HEADER IMMUNE SYSTEM 17-MAR-10 3M7O TITLE CRYSTAL STRUCTURE OF MOUSE MD-1 IN COMPLEX WITH PHOSPHATIDYLCHOLINE CAVEAT 3M7O NAG B 201 HAS WRONG CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYMPHOCYTE ANTIGEN 86; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: LY-86, PROTEIN MD-1; COMPND 5 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: LY86, MD1; SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS BETA SHEET, GLYCOPROTEIN, IMMUNITY, INFLAMMATORY RESPONSE, INNATE KEYWDS 2 IMMUNITY, SECRETED, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR H.HARADA,U.OHTO,Y.SATOW REVDAT 4 16-OCT-24 3M7O 1 HETSYN REVDAT 3 29-JUL-20 3M7O 1 CAVEAT COMPND REMARK HET REVDAT 3 2 1 HETNAM FORMUL LINK SITE REVDAT 3 3 1 ATOM REVDAT 2 22-JAN-14 3M7O 1 JRNL VERSN REVDAT 1 09-JUN-10 3M7O 0 JRNL AUTH H.HARADA,U.OHTO,Y.SATOW JRNL TITL CRYSTAL STRUCTURE OF MOUSE MD-1 WITH ENDOGENOUS PHOSPHOLIPID JRNL TITL 2 BOUND IN ITS CAVITY JRNL REF J.MOL.BIOL. V. 400 838 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20595044 JRNL DOI 10.1016/J.JMB.2010.05.063 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 67139 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3551 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2547 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.12 REMARK 3 BIN R VALUE (WORKING SET) : 0.2160 REMARK 3 BIN FREE R VALUE SET COUNT : 135 REMARK 3 BIN FREE R VALUE : 0.2520 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4135 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 364 REMARK 3 SOLVENT ATOMS : 444 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.01000 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): 0.106 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.104 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.064 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.850 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4611 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6223 ; 1.405 ; 2.046 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 531 ; 6.546 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 200 ;35.484 ;24.800 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 711 ;13.639 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;16.255 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 666 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3524 ; 0.005 ; 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): 2696 ; 2.015 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4280 ; 3.372 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1915 ; 4.481 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1939 ; 7.089 ; 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 : BABINET MODEL WITH 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 3M7O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1000058211. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-DEC-09; NULL REMARK 200 TEMPERATURE (KELVIN) : 95; 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY; PHOTON FACTORY REMARK 200 BEAMLINE : AR-NE3A; AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : NULL; NULL REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270; ADSC QUANTUM REMARK 200 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 82260 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.56600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: AUTOSHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% (W/V) PEG-8000, 0.2 M AMMONIUM REMARK 280 SULFATE AND MES PH 6.5,SUPPLEMENTED WITH 1/10 VOLUME OF 20% (W/V) REMARK 280 BENZAMIDINE HYDROCHLORIDE AS A CRYSTALLIZATION ADDITIVE, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.35700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 65.03550 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 21.67850 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A 1 REMARK 465 ASN A 2 REMARK 465 GLY A 3 REMARK 465 VAL A 4 REMARK 465 ALA A 5 REMARK 465 ALA A 6 REMARK 465 ALA A 7 REMARK 465 LEU A 8 REMARK 465 LEU A 9 REMARK 465 VAL A 10 REMARK 465 TRP A 11 REMARK 465 ILE A 12 REMARK 465 LEU A 13 REMARK 465 THR A 14 REMARK 465 SER A 15 REMARK 465 PRO A 16 REMARK 465 SER A 17 REMARK 465 SER A 18 REMARK 465 SER A 19 REMARK 465 ASP A 20 REMARK 465 HIS A 21 REMARK 465 GLY A 22 REMARK 465 SER A 23 REMARK 465 GLU A 24 REMARK 465 ASN A 25 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 GLY B 3 REMARK 465 VAL B 4 REMARK 465 ALA B 5 REMARK 465 ALA B 6 REMARK 465 ALA B 7 REMARK 465 LEU B 8 REMARK 465 LEU B 9 REMARK 465 VAL B 10 REMARK 465 TRP B 11 REMARK 465 ILE B 12 REMARK 465 LEU B 13 REMARK 465 THR B 14 REMARK 465 SER B 15 REMARK 465 PRO B 16 REMARK 465 SER B 17 REMARK 465 SER B 18 REMARK 465 SER B 19 REMARK 465 ASP B 20 REMARK 465 HIS B 21 REMARK 465 GLY B 22 REMARK 465 SER B 23 REMARK 465 GLU B 24 REMARK 465 ASN B 25 REMARK 465 GLU B 103 REMARK 465 GLU B 104 REMARK 465 ASP B 105 REMARK 465 GLN B 106 REMARK 465 PRO B 107 REMARK 465 LYS B 108 REMARK 465 MET C 1 REMARK 465 ASN C 2 REMARK 465 GLY C 3 REMARK 465 VAL C 4 REMARK 465 ALA C 5 REMARK 465 ALA C 6 REMARK 465 ALA C 7 REMARK 465 LEU C 8 REMARK 465 LEU C 9 REMARK 465 VAL C 10 REMARK 465 TRP C 11 REMARK 465 ILE C 12 REMARK 465 LEU C 13 REMARK 465 THR C 14 REMARK 465 SER C 15 REMARK 465 PRO C 16 REMARK 465 SER C 17 REMARK 465 SER C 18 REMARK 465 SER C 19 REMARK 465 ASP C 20 REMARK 465 HIS C 21 REMARK 465 GLY C 22 REMARK 465 SER C 23 REMARK 465 GLU C 24 REMARK 465 ASN C 25 REMARK 465 GLU C 103 REMARK 465 GLU C 104 REMARK 465 ASP C 105 REMARK 465 GLN C 106 REMARK 465 PRO C 107 REMARK 465 LYS C 108 REMARK 465 MET D 1 REMARK 465 ASN D 2 REMARK 465 GLY D 3 REMARK 465 VAL D 4 REMARK 465 ALA D 5 REMARK 465 ALA D 6 REMARK 465 ALA D 7 REMARK 465 LEU D 8 REMARK 465 LEU D 9 REMARK 465 VAL D 10 REMARK 465 TRP D 11 REMARK 465 ILE D 12 REMARK 465 LEU D 13 REMARK 465 THR D 14 REMARK 465 SER D 15 REMARK 465 PRO D 16 REMARK 465 SER D 17 REMARK 465 SER D 18 REMARK 465 SER D 19 REMARK 465 ASP D 20 REMARK 465 HIS D 21 REMARK 465 GLY D 22 REMARK 465 SER D 23 REMARK 465 GLU D 24 REMARK 465 ASN D 25 REMARK 465 GLU D 103 REMARK 465 GLU D 104 REMARK 465 ASP D 105 REMARK 465 GLN D 106 REMARK 465 PRO D 107 REMARK 465 LYS D 108 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 ASP D 50 CB - CG - OD2 ANGL. DEV. = 5.5 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 127 52.36 -96.82 REMARK 500 ASN A 146 -168.25 -101.69 REMARK 500 ARG B 79 -61.73 -105.24 REMARK 500 ASN D 34 94.10 -163.56 REMARK 500 ASN D 127 63.47 -103.26 REMARK 500 ASN D 146 -167.29 -101.19 REMARK 500 REMARK 500 REMARK: NULL DBREF 3M7O A 1 162 UNP O88188 LY86_MOUSE 1 162 DBREF 3M7O B 1 162 UNP O88188 LY86_MOUSE 1 162 DBREF 3M7O C 1 162 UNP O88188 LY86_MOUSE 1 162 DBREF 3M7O D 1 162 UNP O88188 LY86_MOUSE 1 162 SEQRES 1 A 162 MET ASN GLY VAL ALA ALA ALA LEU LEU VAL TRP ILE LEU SEQRES 2 A 162 THR SER PRO SER SER SER ASP HIS GLY SER GLU ASN GLY SEQRES 3 A 162 TRP PRO LYS HIS THR ALA CYS ASN SER GLY GLY LEU GLU SEQRES 4 A 162 VAL VAL TYR GLN SER CYS ASP PRO LEU GLN ASP PHE GLY SEQRES 5 A 162 LEU SER ILE ASP GLN CYS SER LYS GLN ILE GLN SER ASN SEQRES 6 A 162 LEU ASN ILE ARG PHE GLY ILE ILE LEU ARG GLN ASP ILE SEQRES 7 A 162 ARG LYS LEU PHE LEU ASP ILE THR LEU MET ALA LYS GLY SEQRES 8 A 162 SER SER ILE LEU ASN TYR SER TYR PRO LEU CYS GLU GLU SEQRES 9 A 162 ASP GLN PRO LYS PHE SER PHE CYS GLY ARG ARG LYS GLY SEQRES 10 A 162 GLU GLN ILE TYR TYR ALA GLY PRO VAL ASN ASN PRO GLY SEQRES 11 A 162 LEU ASP VAL PRO GLN GLY GLU TYR GLN LEU LEU LEU GLU SEQRES 12 A 162 LEU TYR ASN GLU ASN ARG ALA THR VAL ALA CYS ALA ASN SEQRES 13 A 162 ALA THR VAL THR SER SER SEQRES 1 B 162 MET ASN GLY VAL ALA ALA ALA LEU LEU VAL TRP ILE LEU SEQRES 2 B 162 THR SER PRO SER SER SER ASP HIS GLY SER GLU ASN GLY SEQRES 3 B 162 TRP PRO LYS HIS THR ALA CYS ASN SER GLY GLY LEU GLU SEQRES 4 B 162 VAL VAL TYR GLN SER CYS ASP PRO LEU GLN ASP PHE GLY SEQRES 5 B 162 LEU SER ILE ASP GLN CYS SER LYS GLN ILE GLN SER ASN SEQRES 6 B 162 LEU ASN ILE ARG PHE GLY ILE ILE LEU ARG GLN ASP ILE SEQRES 7 B 162 ARG LYS LEU PHE LEU ASP ILE THR LEU MET ALA LYS GLY SEQRES 8 B 162 SER SER ILE LEU ASN TYR SER TYR PRO LEU CYS GLU GLU SEQRES 9 B 162 ASP GLN PRO LYS PHE SER PHE CYS GLY ARG ARG LYS GLY SEQRES 10 B 162 GLU GLN ILE TYR TYR ALA GLY PRO VAL ASN ASN PRO GLY SEQRES 11 B 162 LEU ASP VAL PRO GLN GLY GLU TYR GLN LEU LEU LEU GLU SEQRES 12 B 162 LEU TYR ASN GLU ASN ARG ALA THR VAL ALA CYS ALA ASN SEQRES 13 B 162 ALA THR VAL THR SER SER SEQRES 1 C 162 MET ASN GLY VAL ALA ALA ALA LEU LEU VAL TRP ILE LEU SEQRES 2 C 162 THR SER PRO SER SER SER ASP HIS GLY SER GLU ASN GLY SEQRES 3 C 162 TRP PRO LYS HIS THR ALA CYS ASN SER GLY GLY LEU GLU SEQRES 4 C 162 VAL VAL TYR GLN SER CYS ASP PRO LEU GLN ASP PHE GLY SEQRES 5 C 162 LEU SER ILE ASP GLN CYS SER LYS GLN ILE GLN SER ASN SEQRES 6 C 162 LEU ASN ILE ARG PHE GLY ILE ILE LEU ARG GLN ASP ILE SEQRES 7 C 162 ARG LYS LEU PHE LEU ASP ILE THR LEU MET ALA LYS GLY SEQRES 8 C 162 SER SER ILE LEU ASN TYR SER TYR PRO LEU CYS GLU GLU SEQRES 9 C 162 ASP GLN PRO LYS PHE SER PHE CYS GLY ARG ARG LYS GLY SEQRES 10 C 162 GLU GLN ILE TYR TYR ALA GLY PRO VAL ASN ASN PRO GLY SEQRES 11 C 162 LEU ASP VAL PRO GLN GLY GLU TYR GLN LEU LEU LEU GLU SEQRES 12 C 162 LEU TYR ASN GLU ASN ARG ALA THR VAL ALA CYS ALA ASN SEQRES 13 C 162 ALA THR VAL THR SER SER SEQRES 1 D 162 MET ASN GLY VAL ALA ALA ALA LEU LEU VAL TRP ILE LEU SEQRES 2 D 162 THR SER PRO SER SER SER ASP HIS GLY SER GLU ASN GLY SEQRES 3 D 162 TRP PRO LYS HIS THR ALA CYS ASN SER GLY GLY LEU GLU SEQRES 4 D 162 VAL VAL TYR GLN SER CYS ASP PRO LEU GLN ASP PHE GLY SEQRES 5 D 162 LEU SER ILE ASP GLN CYS SER LYS GLN ILE GLN SER ASN SEQRES 6 D 162 LEU ASN ILE ARG PHE GLY ILE ILE LEU ARG GLN ASP ILE SEQRES 7 D 162 ARG LYS LEU PHE LEU ASP ILE THR LEU MET ALA LYS GLY SEQRES 8 D 162 SER SER ILE LEU ASN TYR SER TYR PRO LEU CYS GLU GLU SEQRES 9 D 162 ASP GLN PRO LYS PHE SER PHE CYS GLY ARG ARG LYS GLY SEQRES 10 D 162 GLU GLN ILE TYR TYR ALA GLY PRO VAL ASN ASN PRO GLY SEQRES 11 D 162 LEU ASP VAL PRO GLN GLY GLU TYR GLN LEU LEU LEU GLU SEQRES 12 D 162 LEU TYR ASN GLU ASN ARG ALA THR VAL ALA CYS ALA ASN SEQRES 13 D 162 ALA THR VAL THR SER SER MODRES 3M7O ASN A 96 ASN GLYCOSYLATION SITE MODRES 3M7O ASN A 156 ASN GLYCOSYLATION SITE MODRES 3M7O ASN D 96 ASN GLYCOSYLATION SITE MODRES 3M7O ASN D 156 ASN GLYCOSYLATION SITE MODRES 3M7O ASN C 96 ASN GLYCOSYLATION SITE MODRES 3M7O ASN C 156 ASN GLYCOSYLATION SITE MODRES 3M7O ASN B 156 ASN GLYCOSYLATION SITE MODRES 3M7O ASN B 96 ASN GLYCOSYLATION SITE HET NAG A 201 14 HET NAG A 202 14 HET L9R A 301 54 HET BEN A 163 9 HET BEN A 164 9 HET BEN A 165 9 HET BEN A 166 9 HET BEN A 167 9 HET NAG B 201 14 HET NAG B 202 14 HET BEN B 163 9 HET BEN B 164 9 HET BEN B 165 9 HET NAG C 201 14 HET NAG C 202 14 HET BEN C 163 9 HET BEN C 164 9 HET BEN C 165 9 HET NAG D 201 14 HET NAG D 202 14 HET L9R D 301 54 HET BEN D 163 9 HET BEN D 164 9 HET BEN D 165 9 HET BEN D 166 9 HET BEN D 167 9 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM L9R (2S)-3-(OCTADECANOYLOXY)-2-[(9Z)-OCTADEC-9- HETNAM 2 L9R ENOYLOXY]PROPYL 2-(TRIMETHYLAMMONIO)ETHYL PHOSPHATE HETNAM BEN BENZAMIDINE 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 L9R 1-STEAROYL-2-OLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE FORMUL 5 NAG 8(C8 H15 N O6) FORMUL 7 L9R 2(C44 H86 N O8 P) FORMUL 8 BEN 16(C7 H8 N2) FORMUL 31 HOH *444(H2 O) SHEET 1 A12 HIS A 30 SER A 35 0 SHEET 2 A12 LEU A 38 SER A 44 -1 O VAL A 40 N CYS A 33 SHEET 3 A12 THR A 151 SER A 161 -1 O THR A 158 N VAL A 41 SHEET 4 A12 GLY A 136 ASN A 146 -1 N LEU A 144 O VAL A 152 SHEET 5 A12 LYS A 80 ALA A 89 -1 N MET A 88 O GLN A 139 SHEET 6 A12 SER A 92 GLU A 103 -1 O LEU A 95 N LEU A 87 SHEET 7 A12 SER B 92 PRO B 100 -1 O ASN B 96 N ASN A 96 SHEET 8 A12 PHE B 82 ALA B 89 -1 N ILE B 85 O TYR B 97 SHEET 9 A12 GLY B 136 TYR B 145 -1 O GLU B 143 N ASP B 84 SHEET 10 A12 THR B 151 SER B 161 -1 O ALA B 155 N LEU B 142 SHEET 11 A12 LEU B 38 SER B 44 -1 N GLU B 39 O THR B 160 SHEET 12 A12 HIS B 30 SER B 35 -1 N HIS B 30 O TYR B 42 SHEET 1 B 3 GLY A 52 ILE A 55 0 SHEET 2 B 3 ASN A 67 ILE A 73 -1 O GLY A 71 N GLY A 52 SHEET 3 B 3 GLN A 119 PRO A 125 -1 O ILE A 120 N ILE A 72 SHEET 1 C 4 GLN A 61 ILE A 62 0 SHEET 2 C 4 GLY A 130 ASP A 132 -1 O LEU A 131 N ILE A 62 SHEET 3 C 4 LEU B 131 ASP B 132 -1 O ASP B 132 N GLY A 130 SHEET 4 C 4 GLN B 61 ILE B 62 -1 N ILE B 62 O LEU B 131 SHEET 1 D 3 GLY B 52 ILE B 55 0 SHEET 2 D 3 ASN B 67 ILE B 73 -1 O GLY B 71 N GLY B 52 SHEET 3 D 3 GLN B 119 PRO B 125 -1 O ILE B 120 N ILE B 72 SHEET 1 E12 HIS C 30 SER C 35 0 SHEET 2 E12 LEU C 38 SER C 44 -1 O TYR C 42 N HIS C 30 SHEET 3 E12 THR C 151 SER C 161 -1 O THR C 158 N VAL C 41 SHEET 4 E12 GLY C 136 ASN C 146 -1 N LEU C 142 O ALA C 155 SHEET 5 E12 LEU C 81 ALA C 89 -1 N MET C 88 O GLN C 139 SHEET 6 E12 SER C 92 PRO C 100 -1 O TYR C 97 N ILE C 85 SHEET 7 E12 SER D 92 CYS D 102 -1 O ASN D 96 N ASN C 96 SHEET 8 E12 LEU D 81 ALA D 89 -1 N LEU D 81 O LEU D 101 SHEET 9 E12 GLY D 136 ASN D 146 -1 O GLU D 143 N ASP D 84 SHEET 10 E12 THR D 151 SER D 161 -1 O ALA D 157 N LEU D 140 SHEET 11 E12 LEU D 38 SER D 44 -1 N GLU D 39 O THR D 160 SHEET 12 E12 HIS D 30 SER D 35 -1 N CYS D 33 O VAL D 40 SHEET 1 F 3 GLY C 52 ILE C 55 0 SHEET 2 F 3 ASN C 67 ILE C 73 -1 O GLY C 71 N GLY C 52 SHEET 3 F 3 GLN C 119 PRO C 125 -1 O TYR C 122 N PHE C 70 SHEET 1 G 4 GLN C 61 ILE C 62 0 SHEET 2 G 4 LEU C 131 ASP C 132 -1 O LEU C 131 N ILE C 62 SHEET 3 G 4 GLY D 130 ASP D 132 -1 O GLY D 130 N ASP C 132 SHEET 4 G 4 GLN D 61 ILE D 62 -1 N ILE D 62 O LEU D 131 SHEET 1 H 3 GLY D 52 ILE D 55 0 SHEET 2 H 3 ASN D 67 ILE D 73 -1 O ARG D 69 N SER D 54 SHEET 3 H 3 GLN D 119 PRO D 125 -1 O ILE D 120 N ILE D 72 SSBOND 1 CYS A 33 CYS A 58 1555 1555 2.00 SSBOND 2 CYS A 45 CYS A 154 1555 1555 2.06 SSBOND 3 CYS A 102 CYS A 112 1555 1555 2.03 SSBOND 4 CYS B 33 CYS B 58 1555 1555 2.00 SSBOND 5 CYS B 45 CYS B 154 1555 1555 2.06 SSBOND 6 CYS B 102 CYS B 112 1555 1555 2.04 SSBOND 7 CYS C 33 CYS C 58 1555 1555 2.03 SSBOND 8 CYS C 45 CYS C 154 1555 1555 2.06 SSBOND 9 CYS C 102 CYS C 112 1555 1555 2.00 SSBOND 10 CYS D 33 CYS D 58 1555 1555 2.01 SSBOND 11 CYS D 45 CYS D 154 1555 1555 2.06 SSBOND 12 CYS D 102 CYS D 112 1555 1555 2.02 LINK ND2 ASN A 96 C1 NAG A 202 1555 1555 1.43 LINK ND2 ASN A 156 C1 NAG A 201 1555 1555 1.43 LINK ND2 ASN B 96 C1 NAG B 202 1555 1555 1.45 LINK ND2 ASN B 156 C1 NAG B 201 1555 1555 1.45 LINK ND2 ASN C 96 C1 NAG C 202 1555 1555 1.45 LINK ND2 ASN C 156 C1 NAG C 201 1555 1555 1.45 LINK ND2 ASN D 96 C1 NAG D 202 1555 1555 1.43 LINK ND2 ASN D 156 C1 NAG D 201 1555 1555 1.44 CISPEP 1 GLN A 106 PRO A 107 0 -1.41 CRYST1 90.299 90.299 86.714 90.00 90.00 90.00 P 43 16 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 0.011074 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011074 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011532 0.00000