HEADER IMMUNE SYSTEM 14-MAR-09 3GMM TITLE STRUCTURE OF MOUSE CD1D IN COMPLEX WITH C8PH COMPND MOL_ID: 1; COMPND 2 MOLECULE: T-CELL SURFACE GLYCOPROTEIN CD1D1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 19-297; 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: CD1D1, CD1.1; 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; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PACUW51; 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; 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; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PACUW51 KEYWDS CD1, NKT CELL, GLYCOLIPID, ANTIGEN PRESENTATION, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR A.SCHIEFNER,I.A.WILSON REVDAT 6 30-OCT-24 3GMM 1 REMARK REVDAT 5 06-SEP-23 3GMM 1 HETSYN REVDAT 4 29-JUL-20 3GMM 1 COMPND REMARK SEQADV HETNAM REVDAT 4 2 1 LINK SITE ATOM REVDAT 3 01-NOV-17 3GMM 1 REMARK REVDAT 2 13-JUL-11 3GMM 1 VERSN REVDAT 1 10-NOV-09 3GMM 0 JRNL AUTH A.SCHIEFNER,M.FUJIO,D.WU,C.H.WONG,I.A.WILSON JRNL TITL STRUCTURAL EVALUATION OF POTENT NKT CELL AGONISTS: JRNL TITL 2 IMPLICATIONS FOR DESIGN OF NOVEL STIMULATORY LIGANDS. JRNL REF J.MOL.BIOL. V. 394 71 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19732779 JRNL DOI 10.1016/J.JMB.2009.08.061 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 37348 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1993 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) : 2768 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.2650 REMARK 3 BIN FREE R VALUE SET COUNT : 152 REMARK 3 BIN FREE R VALUE : 0.2830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2975 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 228 REMARK 3 SOLVENT ATOMS : 314 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 34.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.83000 REMARK 3 B22 (A**2) : 1.96000 REMARK 3 B33 (A**2) : -0.97000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.47000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.127 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.124 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.093 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.445 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3376 ; 0.023 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4591 ; 2.144 ; 1.999 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 378 ; 6.610 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 152 ;32.427 ;24.211 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 525 ;15.081 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;20.003 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 506 ; 0.156 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2493 ; 0.011 ; 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): 1877 ; 1.321 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3051 ; 2.175 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1499 ; 3.389 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1540 ; 5.163 ; 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 : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 7 A 184 REMARK 3 ORIGIN FOR THE GROUP (A): -1.7646 -13.2570 10.5992 REMARK 3 T TENSOR REMARK 3 T11: 0.0200 T22: 0.0758 REMARK 3 T33: 0.0207 T12: 0.0090 REMARK 3 T13: 0.0058 T23: -0.0182 REMARK 3 L TENSOR REMARK 3 L11: 3.5750 L22: 1.1282 REMARK 3 L33: 1.2991 L12: 1.0715 REMARK 3 L13: 0.9721 L23: 0.0262 REMARK 3 S TENSOR REMARK 3 S11: 0.0182 S12: -0.4181 S13: 0.0816 REMARK 3 S21: 0.0411 S22: -0.1082 S23: -0.0540 REMARK 3 S31: -0.0273 S32: -0.2114 S33: 0.0899 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 185 A 279 REMARK 3 ORIGIN FOR THE GROUP (A): -19.6270 -35.8383 -13.1994 REMARK 3 T TENSOR REMARK 3 T11: 0.1133 T22: 0.0111 REMARK 3 T33: 0.0983 T12: -0.0133 REMARK 3 T13: 0.0313 T23: 0.0002 REMARK 3 L TENSOR REMARK 3 L11: 2.2439 L22: 4.1610 REMARK 3 L33: 2.8123 L12: 1.4104 REMARK 3 L13: 1.0158 L23: 1.2785 REMARK 3 S TENSOR REMARK 3 S11: -0.0520 S12: 0.0410 S13: -0.3750 REMARK 3 S21: -0.4760 S22: 0.1889 S23: -0.1916 REMARK 3 S31: 0.1451 S32: 0.0894 S33: -0.1369 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 1 B 99 REMARK 3 ORIGIN FOR THE GROUP (A): -16.3481 -14.0117 -13.9424 REMARK 3 T TENSOR REMARK 3 T11: 0.1220 T22: 0.0418 REMARK 3 T33: 0.0444 T12: -0.0172 REMARK 3 T13: -0.0323 T23: 0.0053 REMARK 3 L TENSOR REMARK 3 L11: 3.1700 L22: 0.7218 REMARK 3 L33: 2.3171 L12: 0.4141 REMARK 3 L13: 1.4897 L23: 0.1996 REMARK 3 S TENSOR REMARK 3 S11: -0.2557 S12: 0.1335 S13: 0.2153 REMARK 3 S21: -0.2168 S22: 0.1280 S23: 0.0833 REMARK 3 S31: -0.2302 S32: -0.0080 S33: 0.1277 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3GMM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000052049. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-NOV-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 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) : 0.9795 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : FLAT MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39342 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04300 REMARK 200 FOR THE DATA SET : 17.2000 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) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.48900 REMARK 200 FOR SHELL : 2.800 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: PDB ENTRY 3GML REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MALONATE PH 4.5, 20%(V/V) REMARK 280 PEG3350, VAPOR DIFFUSION, SITTING 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 48.95000 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: 6960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 38.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 VAL A 196 REMARK 465 PRO A 197 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 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 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 436 O HOH A 492 2.01 REMARK 500 O GLY A 272 O HOH A 367 2.09 REMARK 500 O HOH B 105 O HOH B 521 2.09 REMARK 500 OE1 GLU A 83 O HOH A 369 2.18 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 CD1 ILE B 1 O HOH B 392 1655 1.33 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 MET B 54 CG MET B 54 SD -0.188 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 -172.68 -170.21 REMARK 500 PRO A 108 131.26 -26.87 REMARK 500 ASP A 166 -58.20 -128.68 REMARK 500 GLU A 257 42.89 -72.95 REMARK 500 LYS B 48 30.52 -91.59 REMARK 500 TRP B 60 -6.01 77.96 REMARK 500 ARG B 97 2.91 82.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Z5L RELATED DB: PDB REMARK 900 SAME PROTEIN BOUND TO ALPHA-GALACTOSYL CERAMIDE REMARK 900 RELATED ID: 2AKR RELATED DB: PDB REMARK 900 SAME PROTEIN BOUND TO SULFATIDE REMARK 900 RELATED ID: 2FIK RELATED DB: PDB REMARK 900 SAME PROTEIN BOUND TO MICROBIAL ALPHA-GALACTURONOSYL CERAMIDE REMARK 900 RELATED ID: 2Q7Y RELATED DB: PDB REMARK 900 SAME PROTEIN BOUND TO MCD1D REMARK 900 RELATED ID: 3GMR RELATED DB: PDB REMARK 900 SAME PROTEIN BOUND TO C8PH, DIFFERENT SPACE GROUP REMARK 900 RELATED ID: 3GMN RELATED DB: PDB REMARK 900 SAME PROTEIN IN COMPLEX WITH C10PH REMARK 900 RELATED ID: 3GMO RELATED DB: PDB REMARK 900 SAME PROTEIN IN COMPLEX WITH C8PHF REMARK 900 RELATED ID: 3GMP RELATED DB: PDB REMARK 900 SAME PROTEIN IN COMPLEX WITH PBS-25 REMARK 900 RELATED ID: 3GMQ RELATED DB: PDB REMARK 900 SAME PROTEIN NO LIGAND ADDED REMARK 900 RELATED ID: 3GML RELATED DB: PDB REMARK 900 SAME PROTEIN IN COMPLEX WITH C6PH REMARK 999 REMARK 999 SEQUENCE REMARK 999 ASP TO HIS CONFLICT IN UNP ENTRY P11609 DBREF 3GMM A 1 279 UNP P11609 CD1D1_MOUSE 19 297 DBREF 3GMM B 1 99 UNP Q91XJ8 Q91XJ8_MOUSE 21 119 SEQADV 3GMM HIS A 201 UNP P11609 ASP 219 SEE REMARK 999 SEQADV 3GMM GLY A 280 UNP P11609 EXPRESSION TAG SEQADV 3GMM SER A 281 UNP P11609 EXPRESSION TAG SEQADV 3GMM HIS A 282 UNP P11609 EXPRESSION TAG SEQADV 3GMM HIS A 283 UNP P11609 EXPRESSION TAG SEQADV 3GMM HIS A 284 UNP P11609 EXPRESSION TAG SEQADV 3GMM HIS A 285 UNP P11609 EXPRESSION TAG SEQADV 3GMM HIS A 286 UNP P11609 EXPRESSION TAG SEQADV 3GMM HIS A 287 UNP P11609 EXPRESSION TAG 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 3GMM ASN A 20 ASN GLYCOSYLATION SITE MODRES 3GMM ASN A 42 ASN GLYCOSYLATION SITE MODRES 3GMM ASN A 165 ASN GLYCOSYLATION SITE HET NAG C 1 14 HET NAG C 2 14 HET BMA C 3 11 HET MAN C 4 11 HET MAN C 5 11 HET NAG D 1 14 HET NAG D 2 14 HET BMA D 3 11 HET MAN D 4 11 HET MAN D 5 11 HET FUC D 6 10 HET NAG A 288 14 HET C8P A 300 48 HET PLM A 301 18 HET EDO A 302 4 HET EDO A 303 4 HET EDO B 100 4 HET EDO B 101 8 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM C8P N-{(1S,2S,3R)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]- HETNAM 2 C8P 2,3-DIHYDROXYHEPTADECYL}-8-PHENYLOCTANAMIDE HETNAM PLM PALMITIC ACID HETNAM EDO 1,2-ETHANEDIOL 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 BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN C8P (2S,3S,4R)-N-PHENYLOCTANOYL-1-[(ALPHA-D- HETSYN 2 C8P GALACTOPYRANOSYL)OXY]-2-AMINO-OCTADECANE-3,4-DIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 NAG 5(C8 H15 N O6) FORMUL 3 BMA 2(C6 H12 O6) FORMUL 3 MAN 4(C6 H12 O6) FORMUL 4 FUC C6 H12 O5 FORMUL 6 C8P C38 H67 N O9 FORMUL 7 PLM C16 H32 O2 FORMUL 8 EDO 4(C2 H6 O2) FORMUL 12 HOH *314(H2 O) HELIX 1 1 SER A 59 SER A 89 1 31 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 VAL A 30 O THR A 37 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 TYR A 107 -1 O ALA A 102 N CYS A 12 SHEET 6 A 8 ALA A 111 PHE A 120 -1 O GLU A 113 N GLU A 105 SHEET 7 A 8 LYS A 123 TRP A 129 -1 O VAL A 125 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 SER A 194 0 SHEET 2 B 4 ARG A 204 PHE A 213 -1 O HIS A 209 N TRP A 192 SHEET 3 B 4 TRP A 245 VAL A 253 -1 O VAL A 253 N ARG A 204 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 SER A 194 0 SHEET 2 C 4 ARG A 204 PHE A 213 -1 O HIS A 209 N TRP A 192 SHEET 3 C 4 TRP A 245 VAL A 253 -1 O VAL A 253 N ARG A 204 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 ARG A 264 N MET A 221 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 THR B 68 N LEU B 23 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 THR B 68 N LEU B 23 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 ARG B 81 N GLN B 38 SHEET 4 G 4 LYS B 91 TYR B 94 -1 O VAL B 93 N CYS B 80 SSBOND 1 CYS A 104 CYS A 168 1555 1555 2.20 SSBOND 2 CYS A 208 CYS A 263 1555 1555 2.04 SSBOND 3 CYS B 25 CYS B 80 1555 1555 2.02 LINK ND2 ASN A 20 C1 NAG A 288 1555 1555 1.44 LINK ND2 ASN A 42 C1 NAG C 1 1555 1555 1.43 LINK ND2 ASN A 165 C1 NAG D 1 1555 1555 1.44 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.44 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.45 LINK O3 BMA C 3 C1 MAN C 4 1555 1555 1.47 LINK O2 MAN C 4 C1 MAN C 5 1555 1555 1.44 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.45 LINK O6 NAG D 1 C1 FUC D 6 1555 1555 1.48 LINK O4 NAG D 2 C1 BMA D 3 1555 1555 1.41 LINK O3 BMA D 3 C1 MAN D 4 1555 1555 1.44 LINK O6 BMA D 3 C1 MAN D 5 1555 1555 1.44 CISPEP 1 SER A 89 PRO A 90 0 4.07 CISPEP 2 TYR A 94 PRO A 95 0 -4.81 CISPEP 3 TYR A 214 PRO A 215 0 1.21 CISPEP 4 HIS B 31 PRO B 32 0 3.70 CRYST1 41.740 97.900 55.420 90.00 106.57 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 0.023958 0.000000 0.007128 0.00000 SCALE2 0.000000 0.010215 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018826 0.00000