMUNOL. V. 184 141 2010 JRNL REFN ISSN 0022-1767 JRNL PMID 19949076 JRNL DOI 10.4049/JIMMUNOL.0902880 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0066 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 62608 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1292 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4362 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.16 REMARK 3 BIN R VALUE (WORKING SET) : 0.2760 REMARK 3 BIN FREE R VALUE SET COUNT : 92 REMARK 3 BIN FREE R VALUE : 0.2770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2887 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 115 REMARK 3 SOLVENT ATOMS : 477 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 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): 0.085 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.087 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.058 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.660 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3146 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4284 ; 1.466 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 369 ; 5.725 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 143 ;33.252 ;24.056 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 493 ;11.966 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;21.169 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 464 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2374 ; 0.008 ; 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): 1819 ; 0.829 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2948 ; 1.460 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1327 ; 2.289 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1329 ; 3.505 ; 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 7 A 182 REMARK 3 RESIDUE RANGE : E 500 E 512 REMARK 3 RESIDUE RANGE : R 1 R 1 REMARK 3 RESIDUE RANGE : S 1 S 1 REMARK 3 ORIGIN FOR THE GROUP (A): -6.7518 0.0212 -31.0038 REMARK 3 T TENSOR REMARK 3 T11: 0.1124 T22: 0.0650 REMARK 3 T33: 0.0626 T12: -0.0161 REMARK 3 T13: 0.0011 T23: -0.0400 REMARK 3 L TENSOR REMARK 3 L11: 2.6071 L22: 1.8256 REMARK 3 L33: 1.0065 L12: 0.0018 REMARK 3 L13: 0.2273 L23: 0.3573 REMARK 3 S TENSOR REMARK 3 S11: 0.0047 S12: 0.1117 S13: -0.0779 REMARK 3 S21: -0.0212 S22: -0.0367 S23: 0.0114 REMARK 3 S31: 0.0512 S32: -0.1088 S33: 0.0320 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 : A 183 A 279 REMARK 3 ORIGIN FOR THE GROUP (A): 10.6659 21.5636 -5.2834 REMARK 3 T TENSOR REMARK 3 T11: 0.0177 T22: 0.0768 REMARK 3 T33: 0.0363 T12: -0.0128 REMARK 3 T13: -0.0029 T23: -0.0214 REMARK 3 L TENSOR REMARK 3 L11: 1.9308 L22: 3.7960 REMARK 3 L33: 4.1281 L12: -0.2009 REMARK 3 L13: 0.1502 L23: 2.4223 REMARK 3 S TENSOR REMARK 3 S11: 0.0381 S12: -0.2173 S13: 0.1037 REMARK 3 S21: 0.1632 S22: -0.0448 S23: 0.0418 REMARK 3 S31: 0.0778 S32: -0.1363 S33: 0.0067 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 2 B 98 REMARK 3 ORIGIN FOR THE GROUP (A): 7.8495 24.5901 -26.3657 REMARK 3 T TENSOR REMARK 3 T11: 0.0882 T22: 0.0462 REMARK 3 T33: 0.0773 T12: 0.0095 REMARK 3 T13: -0.0084 T23: -0.0071 REMARK 3 L TENSOR REMARK 3 L11: 3.1911 L22: 2.0339 REMARK 3 L33: 1.6974 L12: 0.7633 REMARK 3 L13: 0.9973 L23: 0.1868 REMARK 3 S TENSOR REMARK 3 S11: -0.1325 S12: 0.1221 S13: 0.2315 REMARK 3 S21: -0.1644 S22: 0.0071 S23: 0.0042 REMARK 3 S31: -0.1446 S32: 0.0668 S33: 0.1254 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3G08 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000051258. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JAN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97976 REMARK 200 MONOCHROMATOR : SIDE SCATTERING BENT CUBE-ROOT I REMARK 200 -BEAM SINGLE CRYSTAL REMARK 200 OPTICS : FLAT MIRROR (VERTICAL FOCUSING); REMARK 200 SINGLE CRYSTAL SI(111) BENT REMARK 200 MONOCHROMATOR (HO RIZONTAL REMARK 200 FOCUSING) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 63903 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 29.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.63200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2Q7Y REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% POLYETHYLENE GLYCOL 3350, 100MM REMARK 280 TRIS PH8.5, 2% TACSIMATE PH8.0 , VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 21.12000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.33150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.54850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.33150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.12000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.54850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 3960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 7.0 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 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 1 REMARK 465 GLU A 2 REMARK 465 ALA A 3 REMARK 465 GLN A 4 REMARK 465 GLN A 5 REMARK 465 LYS A 6 REMARK 465 SER A 89 REMARK 465 PRO A 90 REMARK 465 LYS A 91 REMARK 465 PRO A 108 REMARK 465 GLY A 109 REMARK 465 ASN A 110 REMARK 465 SER A 198 REMARK 465 SER A 199 REMARK 465 ALA A 200 REMARK 465 HIS A 201 REMARK 465 GLY A 202 REMARK 465 HIS A 280 REMARK 465 HIS A 281 REMARK 465 HIS A 282 REMARK 465 HIS A 283 REMARK 465 HIS A 284 REMARK 465 HIS A 285 REMARK 465 ILE B 1 REMARK 465 MET B 99 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 ARG A 21 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 86 CG CD CE NZ REMARK 470 GLU A 105 CG CD OE1 OE2 REMARK 470 GLU A 113 CG CD OE1 OE2 REMARK 470 LYS B 44 CG CD CE NZ REMARK 470 LYS B 48 CG CD CE NZ REMARK 470 LYS B 58 CG CD CE NZ REMARK 470 GLU B 74 CG CD OE1 OE2 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 427 O HOH B 220 1.79 REMARK 500 O HOH A 304 O HOH A 376 1.79 REMARK 500 O HOH B 127 O HOH B 519 2.01 REMARK 500 O HOH A 376 O HOH A 390 2.01 REMARK 500 O HOH A 390 O HOH A 562 2.10 REMARK 500 O HOH A 489 O HOH B 101 2.15 REMARK 500 O HOH A 334 O HOH A 475 2.19 REMARK 500 O HOH A 584 O HOH A 616 2.19 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 ASN A 20 -169.92 -160.58 REMARK 500 TRP B 60 -10.32 77.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PLM A 287 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Z5L RELATED DB: PDB REMARK 900 STRUCTURE OF SHORT CHAIN ALPHA-GALACTOSYLCERAMIDE PBS-25 IN COMPLEX REMARK 900 WITH MCD1D REMARK 900 RELATED ID: 1ZT4 RELATED DB: PDB REMARK 900 STRUCTURE OF ALPHA-GALACTOSYLCERAMIDE BOUND TO HUMAN CD1D DBREF 3G08 A 1 279 UNP P11609 CD1D1_MOUSE 19 297 DBREF 3G08 B 1 99 UNP Q91XJ8 Q91XJ8_MOUSE 20 118 SEQADV 3G08 HIS A 201 UNP P11609 ASP 219 VARIANT SEQADV 3G08 HIS A 280 UNP P11609 EXPRESSION TAG SEQADV 3G08 HIS A 281 UNP P11609 EXPRESSION TAG SEQADV 3G08 HIS A 282 UNP P11609 EXPRESSION TAG SEQADV 3G08 HIS A 283 UNP P11609 EXPRESSION TAG SEQADV 3G08 HIS A 284 UNP P11609 EXPRESSION TAG SEQADV 3G08 HIS A 285 UNP P11609 EXPRESSION TAG SEQRES 1 A 285 SER GLU ALA GLN GLN LYS ASN TYR THR PHE ARG CYS LEU SEQRES 2 A 285 GLN MET SER SER PHE ALA ASN ARG SER TRP SER ARG THR SEQRES 3 A 285 ASP SER VAL VAL TRP LEU GLY ASP LEU GLN THR HIS ARG SEQRES 4 A 285 TRP SER ASN ASP SER ALA THR ILE SER PHE THR LYS PRO SEQRES 5 A 285 TRP SER GLN GLY LYS LEU SER ASN GLN GLN TRP GLU LYS SEQRES 6 A 285 LEU GLN HIS MET PHE GLN VAL TYR ARG VAL SER PHE THR SEQRES 7 A 285 ARG ASP ILE GLN GLU LEU VAL LYS MET MET SER PRO LYS SEQRES 8 A 285 GLU ASP TYR PRO ILE GLU ILE GLN LEU SER ALA GLY CYS SEQRES 9 A 285 GLU MET TYR PRO GLY ASN ALA SER GLU SER PHE LEU HIS SEQRES 10 A 285 VAL ALA PHE GLN GLY LYS TYR VAL VAL ARG PHE TRP GLY SEQRES 11 A 285 THR SER TRP GLN THR VAL PRO GLY ALA PRO SER TRP LEU SEQRES 12 A 285 ASP LEU PRO ILE LYS VAL LEU ASN ALA ASP GLN GLY THR SEQRES 13 A 285 SER ALA THR VAL GLN MET LEU LEU ASN ASP THR CYS PRO SEQRES 14 A 285 LEU PHE VAL ARG GLY LEU LEU GLU ALA GLY LYS SER ASP SEQRES 15 A 285 LEU GLU LYS GLN GLU LYS PRO VAL ALA TRP LEU SER SER SEQRES 16 A 285 VAL PRO SER SER ALA HIS GLY HIS ARG GLN LEU VAL CYS SEQRES 17 A 285 HIS VAL SER GLY PHE TYR PRO LYS PRO VAL TRP VAL MET SEQRES 18 A 285 TRP MET ARG GLY ASP GLN GLU GLN GLN GLY THR HIS ARG SEQRES 19 A 285 GLY ASP PHE LEU PRO ASN ALA ASP GLU THR TRP TYR LEU SEQRES 20 A 285 GLN ALA THR LEU ASP VAL GLU ALA GLY GLU GLU ALA GLY SEQRES 21 A 285 LEU ALA CYS ARG VAL LYS HIS SER SER LEU GLY GLY GLN SEQRES 22 A 285 ASP ILE ILE LEU TYR TRP HIS HIS HIS HIS HIS HIS SEQRES 1 B 99 ILE GLN LYS THR PRO GLN ILE GLN VAL TYR SER ARG HIS SEQRES 2 B 99 PRO PRO GLU ASN GLY LYS PRO ASN ILE LEU ASN CYS TYR SEQRES 3 B 99 VAL THR GLN PHE HIS PRO PRO HIS ILE GLU ILE GLN MET SEQRES 4 B 99 LEU LYS ASN GLY LYS LYS ILE PRO LYS VAL GLU MET SER SEQRES 5 B 99 ASP MET SER PHE SER LYS ASP TRP SER PHE TYR ILE LEU SEQRES 6 B 99 ALA HIS THR GLU PHE THR PRO THR GLU THR ASP THR TYR SEQRES 7 B 99 ALA CYS ARG VAL LYS HIS ALA SER MET ALA GLU PRO LYS SEQRES 8 B 99 THR VAL TYR TRP ASP ARG ASP MET MODRES 3G08 ASN A 20 ASN GLYCOSYLATION SITE MODRES 3G08 ASN A 42 ASN GLYCOSYLATION SITE MODRES 3G08 ASN A 165 ASN GLYCOSYLATION SITE HET NAG C 1 14 HET NAG C 2 14 HET NAG A 500 14 HET NAG A 501 14 HET FEE A 286 49 HET PLM A 287 10 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM FEE N-{(1S,2S,3R)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]- HETNAM 2 FEE 2,3-DIHYDROXYOCTYL}TETRACOSANAMIDE HETNAM PLM PALMITIC ACID 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 6 FEE C39 H77 N O9 FORMUL 7 PLM C16 H32 O2 FORMUL 8 HOH *477(H2 O) HELIX 1 1 SER A 59 MET A 88 1 30 HELIX 2 2 PRO A 140 TRP A 142 5 3 HELIX 3 3 LEU A 143 ASP A 153 1 11 HELIX 4 4 ASP A 153 ASP A 166 1 14 HELIX 5 5 ASP A 166 GLY A 179 1 14 HELIX 6 6 GLY A 179 GLU A 184 1 6 HELIX 7 7 HIS A 267 GLY A 271 5 5 SHEET 1 A 8 SER A 48 PHE A 49 0 SHEET 2 A 8 LEU A 35 TRP A 40 -1 N ARG A 39 O SER A 48 SHEET 3 A 8 TRP A 23 LEU A 32 -1 N SER A 28 O TRP A 40 SHEET 4 A 8 TYR A 8 ASN A 20 -1 N LEU A 13 O VAL A 29 SHEET 5 A 8 ILE A 96 MET A 106 -1 O ALA A 102 N CYS A 12 SHEET 6 A 8 GLU A 113 PHE A 120 -1 O ALA A 119 N GLN A 99 SHEET 7 A 8 LYS A 123 TRP A 129 -1 O VAL A 126 N VAL A 118 SHEET 8 A 8 SER A 132 THR A 135 -1 O SER A 132 N TRP A 129 SHEET 1 B 4 VAL A 190 VAL A 196 0 SHEET 2 B 4 ARG A 204 PHE A 213 -1 O GLN A 205 N VAL A 196 SHEET 3 B 4 TRP A 245 VAL A 253 -1 O LEU A 251 N LEU A 206 SHEET 4 B 4 HIS A 233 ARG A 234 -1 N HIS A 233 O THR A 250 SHEET 1 C 4 VAL A 190 VAL A 196 0 SHEET 2 C 4 ARG A 204 PHE A 213 -1 O GLN A 205 N VAL A 196 SHEET 3 C 4 TRP A 245 VAL A 253 -1 O LEU A 251 N LEU A 206 SHEET 4 C 4 LEU A 238 PRO A 239 -1 N LEU A 238 O TYR A 246 SHEET 1 D 4 GLN A 227 GLU A 228 0 SHEET 2 D 4 TRP A 219 ARG A 224 -1 N ARG A 224 O GLN A 227 SHEET 3 D 4 LEU A 261 LYS A 266 -1 O ALA A 262 N MET A 223 SHEET 4 D 4 ILE A 275 TYR A 278 -1 O LEU A 277 N CYS A 263 SHEET 1 E 4 GLN B 6 SER B 11 0 SHEET 2 E 4 ASN B 21 PHE B 30 -1 O ASN B 24 N TYR B 10 SHEET 3 E 4 PHE B 62 PHE B 70 -1 O ALA B 66 N CYS B 25 SHEET 4 E 4 GLU B 50 MET B 51 -1 N GLU B 50 O HIS B 67 SHEET 1 F 4 GLN B 6 SER B 11 0 SHEET 2 F 4 ASN B 21 PHE B 30 -1 O ASN B 24 N TYR B 10 SHEET 3 F 4 PHE B 62 PHE B 70 -1 O ALA B 66 N CYS B 25 SHEET 4 F 4 SER B 55 PHE B 56 -1 N SER B 55 O TYR B 63 SHEET 1 G 4 LYS B 44 LYS B 45 0 SHEET 2 G 4 ILE B 35 LYS B 41 -1 N LYS B 41 O LYS B 44 SHEET 3 G 4 TYR B 78 HIS B 84 -1 O ALA B 79 N LEU B 40 SHEET 4 G 4 LYS B 91 TYR B 94 -1 O LYS B 91 N VAL B 82 SSBOND 1 CYS A 104 CYS A 168 1555 1555 2.11 SSBOND 2 CYS A 208 CYS A 263 1555 1555 2.01 SSBOND 3 CYS B 25 CYS B 80 1555 1555 2.05 LINK ND2 ASN A 20 C1 NAG A 500 1555 1555 1.44 LINK ND2 ASN A 42 C1 NAG A 501 1555 1555 1.43 LINK ND2 ASN A 165 C1 NAG C 1 1555 1555 1.44 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.44 CISPEP 1 TYR A 94 PRO A 95 0 0.75 CISPEP 2 TYR A 214 PRO A 215 0 -0.69 CISPEP 3 HIS B 31 PRO B 32 0 0.87 CRYST1 42.240 107.097 106.663 90.00 90.00 90.00 P 21 21 21 4 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 0.023674 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009337 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009375 0.00000