HEADER IMMUNE SYSTEM 29-DEC-05 2FIK TITLE STRUCTURE OF A MICROBIAL GLYCOSPHINGOLIPID BOUND TO MOUSE CD1D COMPND MOL_ID: 1; COMPND 2 MOLECULE: T-CELL SURFACE GLYCOPROTEIN CD1D1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EXTRACELLULAR DOMAIN OF CD1D, RESIDUES 19-297; COMPND 5 SYNONYM: CD1.1 ANTIGEN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: B(2)-MICROGLOBULIN; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: CD1D1, CD1.1; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: SF9 CELLS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PBACP10PH; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 14 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 15 ORGANISM_TAXID: 10090; SOURCE 16 GENE: BETA-2-MICROGLOBULIN; SOURCE 17 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 18 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 20 EXPRESSION_SYSTEM_STRAIN: SF9 CELLS; SOURCE 21 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: PBACP10PH KEYWDS NKT CELLS, CD1D, MHC-FOLD, IMMUNE SYSTEM, BACTERIAL ANTIGEN, TCR EXPDTA X-RAY DIFFRACTION AUTHOR D.WU,D.M.ZAJONC REVDAT 5 30-AUG-23 2FIK 1 REMARK HETSYN REVDAT 4 29-JUL-20 2FIK 1 COMPND REMARK SEQADV HETNAM REVDAT 4 2 1 SSBOND LINK SITE ATOM REVDAT 3 13-JUL-11 2FIK 1 VERSN REVDAT 2 24-FEB-09 2FIK 1 VERSN REVDAT 1 21-MAR-06 2FIK 0 JRNL AUTH D.WU,D.M.ZAJONC,M.FUJIO,B.A.SULLIVAN,Y.KINJO,M.KRONENBERG, JRNL AUTH 2 I.A.WILSON,C.H.WONG JRNL TITL DESIGN OF NATURAL KILLER T CELL ACTIVATORS: STRUCTURE AND JRNL TITL 2 FUNCTION OF A MICROBIAL GLYCOSPHINGOLIPID BOUND TO MOUSE JRNL TITL 3 CD1D. JRNL REF PROC.NATL.ACAD.SCI.USA V. 103 3972 2006 JRNL REFN ISSN 0027-8424 JRNL PMID 16537470 JRNL DOI 10.1073/PNAS.0600285103 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 34.14 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 46570 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) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.600 REMARK 3 FREE R VALUE TEST SET COUNT : 1230 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) : 3417 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.97 REMARK 3 BIN R VALUE (WORKING SET) : 0.2780 REMARK 3 BIN FREE R VALUE SET COUNT : 83 REMARK 3 BIN FREE R VALUE : 0.3460 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2930 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 122 REMARK 3 SOLVENT ATOMS : 379 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.29 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): 0.122 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.119 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.088 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.801 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 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): 3120 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4236 ; 1.568 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 359 ; 6.969 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 141 ;34.626 ;24.043 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 478 ;15.029 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;22.177 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 451 ; 0.129 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2340 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1337 ; 0.211 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2070 ; 0.305 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 304 ; 0.175 ; 0.200 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): 33 ; 0.180 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 21 ; 0.207 ; 0.200 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): 1860 ; 1.099 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2926 ; 1.804 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1474 ; 2.485 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1310 ; 3.861 ; 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 : 1.20 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 2FIK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-DEC-05. REMARK 100 THE DEPOSITION ID IS D_1000035919. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAY-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95369 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47802 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 37.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.5000 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) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.72200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 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 (%): 56.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 % POLYETHYLENE GLYCOL 4000, 0.1 M REMARK 280 SODIUM CITRATE, 10% ISOPROPANOL, PH 5.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277.0K 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 21.14750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.34950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.83050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.34950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.14750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.83050 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 300 REMARK: HETERODIMER FORMED BY CD1D AND BETA-2-MICROGLOBULIN 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: 5930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 ASN A 7 REMARK 465 MET A 87 REMARK 465 MET A 88 REMARK 465 SER A 89 REMARK 465 PRO A 90 REMARK 465 LYS A 91 REMARK 465 GLU A 92 REMARK 465 ASP A 93 REMARK 465 GLY A 280 REMARK 465 SER A 281 REMARK 465 HIS A 282 REMARK 465 HIS A 283 REMARK 465 HIS A 284 REMARK 465 HIS A 285 REMARK 465 HIS A 286 REMARK 465 HIS A 287 REMARK 465 ILE B 1 REMARK 465 MET B 99 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASN A 110 CB CG OD1 ND2 REMARK 480 GLU A 257 CG CD OE1 OE2 REMARK 480 LYS B 19 CD CE NZ REMARK 480 LYS B 48 CG CD CE NZ REMARK 480 LYS B 58 CG CD CE NZ REMARK 480 ARG B 97 CB CG CD NE CZ NH1 NH2 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 598 O HOH A 648 1.94 REMARK 500 OG1 THR A 9 OE1 GLU A 105 2.09 REMARK 500 O HOH A 653 O HOH A 715 2.16 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 OD2 ASP A 166 OH TYR B 94 3655 2.10 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 ASN A 110 CA ASN A 110 CB 0.221 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 ASN A 110 N - CA - CB ANGL. DEV. = -12.7 DEGREES REMARK 500 ASN A 110 CA - CB - CG ANGL. DEV. = -14.5 DEGREES REMARK 500 ARG B 12 NE - CZ - NH1 ANGL. DEV. = 7.2 DEGREES REMARK 500 ARG B 12 NE - CZ - NH2 ANGL. DEV. = -8.5 DEGREES REMARK 500 LYS B 58 CA - CB - CG ANGL. DEV. = 19.3 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 ASN A 20 -170.26 -170.23 REMARK 500 PRO A 95 122.81 -22.21 REMARK 500 ALA A 200 103.37 145.85 REMARK 500 TRP B 60 -6.73 75.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 TYR A 94 PRO A 95 -114.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Z5L RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A HIGHLY POTENT SHORT-CHAIN GALACTOSYL REMARK 900 CERAMIDE AGONIST BOUND TO CD1D REMARK 900 RELATED ID: 2AKR RELATED DB: PDB REMARK 900 STRUCTURAL BASIS OF SULFATIDE PRESENTATION BY MOUSE CD1D REMARK 900 RELATED ID: 1ZHN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MOUSE CD1D BOUND TO THE SELF LIGAND REMARK 900 PHOSPHATIDYLCHOLINE REMARK 900 RELATED ID: 1ZT4 RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF HUMAN CD1D WITH AND WITHOUT- REMARK 900 GALACTOSYLCERAMIDE REMARK 900 RELATED ID: 1CD1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CD1(MOUSE) ANTIGEN PRESENTING MOLECULE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE MUTATION IS A RESULT OF AN EARLY CLONING ARTIFACT DBREF 2FIK A 1 279 UNP P11609 CD1D1_MOUSE 19 297 DBREF 2FIK B 1 99 GB 199582 AAA39671 21 119 SEQADV 2FIK HIS A 201 UNP P11609 ASP 219 SEE REMARK 999 SEQADV 2FIK GLY A 280 UNP P11609 CLONING ARTIFACT SEQADV 2FIK SER A 281 UNP P11609 CLONING ARTIFACT SEQADV 2FIK HIS A 282 UNP P11609 EXPRESSION TAG SEQADV 2FIK HIS A 283 UNP P11609 EXPRESSION TAG SEQADV 2FIK HIS A 284 UNP P11609 EXPRESSION TAG SEQADV 2FIK HIS A 285 UNP P11609 EXPRESSION TAG SEQADV 2FIK HIS A 286 UNP P11609 EXPRESSION TAG SEQADV 2FIK HIS A 287 UNP P11609 EXPRESSION TAG SEQADV 2FIK ALA B 85 GB 199582 VAL 105 SEE REMARK 999 SEQRES 1 A 287 SER GLU ALA GLN GLN LYS ASN TYR THR PHE ARG CYS LEU SEQRES 2 A 287 GLN MET SER SER PHE ALA ASN ARG SER TRP SER ARG THR SEQRES 3 A 287 ASP SER VAL VAL TRP LEU GLY ASP LEU GLN THR HIS ARG SEQRES 4 A 287 TRP SER ASN ASP SER ALA THR ILE SER PHE THR LYS PRO SEQRES 5 A 287 TRP SER GLN GLY LYS LEU SER ASN GLN GLN TRP GLU LYS SEQRES 6 A 287 LEU GLN HIS MET PHE GLN VAL TYR ARG VAL SER PHE THR SEQRES 7 A 287 ARG ASP ILE GLN GLU LEU VAL LYS MET MET SER PRO LYS SEQRES 8 A 287 GLU ASP TYR PRO ILE GLU ILE GLN LEU SER ALA GLY CYS SEQRES 9 A 287 GLU MET TYR PRO GLY ASN ALA SER GLU SER PHE LEU HIS SEQRES 10 A 287 VAL ALA PHE GLN GLY LYS TYR VAL VAL ARG PHE TRP GLY SEQRES 11 A 287 THR SER TRP GLN THR VAL PRO GLY ALA PRO SER TRP LEU SEQRES 12 A 287 ASP LEU PRO ILE LYS VAL LEU ASN ALA ASP GLN GLY THR SEQRES 13 A 287 SER ALA THR VAL GLN MET LEU LEU ASN ASP THR CYS PRO SEQRES 14 A 287 LEU PHE VAL ARG GLY LEU LEU GLU ALA GLY LYS SER ASP SEQRES 15 A 287 LEU GLU LYS GLN GLU LYS PRO VAL ALA TRP LEU SER SER SEQRES 16 A 287 VAL PRO SER SER ALA HIS GLY HIS ARG GLN LEU VAL CYS SEQRES 17 A 287 HIS VAL SER GLY PHE TYR PRO LYS PRO VAL TRP VAL MET SEQRES 18 A 287 TRP MET ARG GLY ASP GLN GLU GLN GLN GLY THR HIS ARG SEQRES 19 A 287 GLY ASP PHE LEU PRO ASN ALA ASP GLU THR TRP TYR LEU SEQRES 20 A 287 GLN ALA THR LEU ASP VAL GLU ALA GLY GLU GLU ALA GLY SEQRES 21 A 287 LEU ALA CYS ARG VAL LYS HIS SER SER LEU GLY GLY GLN SEQRES 22 A 287 ASP ILE ILE LEU TYR TRP GLY SER HIS HIS HIS HIS HIS SEQRES 23 A 287 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 2FIK ASN A 20 ASN GLYCOSYLATION SITE MODRES 2FIK ASN A 42 ASN GLYCOSYLATION SITE MODRES 2FIK ASN A 165 ASN GLYCOSYLATION SITE HET NAG C 1 14 HET NAG C 2 14 HET NAG A 303 14 HET NAG A 304 14 HET GSL A 501 48 HET PLM A 502 18 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM GSL (2S,3R)-3-HYDROXY-2-(TETRADECANOYLAMINO)OCTADECYL HETNAM 2 GSL ALPHA-D-GALACTOPYRANOSIDURONIC ACID 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 HETSYN GSL (2S,3R)-N-MYRISTOYL-1-O-(ALPHA-D-GALACTURONOSYL)-2-N- HETSYN 2 GSL OCTADECANE-3-OL FORMUL 3 NAG 4(C8 H15 N O6) FORMUL 6 GSL C38 H73 N O9 FORMUL 7 PLM C16 H32 O2 FORMUL 8 HOH *379(H2 O) HELIX 1 1 SER A 59 LYS A 86 1 28 HELIX 2 2 PRO A 140 TRP A 142 5 3 HELIX 3 3 LEU A 143 ALA A 152 1 10 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 THR A 9 ASN A 20 -1 N LEU A 13 O VAL A 29 SHEET 5 A 8 ILE A 96 TYR A 107 -1 O CYS A 104 N PHE A 10 SHEET 6 A 8 ALA A 111 PHE A 120 -1 O ALA A 111 N TYR A 107 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 GLN A 134 N ARG A 127 SHEET 1 B 4 VAL A 190 PRO A 197 0 SHEET 2 B 4 HIS A 203 PHE A 213 -1 O VAL A 207 N SER A 194 SHEET 3 B 4 TRP A 245 GLU A 254 -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 PRO A 197 0 SHEET 2 C 4 HIS A 203 PHE A 213 -1 O VAL A 207 N SER A 194 SHEET 3 C 4 TRP A 245 GLU A 254 -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 ILE A 275 N VAL A 265 SHEET 1 E 4 GLN B 6 SER B 11 0 SHEET 2 E 4 ASN B 21 PHE B 30 -1 O TYR B 26 N GLN B 8 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 TYR B 26 N GLN B 8 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 GLU B 36 LYS B 41 -1 N LYS B 41 O LYS B 44 SHEET 3 G 4 TYR B 78 LYS B 83 -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 208 CYS A 263 1555 1555 2.07 SSBOND 2 CYS B 25 CYS B 80 1555 1555 2.03 LINK ND2 ASN A 20 C1 NAG A 304 1555 1555 1.45 LINK ND2 ASN A 42 C1 NAG A 303 1555 1555 1.45 LINK ND2 ASN A 165 C1 NAG C 1 1555 1555 1.43 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.43 CISPEP 1 TYR A 214 PRO A 215 0 1.35 CISPEP 2 HIS B 31 PRO B 32 0 0.51 CRYST1 42.295 107.661 110.699 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 0.023643 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009288 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009034 0.00000