HEADER IMMUNE SYSTEM 07-AUG-09 3ILQ TITLE STRUCTURE OF MCD1D WITH BOUND GLYCOLIPID BBGL-2C FROM BORRELIA TITLE 2 BURGDORFERI COMPND MOL_ID: 1; COMPND 2 MOLECULE: T-CELL SURFACE GLYCOPROTEIN CD1D1; COMPND 3 CHAIN: C; 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: D; 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: DUAL PROMOTOR BACULOVIRUS TRANSFER SOURCE 10 VECTOR; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PBACPHP10; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 14 ORGANISM_COMMON: MOUSE; SOURCE 15 ORGANISM_TAXID: 10090; SOURCE 16 GENE: B2M, BETA 2 MICROBLOBULIN, MCG_11606, RP23-34E24.5-001; SOURCE 17 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 19 EXPRESSION_SYSTEM_STRAIN: SF9; SOURCE 20 EXPRESSION_SYSTEM_VECTOR_TYPE: DUAL PROMOTOR BACULOVIRUS TRANSFER SOURCE 21 VECTOR; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: PBACPHP10 KEYWDS ANTIGEN PRESENTATION, INKT CELLS, HOST DEFENSE, BORRELIA BURGDORFERI, KEYWDS 2 CD1, CELL MEMBRANE, DISULFIDE BOND, ENDOSOME, GLYCOPROTEIN, IMMUNE KEYWDS 3 RESPONSE, IMMUNOGLOBULIN DOMAIN, INNATE IMMUNITY, LYSOSOME, KEYWDS 4 MEMBRANE, TRANSMEMBRANE, MHC I, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR D.M.ZAJONC REVDAT 4 06-SEP-23 3ILQ 1 HETSYN REVDAT 3 29-JUL-20 3ILQ 1 COMPND REMARK SEQADV HETNAM REVDAT 3 2 1 LINK SITE ATOM REVDAT 2 02-MAR-10 3ILQ 1 JRNL REVDAT 1 26-JAN-10 3ILQ 0 JRNL AUTH J.WANG,Y.LI,Y.KINJO,T.T.MAC,D.GIBSON,G.F.PAINTER, JRNL AUTH 2 M.KRONENBERG,D.M.ZAJONC JRNL TITL LIPID BINDING ORIENTATION WITHIN CD1D AFFECTS RECOGNITION OF JRNL TITL 2 BORRELIA BURGORFERI ANTIGENS BY NKT CELLS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 107 1535 2010 JRNL REFN ISSN 0027-8424 JRNL PMID 20080535 JRNL DOI 10.1073/PNAS.0909479107 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0088 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.07 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 23963 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) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1023 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1651 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.16 REMARK 3 BIN R VALUE (WORKING SET) : 0.3100 REMARK 3 BIN FREE R VALUE SET COUNT : 69 REMARK 3 BIN FREE R VALUE : 0.3200 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2909 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 109 REMARK 3 SOLVENT ATOMS : 131 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : -0.03000 REMARK 3 B33 (A**2) : 0.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.232 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.193 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.152 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.773 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3112 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4224 ; 1.479 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 356 ; 6.505 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 141 ;36.627 ;24.043 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 494 ;15.399 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;15.189 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 452 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2347 ; 0.007 ; 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): 1800 ; 0.618 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2912 ; 1.147 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1312 ; 1.934 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1312 ; 2.873 ; 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 : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 7 C 185 REMARK 3 RESIDUE RANGE : E 500 E 521 REMARK 3 RESIDUE RANGE : L 1 L 1 REMARK 3 ORIGIN FOR THE GROUP (A): -9.6589 6.4945 37.3213 REMARK 3 T TENSOR REMARK 3 T11: 0.1930 T22: 0.1697 REMARK 3 T33: 0.1425 T12: 0.0509 REMARK 3 T13: 0.0048 T23: -0.0312 REMARK 3 L TENSOR REMARK 3 L11: 6.1408 L22: 0.9990 REMARK 3 L33: 2.3482 L12: 0.9577 REMARK 3 L13: 0.9586 L23: 0.2855 REMARK 3 S TENSOR REMARK 3 S11: -0.0014 S12: -0.6728 S13: 0.1530 REMARK 3 S21: 0.0992 S22: -0.0500 S23: -0.0781 REMARK 3 S31: -0.1468 S32: -0.2856 S33: 0.0514 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 : C 186 C 279 REMARK 3 ORIGIN FOR THE GROUP (A): -27.6941 -16.4437 13.1388 REMARK 3 T TENSOR REMARK 3 T11: 0.3261 T22: 0.0297 REMARK 3 T33: 0.3541 T12: 0.0196 REMARK 3 T13: 0.0260 T23: -0.0069 REMARK 3 L TENSOR REMARK 3 L11: 3.0488 L22: 7.1982 REMARK 3 L33: 3.9203 L12: 1.3048 REMARK 3 L13: 1.3057 L23: 2.6711 REMARK 3 S TENSOR REMARK 3 S11: -0.0052 S12: 0.2046 S13: -0.5925 REMARK 3 S21: -0.8402 S22: 0.0804 S23: -0.1302 REMARK 3 S31: 0.1598 S32: 0.1553 S33: -0.0752 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 : D 2 D 99 REMARK 3 ORIGIN FOR THE GROUP (A): -24.4222 5.4069 12.9309 REMARK 3 T TENSOR REMARK 3 T11: 0.2773 T22: 0.0637 REMARK 3 T33: 0.1556 T12: -0.0035 REMARK 3 T13: 0.0002 T23: 0.0133 REMARK 3 L TENSOR REMARK 3 L11: 6.4045 L22: 1.2605 REMARK 3 L33: 3.8059 L12: 0.7746 REMARK 3 L13: 3.0783 L23: 0.2258 REMARK 3 S TENSOR REMARK 3 S11: -0.2360 S12: 0.4520 S13: 0.1601 REMARK 3 S21: -0.2655 S22: 0.1855 S23: 0.0688 REMARK 3 S31: -0.2897 S32: 0.0320 S33: 0.0505 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 3ILQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1000054568. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SIDE SCATTERING I-BEAM BENT REMARK 200 SINGLE CRYSTAL, ASYMMETRIC CUT REMARK 200 4.9650 DEG. REMARK 200 OPTICS : VERTICAL FOCUSING MIRROR; SINGLE REMARK 200 CRYSTAL (SI111) BENT REMARK 200 MONOCHROMATOR (HORIZONTAL REMARK 200 FOCUSING). REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25018 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 35.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.60400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.600 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 2AKR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 17% POLYETHYLENE GLYCOL 3350, 150MM DI REMARK 280 -AMMONIUM HYDROGEN CITRATE, PH 5.0, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 48.89550 REMARK 290 SMTRY3 2 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: 3380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, 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 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 C 1 REMARK 465 GLU C 2 REMARK 465 ALA C 3 REMARK 465 GLN C 4 REMARK 465 GLN C 5 REMARK 465 LYS C 6 REMARK 465 PRO C 108 REMARK 465 GLY C 109 REMARK 465 ASN C 110 REMARK 465 VAL C 196 REMARK 465 PRO C 197 REMARK 465 SER C 198 REMARK 465 SER C 199 REMARK 465 ALA C 200 REMARK 465 ASP C 201 REMARK 465 GLY C 202 REMARK 465 HIS C 203 REMARK 465 HIS C 280 REMARK 465 HIS C 281 REMARK 465 HIS C 282 REMARK 465 HIS C 283 REMARK 465 HIS C 284 REMARK 465 HIS C 285 REMARK 465 ILE D 1 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 GLN C 61 CG CD OE1 NE2 REMARK 470 LYS C 91 CG CD CE NZ REMARK 470 ASP C 93 CG OD1 OD2 REMARK 470 GLN C 230 CG CD OE1 NE2 REMARK 470 LYS D 48 CG CD CE NZ 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 O6 NAG A 1 O HOH C 315 2.03 REMARK 500 O4 NAG C 501 O HOH C 321 2.13 REMARK 500 O HOH C 293 O HOH C 366 2.15 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 OD1 ASN C 42 O HOH C 319 2456 1.99 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 C 21 140.20 -37.37 REMARK 500 ALA C 255 40.51 -62.79 REMARK 500 TRP D 60 -7.46 81.45 REMARK 500 ARG D 97 -0.68 74.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2FIK RELATED DB: PDB REMARK 900 STRUCTURE OF MCD1D WITH BOUND PIM-2 REMARK 900 RELATED ID: 1ZHN RELATED DB: PDB REMARK 900 STRUCTURE OF MCD1D WITH BOUND SELF ANTIGEN PC REMARK 900 RELATED ID: 3ILP RELATED DB: PDB REMARK 900 STRUCTURE OF MCD1D WITH BOUND GLYCOLIPID BBGL-2F FROM BORRELIA REMARK 900 BURGDORFERI DBREF 3ILQ C 1 279 UNP P11609 CD1D1_MOUSE 19 297 DBREF 3ILQ D 1 99 UNP Q91XJ8 Q91XJ8_MOUSE 21 119 SEQADV 3ILQ HIS C 280 UNP P11609 EXPRESSION TAG SEQADV 3ILQ HIS C 281 UNP P11609 EXPRESSION TAG SEQADV 3ILQ HIS C 282 UNP P11609 EXPRESSION TAG SEQADV 3ILQ HIS C 283 UNP P11609 EXPRESSION TAG SEQADV 3ILQ HIS C 284 UNP P11609 EXPRESSION TAG SEQADV 3ILQ HIS C 285 UNP P11609 EXPRESSION TAG SEQRES 1 C 285 SER GLU ALA GLN GLN LYS ASN TYR THR PHE ARG CYS LEU SEQRES 2 C 285 GLN MET SER SER PHE ALA ASN ARG SER TRP SER ARG THR SEQRES 3 C 285 ASP SER VAL VAL TRP LEU GLY ASP LEU GLN THR HIS ARG SEQRES 4 C 285 TRP SER ASN ASP SER ALA THR ILE SER PHE THR LYS PRO SEQRES 5 C 285 TRP SER GLN GLY LYS LEU SER ASN GLN GLN TRP GLU LYS SEQRES 6 C 285 LEU GLN HIS MET PHE GLN VAL TYR ARG VAL SER PHE THR SEQRES 7 C 285 ARG ASP ILE GLN GLU LEU VAL LYS MET MET SER PRO LYS SEQRES 8 C 285 GLU ASP TYR PRO ILE GLU ILE GLN LEU SER ALA GLY CYS SEQRES 9 C 285 GLU MET TYR PRO GLY ASN ALA SER GLU SER PHE LEU HIS SEQRES 10 C 285 VAL ALA PHE GLN GLY LYS TYR VAL VAL ARG PHE TRP GLY SEQRES 11 C 285 THR SER TRP GLN THR VAL PRO GLY ALA PRO SER TRP LEU SEQRES 12 C 285 ASP LEU PRO ILE LYS VAL LEU ASN ALA ASP GLN GLY THR SEQRES 13 C 285 SER ALA THR VAL GLN MET LEU LEU ASN ASP THR CYS PRO SEQRES 14 C 285 LEU PHE VAL ARG GLY LEU LEU GLU ALA GLY LYS SER ASP SEQRES 15 C 285 LEU GLU LYS GLN GLU LYS PRO VAL ALA TRP LEU SER SER SEQRES 16 C 285 VAL PRO SER SER ALA ASP GLY HIS ARG GLN LEU VAL CYS SEQRES 17 C 285 HIS VAL SER GLY PHE TYR PRO LYS PRO VAL TRP VAL MET SEQRES 18 C 285 TRP MET ARG GLY ASP GLN GLU GLN GLN GLY THR HIS ARG SEQRES 19 C 285 GLY ASP PHE LEU PRO ASN ALA ASP GLU THR TRP TYR LEU SEQRES 20 C 285 GLN ALA THR LEU ASP VAL GLU ALA GLY GLU GLU ALA GLY SEQRES 21 C 285 LEU ALA CYS ARG VAL LYS HIS SER SER LEU GLY GLY GLN SEQRES 22 C 285 ASP ILE ILE LEU TYR TRP HIS HIS HIS HIS HIS HIS SEQRES 1 D 99 ILE GLN LYS THR PRO GLN ILE GLN VAL TYR SER ARG HIS SEQRES 2 D 99 PRO PRO GLU ASN GLY LYS PRO ASN ILE LEU ASN CYS TYR SEQRES 3 D 99 VAL THR GLN PHE HIS PRO PRO HIS ILE GLU ILE GLN MET SEQRES 4 D 99 LEU LYS ASN GLY LYS LYS ILE PRO LYS VAL GLU MET SER SEQRES 5 D 99 ASP MET SER PHE SER LYS ASP TRP SER PHE TYR ILE LEU SEQRES 6 D 99 ALA HIS THR GLU PHE THR PRO THR GLU THR ASP THR TYR SEQRES 7 D 99 ALA CYS ARG VAL LYS HIS ALA SER MET ALA GLU PRO LYS SEQRES 8 D 99 THR VAL TYR TRP ASP ARG ASP MET MODRES 3ILQ ASN C 20 ASN GLYCOSYLATION SITE MODRES 3ILQ ASN C 42 ASN GLYCOSYLATION SITE MODRES 3ILQ ASN C 165 ASN GLYCOSYLATION SITE HET NAG A 1 14 HET NAG A 2 14 HET NAG C 501 14 HET NAG C 510 14 HET 1O2 C 286 53 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM 1O2 (2S)-3-(ALPHA-D-GALACTOPYRANOSYLOXY)-2- HETNAM 2 1O2 (HEXADECANOYLOXY)PROPYL (9Z)-OCTADEC-9-ENOATE 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 1O2 1-OLEOYL,2-PALMITOYL-3-O(ALPHA-D-GALACTOPYRANOSYL)-SN- HETSYN 2 1O2 GLYCEROL FORMUL 3 NAG 4(C8 H15 N O6) FORMUL 6 1O2 C43 H80 O10 FORMUL 7 HOH *131(H2 O) HELIX 1 1 SER C 59 SER C 89 1 31 HELIX 2 2 PRO C 140 TRP C 142 5 3 HELIX 3 3 LEU C 143 ASP C 153 1 11 HELIX 4 4 ASP C 153 ASP C 166 1 14 HELIX 5 5 ASP C 166 GLY C 179 1 14 HELIX 6 6 GLY C 179 GLU C 184 1 6 HELIX 7 7 HIS C 267 GLY C 271 5 5 SHEET 1 A 8 SER C 48 PHE C 49 0 SHEET 2 A 8 LEU C 35 TRP C 40 -1 N ARG C 39 O SER C 48 SHEET 3 A 8 TRP C 23 LEU C 32 -1 N VAL C 30 O THR C 37 SHEET 4 A 8 THR C 9 ASN C 20 -1 N LEU C 13 O VAL C 29 SHEET 5 A 8 ILE C 96 GLU C 105 -1 O ILE C 96 N PHE C 18 SHEET 6 A 8 GLU C 113 PHE C 120 -1 O HIS C 117 N SER C 101 SHEET 7 A 8 LYS C 123 TRP C 129 -1 O VAL C 125 N VAL C 118 SHEET 8 A 8 SER C 132 THR C 135 -1 O SER C 132 N TRP C 129 SHEET 1 B 4 VAL C 190 SER C 194 0 SHEET 2 B 4 GLN C 205 PHE C 213 -1 O HIS C 209 N TRP C 192 SHEET 3 B 4 TRP C 245 ASP C 252 -1 O LEU C 251 N LEU C 206 SHEET 4 B 4 HIS C 233 ARG C 234 -1 N HIS C 233 O THR C 250 SHEET 1 C 4 VAL C 190 SER C 194 0 SHEET 2 C 4 GLN C 205 PHE C 213 -1 O HIS C 209 N TRP C 192 SHEET 3 C 4 TRP C 245 ASP C 252 -1 O LEU C 251 N LEU C 206 SHEET 4 C 4 LEU C 238 PRO C 239 -1 N LEU C 238 O TYR C 246 SHEET 1 D 4 GLN C 227 GLU C 228 0 SHEET 2 D 4 TRP C 219 ARG C 224 -1 N ARG C 224 O GLN C 227 SHEET 3 D 4 LEU C 261 LYS C 266 -1 O ARG C 264 N MET C 221 SHEET 4 D 4 ILE C 275 TYR C 278 -1 O LEU C 277 N CYS C 263 SHEET 1 E 4 GLN D 6 SER D 11 0 SHEET 2 E 4 ASN D 21 PHE D 30 -1 O ASN D 24 N TYR D 10 SHEET 3 E 4 PHE D 62 PHE D 70 -1 O THR D 68 N LEU D 23 SHEET 4 E 4 GLU D 50 MET D 51 -1 N GLU D 50 O HIS D 67 SHEET 1 F 4 GLN D 6 SER D 11 0 SHEET 2 F 4 ASN D 21 PHE D 30 -1 O ASN D 24 N TYR D 10 SHEET 3 F 4 PHE D 62 PHE D 70 -1 O THR D 68 N LEU D 23 SHEET 4 F 4 SER D 55 PHE D 56 -1 N SER D 55 O TYR D 63 SHEET 1 G 4 LYS D 44 LYS D 45 0 SHEET 2 G 4 GLU D 36 LYS D 41 -1 N LYS D 41 O LYS D 44 SHEET 3 G 4 TYR D 78 LYS D 83 -1 O ALA D 79 N LEU D 40 SHEET 4 G 4 LYS D 91 TYR D 94 -1 O LYS D 91 N VAL D 82 SSBOND 1 CYS C 104 CYS C 168 1555 1555 2.11 SSBOND 2 CYS C 208 CYS C 263 1555 1555 2.02 SSBOND 3 CYS D 25 CYS D 80 1555 1555 2.00 LINK ND2 ASN C 20 C1 NAG C 501 1555 1555 1.44 LINK ND2 ASN C 42 C1 NAG C 510 1555 1555 1.46 LINK ND2 ASN C 165 C1 NAG A 1 1555 1555 1.44 LINK O4 NAG A 1 C1 NAG A 2 1555 1555 1.45 CISPEP 1 SER C 89 PRO C 90 0 3.76 CISPEP 2 TYR C 94 PRO C 95 0 0.98 CISPEP 3 TYR C 214 PRO C 215 0 0.36 CISPEP 4 HIS D 31 PRO D 32 0 1.69 CRYST1 41.706 97.791 55.421 90.00 106.94 90.00 P 1 21 1 2 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 0.023977 0.000000 0.007303 0.00000 SCALE2 0.000000 0.010226 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018862 0.00000