HEADER IMMUNE SYSTEM 25-SEP-13 4MX7 TITLE STRUCTURE OF MOUSE CD1D IN COMPLEX WITH DIOLEOYL-PHOSPHATIDIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTIGEN-PRESENTING GLYCOPROTEIN CD1D1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CD1D ECTDOMAIN, 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: B2M ECTODOMAIN, 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, CD1D1, MCD1D; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SF9 CELLS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PBACPHP10 TRANSFER VECTOR; 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 CELLS; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PBACPHP10 TRANSFER VECTOR KEYWDS MHC FOLD, ANTIGEN PRESENTATION, LIPID ANTIGEN, MEMBRANE, IMMUNE KEYWDS 2 SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR D.M.ZAJONC,J.WANG REVDAT 5 13-MAR-24 4MX7 1 COMPND SOURCE REVDAT 4 20-SEP-23 4MX7 1 HETSYN REVDAT 3 29-JUL-20 4MX7 1 COMPND SOURCE REMARK SEQADV REVDAT 3 2 1 HETNAM LINK SITE ATOM REVDAT 2 15-NOV-17 4MX7 1 REMARK REVDAT 1 01-OCT-14 4MX7 0 JRNL AUTH J.WANG,D.M.ZAJONC JRNL TITL TBN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.24 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0104 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) : 2.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 75.58 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 22578 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) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1221 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) : 2.24 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.30 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1480 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.81 REMARK 3 BIN R VALUE (WORKING SET) : 0.2550 REMARK 3 BIN FREE R VALUE SET COUNT : 84 REMARK 3 BIN FREE R VALUE : 0.3050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2964 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 104 REMARK 3 SOLVENT ATOMS : 115 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.06000 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) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.279 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.216 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.163 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.083 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.925 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.896 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3165 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4300 ; 1.421 ; 1.957 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 366 ; 6.320 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 145 ;35.840 ;24.276 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 498 ;16.524 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;27.215 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 454 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2412 ; 0.006 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 7 A 185 REMARK 3 RESIDUE RANGE : A 301 A 305 REMARK 3 ORIGIN FOR THE GROUP (A): -3.6326 -4.1466 -26.2728 REMARK 3 T TENSOR REMARK 3 T11: 0.1423 T22: 0.0824 REMARK 3 T33: 0.0941 T12: 0.0023 REMARK 3 T13: 0.0239 T23: -0.0603 REMARK 3 L TENSOR REMARK 3 L11: 3.5347 L22: 0.6634 REMARK 3 L33: 2.1576 L12: 0.1093 REMARK 3 L13: -0.0020 L23: 0.4728 REMARK 3 S TENSOR REMARK 3 S11: 0.0173 S12: 0.2065 S13: -0.1380 REMARK 3 S21: -0.1663 S22: 0.0103 S23: -0.1571 REMARK 3 S31: 0.0048 S32: 0.0774 S33: -0.0275 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 186 A 279 REMARK 3 ORIGIN FOR THE GROUP (A): -20.7436 21.4451 -3.7906 REMARK 3 T TENSOR REMARK 3 T11: 0.0245 T22: 0.0252 REMARK 3 T33: 0.0471 T12: -0.0058 REMARK 3 T13: 0.0034 T23: -0.0112 REMARK 3 L TENSOR REMARK 3 L11: 2.9305 L22: 4.8628 REMARK 3 L33: 2.1554 L12: 0.4541 REMARK 3 L13: -0.4102 L23: 1.8886 REMARK 3 S TENSOR REMARK 3 S11: 0.0571 S12: -0.1746 S13: 0.2273 REMARK 3 S21: 0.1425 S22: 0.0063 S23: -0.1204 REMARK 3 S31: -0.0638 S32: 0.1531 S33: -0.0634 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 96 REMARK 3 ORIGIN FOR THE GROUP (A): -18.1088 0.2048 -2.4261 REMARK 3 T TENSOR REMARK 3 T11: 0.0742 T22: 0.0432 REMARK 3 T33: 0.0349 T12: -0.0009 REMARK 3 T13: -0.0050 T23: 0.0027 REMARK 3 L TENSOR REMARK 3 L11: 4.2492 L22: 1.9203 REMARK 3 L33: 2.1991 L12: -1.2272 REMARK 3 L13: -0.5895 L23: 0.2372 REMARK 3 S TENSOR REMARK 3 S11: -0.1102 S12: -0.3358 S13: -0.2313 REMARK 3 S21: 0.1718 S22: 0.0868 S23: 0.0584 REMARK 3 S31: 0.2009 S32: -0.0368 S33: 0.0235 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4MX7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000082478. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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) : 0.97945 REMARK 200 MONOCHROMATOR : SIDE SCATTERING BENT CUBE-ROOT I REMARK 200 -BEAM SINGLE CRYSTAL, ASYMMETRIC REMARK 200 CUT 4.965 DEGS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23843 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.240 REMARK 200 RESOLUTION RANGE LOW (A) : 75.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.12300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.24 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.55200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.100 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 (%): 54.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 4000, 0.2M AMMONIUM ACETATE, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 21.10000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.74000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.15000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.74000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.10000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.15000 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: 3420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 2.0 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 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 ARG B 97 REMARK 465 ASP B 98 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 LYS A 86 CG CD CE NZ REMARK 470 LYS B 48 CG CD CE NZ 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 HIS B 34 CG HIS B 34 CD2 0.057 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 PRO A 108 -80.34 -35.12 REMARK 500 VAL A 125 -33.27 -132.62 REMARK 500 ASP A 166 -56.91 -120.76 REMARK 500 LYS A 180 -65.50 -27.88 REMARK 500 TRP B 60 -11.99 83.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ZHN RELATED DB: PDB REMARK 900 STRUCTURE OF MOUSE CD1D IN COMPLEX WITH PHOSPHATIDYL CHOLINE REMARK 900 RELATED ID: 2GAZ RELATED DB: PDB REMARK 900 STRUCTURE OF MOUSE CD1D IN COMPLEX WITH PHOSPHATIDYL INOSITOL REMARK 900 DIMANNOSIDE DBREF 4MX7 A 1 279 UNP P11609 CD1D1_MOUSE 19 297 DBREF 4MX7 B 1 99 UNP P01887 B2MG_MOUSE 21 119 SEQADV 4MX7 HIS A 280 UNP P11609 EXPRESSION TAG SEQADV 4MX7 HIS A 281 UNP P11609 EXPRESSION TAG SEQADV 4MX7 HIS A 282 UNP P11609 EXPRESSION TAG SEQADV 4MX7 HIS A 283 UNP P11609 EXPRESSION TAG SEQADV 4MX7 HIS A 284 UNP P11609 EXPRESSION TAG SEQADV 4MX7 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 ASP 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 4MX7 ASN A 42 ASN GLYCOSYLATION SITE MODRES 4MX7 ASN A 20 ASN GLYCOSYLATION SITE MODRES 4MX7 ASN A 165 ASN GLYCOSYLATION SITE HET NAG C 1 14 HET NAG C 2 14 HET NAG A 301 14 HET NAG A 302 14 HET MX7 A 305 48 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM MX7 (2R)-3-(PHOSPHONOOXY)PROPANE-1,2-DIYL (9Z,9'Z)BIS- HETNAM 2 MX7 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 MX7 DIOLEOYL-PHOSPHATIDIC ACID FORMUL 3 NAG 4(C8 H15 N O6) FORMUL 6 MX7 C39 H73 O8 P FORMUL 7 HOH *115(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 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 MET A 106 -1 O ALA A 102 N CYS A 12 SHEET 6 A 8 SER A 112 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 PRO A 197 0 SHEET 2 B 4 HIS A 203 PHE A 213 -1 O HIS A 209 N TRP A 192 SHEET 3 B 4 TRP A 245 GLU A 254 -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 PRO A 197 0 SHEET 2 C 4 HIS A 203 PHE A 213 -1 O HIS A 209 N TRP A 192 SHEET 3 C 4 TRP A 245 GLU A 254 -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 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 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 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 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 2.05 SSBOND 3 CYS B 25 CYS B 80 1555 1555 2.03 LINK ND2 ASN A 20 C1 NAG A 301 1555 1555 1.45 LINK ND2 ASN A 42 C1 NAG A 302 1555 1555 1.44 LINK ND2 ASN A 165 C1 NAG C 1 1555 1555 1.46 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.45 CISPEP 1 SER A 89 PRO A 90 0 5.75 CISPEP 2 TYR A 94 PRO A 95 0 -5.14 CISPEP 3 TYR A 214 PRO A 215 0 2.28 CISPEP 4 HIS B 31 PRO B 32 0 5.63 CRYST1 42.200 106.300 107.480 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 0.023697 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009407 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009304 0.00000