HEADER IMMUNE SYSTEM 18-MAY-06 2H26
TITLE HUMAN CD1B IN COMPLEX WITH ENDOGENOUS PHOSPHATIDYLCHOLINE AND SPACER
CAVEAT 2H26 FUC C 2 HAS WRONG CHIRALITY AT ATOM C1 FUC D 2 HAS WRONG
CAVEAT 2 2H26 CHIRALITY AT ATOM C1
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: T-CELL SURFACE GLYCOPROTEIN CD1B;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: EXTRACELLULAR DOMAIN OF CD1B ANTIGEN;
COMPND 5 SYNONYM: CD1B ANTIGEN;
COMPND 6 ENGINEERED: YES;
COMPND 7 MUTATION: YES;
COMPND 8 MOL_ID: 2;
COMPND 9 MOLECULE: BETA-2-MICROGLOBULIN;
COMPND 10 CHAIN: B;
COMPND 11 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: CD1B;
SOURCE 6 EXPRESSION_SYSTEM: MUS MUSCULUS;
SOURCE 7 EXPRESSION_SYSTEM_COMMON: HOUSE MOUSE;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 10090;
SOURCE 9 EXPRESSION_SYSTEM_STRAIN: J558 CELL;
SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 11 EXPRESSION_SYSTEM_PLASMID: BCMGSNEO;
SOURCE 12 MOL_ID: 2;
SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 14 ORGANISM_COMMON: HUMAN;
SOURCE 15 ORGANISM_TAXID: 9606;
SOURCE 16 GENE: B2M;
SOURCE 17 EXPRESSION_SYSTEM: MUS MUSCULUS;
SOURCE 18 EXPRESSION_SYSTEM_COMMON: HOUSE MOUSE;
SOURCE 19 EXPRESSION_SYSTEM_TAXID: 10090;
SOURCE 20 EXPRESSION_SYSTEM_STRAIN: J558 CELL
KEYWDS LIPID, ENDOGENOUS LIGAND, PHOSPHATIDYLCHOLINE, MHC, ANTIGEN
KEYWDS 2 PRESENTATION, GLYCOPROTEIN, IMMUNE SYSTEM
EXPDTA X-RAY DIFFRACTION
AUTHOR L.F.GARCIA-ALLES,L.MAVEYRAUD,A.T.VALLINA,V.GUILLET,L.MOUREY
REVDAT 6 30-AUG-23 2H26 1 HETSYN
REVDAT 5 29-JUL-20 2H26 1 CAVEAT COMPND REMARK HETNAM
REVDAT 5 2 1 LINK SITE ATOM
REVDAT 4 13-JUL-11 2H26 1 VERSN
REVDAT 3 24-FEB-09 2H26 1 VERSN
REVDAT 2 22-AUG-06 2H26 1 JRNL
REVDAT 1 04-JUL-06 2H26 0
JRNL AUTH L.F.GARCIA-ALLES,K.VERSLUIS,L.MAVEYRAUD,A.T.VALLINA,
JRNL AUTH 2 S.SANSANO,N.F.BELLO,H.J.GOBER,V.GUILLET,H.DE LA SALLE,
JRNL AUTH 3 G.PUZO,L.MORI,A.J.HECK,G.DE LIBERO,L.MOUREY
JRNL TITL ENDOGENOUS PHOSPHATIDYLCHOLINE AND A LONG SPACER LIGAND
JRNL TITL 2 STABILIZE THE LIPID-BINDING GROOVE OF CD1B.
JRNL REF EMBO J. V. 25 3684 2006
JRNL REFN ISSN 0261-4189
JRNL PMID 16874306
JRNL DOI 10.1038/SJ.EMBOJ.7601244
REMARK 2
REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0019
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) : 20.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0
REMARK 3 NUMBER OF REFLECTIONS : 41074
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) : 0.207
REMARK 3 R VALUE (WORKING SET) : 0.205
REMARK 3 FREE R VALUE : 0.241
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 2181
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) : 2516
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.60
REMARK 3 BIN R VALUE (WORKING SET) : 0.2520
REMARK 3 BIN FREE R VALUE SET COUNT : 123
REMARK 3 BIN FREE R VALUE : 0.3000
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2980
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 158
REMARK 3 SOLVENT ATOMS : 265
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 27.00
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.61
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 1.57000
REMARK 3 B22 (A**2) : 0.32000
REMARK 3 B33 (A**2) : -1.89000
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): 0.135
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.129
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.090
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.867
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953
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): 3246 ; 0.016 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4401 ; 1.608 ; 1.977
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 383 ; 6.221 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 146 ;34.634 ;23.904
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 467 ;12.778 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;21.193 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 464 ; 0.113 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2447 ; 0.007 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1361 ; 0.202 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2185 ; 0.313 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 268 ; 0.154 ; 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): 44 ; 0.184 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.278 ; 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): 1973 ; 1.150 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3058 ; 1.755 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1482 ; 2.686 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1343 ; 4.076 ; 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 : 1.20
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 2H26 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAY-06.
REMARK 100 THE DEPOSITION ID IS D_1000037835.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 04-JUL-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 : ESRF
REMARK 200 BEAMLINE : ID14-4
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9756
REMARK 200 MONOCHROMATOR : KHOZU MONOCHROMATOR WITH DUAL
REMARK 200 PARALLEL SI(111) CRYSTALS
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA)
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43311
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800
REMARK 200 RESOLUTION RANGE LOW (A) : 32.720
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4
REMARK 200 DATA REDUNDANCY : 3.500
REMARK 200 R MERGE (I) : 0.06800
REMARK 200 R SYM (I) : 0.06800
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.8000
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 (%) : 85.5
REMARK 200 DATA REDUNDANCY IN SHELL : 2.30
REMARK 200 R MERGE FOR SHELL (I) : 0.19800
REMARK 200 R SYM FOR SHELL (I) : 0.19800
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.500
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 1GZP
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 54.50
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M AMMONIUM SULFATE 5 % (V/V)
REMARK 280 ISOPROPANOL 0.1 M NA CITRATE, PH 5.5, VAPOR DIFFUSION, HANGING
REMARK 280 DROP, TEMPERATURE 293K
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 19.91400
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.41450
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.94900
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.41450
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.91400
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.94900
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: THE ASYMMETRIC UNIT CONTAINS THE BIOLOGICAL HETERODIMER
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: 8090 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 17750 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -78.0 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 GLU A 1
REMARK 465 HIS A 2
REMARK 465 ALA A 3
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 61 CG CD CE NZ
REMARK 470 LYS A 91 CG CD CE NZ
REMARK 470 LYS A 127 CD CE NZ
REMARK 470 ASN A 128 OD1 ND2
REMARK 470 GLN A 142 CD OE1 NE2
REMARK 470 LYS A 143 NZ
REMARK 470 ILE A 148 CD1
REMARK 470 LYS A 178 CE NZ
REMARK 470 ILE B 1 CG1 CG2 CD1
REMARK 470 LYS B 19 CD CE NZ
REMARK 470 ARG B 45 CZ NH1 NH2
REMARK 470 GLU B 47 CD OE1 OE2
REMARK 470 LYS B 48 CG CD CE NZ
REMARK 470 LYS B 58 CD CE NZ
REMARK 470 LYS B 75 CG CD CE NZ
REMARK 470 GLU B 77 CD OE1 OE2
REMARK 470 LYS B 91 CD CE NZ
REMARK 470 LYS B 94 CE NZ
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 ND2 ASN A 20 C2 NAG C 1 2.17
REMARK 500 O GLU A 224 O HOH A 1080 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 O HOH A 976 O HOH A 1079 3545 1.94
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 ARG B 12 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 ARG B 12 NE - CZ - NH2 ANGL. DEV. = -3.0 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 ASP A 33 -117.26 45.57
REMARK 500 SER A 106 -112.80 24.89
REMARK 500 ASN A 128 57.79 37.60
REMARK 500 GLN A 271 29.06 -140.82
REMARK 500 TRP B 60 -2.32 77.01
REMARK 500
REMARK 500 REMARK: NULL
REMARK 600
REMARK 600 HETEROGEN
REMARK 600 AUTHOR STATES THAT THIS LIGAND IS FROM UNKNOWN
REMARK 600 ENDOGENOUS LIGAND. TETRACOSYL PALMITATE WAS
REMARK 600 MODELLED AS PROPOSITION. THIS STRUCTURE IS
REMARK 600 PROVIDED JUST AS STARTING HYPOTHESIS. THE REAL
REMARK 600 IDENTITY OF THIS LIGAND IS A MATTER OF SPECULATION.
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 THE C-TERMINAL RESIDUES ON CD1B ANTIGEN,
REMARK 999 IDKLGGGLNDIFEAQKIEWHE, IS A BIRA PEPTIDE TAG.
REMARK 999 HOWEVER, AMONG THE LAST 20 RESIDUES, ONLY 5 RESIDUES
REMARK 999 ARE OBSERVED. THESE 5 RESIDUES ARE MODELLED AS ALA
REMARK 999 AND NUMBERED 901-905. THE SEQUENCE ALIGNMENT OF THESE
REMARK 999 FIVE ALA RESIDUES ARE UNKNOWN. THESE RESIDUES ARE
REMARK 999 CHANGED TO UNK AS UNKNOWN AMINO ACIDS.
DBREF 2H26 A 1 280 UNP P29016 CD1B_HUMAN 19 298
DBREF 2H26 B 1 99 UNP P61769 B2MG_HUMAN 21 119
SEQADV 2H26 ILE A 281 UNP P29016 SEE REMARK 999
SEQADV 2H26 UNK A 901 UNP P29016 SEE REMARK 999
SEQADV 2H26 UNK A 902 UNP P29016 SEE REMARK 999
SEQADV 2H26 UNK A 903 UNP P29016 SEE REMARK 999
SEQADV 2H26 UNK A 904 UNP P29016 SEE REMARK 999
SEQADV 2H26 UNK A 905 UNP P29016 SEE REMARK 999
SEQRES 1 A 286 GLU HIS ALA PHE GLN GLY PRO THR SER PHE HIS VAL ILE
SEQRES 2 A 286 GLN THR SER SER PHE THR ASN SER THR TRP ALA GLN THR
SEQRES 3 A 286 GLN GLY SER GLY TRP LEU ASP ASP LEU GLN ILE HIS GLY
SEQRES 4 A 286 TRP ASP SER ASP SER GLY THR ALA ILE PHE LEU LYS PRO
SEQRES 5 A 286 TRP SER LYS GLY ASN PHE SER ASP LYS GLU VAL ALA GLU
SEQRES 6 A 286 LEU GLU GLU ILE PHE ARG VAL TYR ILE PHE GLY PHE ALA
SEQRES 7 A 286 ARG GLU VAL GLN ASP PHE ALA GLY ASP PHE GLN MET LYS
SEQRES 8 A 286 TYR PRO PHE GLU ILE GLN GLY ILE ALA GLY CYS GLU LEU
SEQRES 9 A 286 HIS SER GLY GLY ALA ILE VAL SER PHE LEU ARG GLY ALA
SEQRES 10 A 286 LEU GLY GLY LEU ASP PHE LEU SER VAL LYS ASN ALA SER
SEQRES 11 A 286 CYS VAL PRO SER PRO GLU GLY GLY SER ARG ALA GLN LYS
SEQRES 12 A 286 PHE CYS ALA LEU ILE ILE GLN TYR GLN GLY ILE MET GLU
SEQRES 13 A 286 THR VAL ARG ILE LEU LEU TYR GLU THR CYS PRO ARG TYR
SEQRES 14 A 286 LEU LEU GLY VAL LEU ASN ALA GLY LYS ALA ASP LEU GLN
SEQRES 15 A 286 ARG GLN VAL LYS PRO GLU ALA TRP LEU SER SER GLY PRO
SEQRES 16 A 286 SER PRO GLY PRO GLY ARG LEU GLN LEU VAL CYS HIS VAL
SEQRES 17 A 286 SER GLY PHE TYR PRO LYS PRO VAL TRP VAL MET TRP MET
SEQRES 18 A 286 ARG GLY GLU GLN GLU GLN GLN GLY THR GLN LEU GLY ASP
SEQRES 19 A 286 ILE LEU PRO ASN ALA ASN TRP THR TRP TYR LEU ARG ALA
SEQRES 20 A 286 THR LEU ASP VAL ALA ASP GLY GLU ALA ALA GLY LEU SER
SEQRES 21 A 286 CYS ARG VAL LYS HIS SER SER LEU GLU GLY GLN ASP ILE
SEQRES 22 A 286 ILE LEU TYR TRP ARG ASN PRO ILE UNK UNK UNK UNK UNK
SEQRES 1 B 99 ILE GLN ARG THR PRO LYS ILE GLN VAL TYR SER ARG HIS
SEQRES 2 B 99 PRO ALA GLU ASN GLY LYS SER ASN PHE LEU ASN CYS TYR
SEQRES 3 B 99 VAL SER GLY PHE HIS PRO SER ASP ILE GLU VAL ASP LEU
SEQRES 4 B 99 LEU LYS ASN GLY GLU ARG ILE GLU LYS VAL GLU HIS SER
SEQRES 5 B 99 ASP LEU SER PHE SER LYS ASP TRP SER PHE TYR LEU LEU
SEQRES 6 B 99 TYR TYR THR GLU PHE THR PRO THR GLU LYS ASP GLU TYR
SEQRES 7 B 99 ALA CYS ARG VAL ASN HIS VAL THR LEU SER GLN PRO LYS
SEQRES 8 B 99 ILE VAL LYS TRP ASP ARG ASP MET
MODRES 2H26 ASN A 20 ASN GLYCOSYLATION SITE
MODRES 2H26 ASN A 57 ASN GLYCOSYLATION SITE
HET NAG C 1 14
HET FUC C 2 10
HET NAG D 1 14
HET FUC D 2 10
HET 6PL A 311 52
HET 6UL A 312 42
HET GOL A 303 6
HET SO4 B 301 5
HET SO4 B 302 5
HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE
HETNAM FUC ALPHA-L-FUCOPYRANOSE
HETNAM 6PL (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-
HETNAM 2 6PL [(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-
HETNAM 3 6PL PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
HETNAM 6UL TETRACOSYL PALMITATE
HETNAM GOL GLYCEROL
HETNAM SO4 SULFATE ION
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 FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L-
HETSYN 2 FUC FUCOSE; FUCOSE
HETSYN 6PL 1-PALMITOYL-2-STEAROYL-SN-GLYCERO-3-PHOSPHOCHOLINE
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 3 NAG 2(C8 H15 N O6)
FORMUL 3 FUC 2(C6 H12 O5)
FORMUL 5 6PL C42 H85 N O8 P 1+
FORMUL 6 6UL C40 H80 O2
FORMUL 7 GOL C3 H8 O3
FORMUL 8 SO4 2(O4 S 2-)
FORMUL 10 HOH *265(H2 O)
HELIX 1 1 SER A 59 ALA A 85 1 27
HELIX 2 2 GLY A 137 ILE A 149 1 13
HELIX 3 3 TYR A 151 GLU A 164 1 14
HELIX 4 4 GLU A 164 GLY A 177 1 14
HELIX 5 5 GLY A 177 GLN A 182 1 6
HELIX 6 6 GLY A 254 ALA A 256 5 3
HELIX 7 7 SER A 267 GLU A 269 5 3
SHEET 1 A 8 THR A 46 PHE A 49 0
SHEET 2 A 8 LEU A 35 ASP A 41 -1 N ASP A 41 O THR A 46
SHEET 3 A 8 TRP A 23 LEU A 32 -1 N LEU A 32 O LEU A 35
SHEET 4 A 8 SER A 9 ASN A 20 -1 N THR A 15 O GLN A 27
SHEET 5 A 8 PHE A 94 LEU A 104 -1 O ILE A 96 N SER A 16
SHEET 6 A 8 ILE A 110 LEU A 118 -1 O PHE A 113 N GLY A 101
SHEET 7 A 8 LEU A 121 LYS A 127 -1 O PHE A 123 N GLY A 116
SHEET 8 A 8 SER A 130 PRO A 133 -1 O VAL A 132 N SER A 125
SHEET 1 B 3 GLN A 231 LEU A 232 0
SHEET 2 B 3 TRP A 243 ALA A 252 -1 O THR A 248 N GLN A 231
SHEET 3 B 3 LEU A 236 PRO A 237 -1 N LEU A 236 O TYR A 244
SHEET 1 C 5 GLN A 231 LEU A 232 0
SHEET 2 C 5 TRP A 243 ALA A 252 -1 O THR A 248 N GLN A 231
SHEET 3 C 5 ARG A 201 PHE A 211 -1 N LEU A 204 O LEU A 249
SHEET 4 C 5 GLU A 188 GLY A 194 -1 N TRP A 190 O HIS A 207
SHEET 5 C 5 UNK A 903 UNK A 904 -1 O UNK A 904 N ALA A 189
SHEET 1 D 4 GLN A 225 GLU A 226 0
SHEET 2 D 4 VAL A 216 ARG A 222 -1 N ARG A 222 O GLN A 225
SHEET 3 D 4 LEU A 259 HIS A 265 -1 O ARG A 262 N MET A 219
SHEET 4 D 4 ILE A 273 TYR A 276 -1 O LEU A 275 N CYS A 261
SHEET 1 E 4 LYS 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 TYR B 66 N CYS B 25
SHEET 4 E 4 GLU B 50 HIS B 51 -1 N GLU B 50 O TYR B 67
SHEET 1 F 4 LYS 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 TYR 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 GLU B 44 ARG B 45 0
SHEET 2 G 4 GLU B 36 LYS B 41 -1 N LYS B 41 O GLU B 44
SHEET 3 G 4 TYR B 78 ASN B 83 -1 O ARG B 81 N ASP B 38
SHEET 4 G 4 LYS B 91 LYS B 94 -1 O LYS B 91 N VAL B 82
SSBOND 1 CYS A 102 CYS A 166 1555 1555 2.17
SSBOND 2 CYS A 131 CYS A 145 1555 1555 2.06
SSBOND 3 CYS A 206 CYS A 261 1555 1555 2.03
SSBOND 4 CYS B 25 CYS B 80 1555 1555 2.06
LINK ND2 ASN A 20 C1 NAG C 1 1555 1555 1.43
LINK ND2 ASN A 57 C1 NAG D 1 1555 1555 1.43
LINK O6 NAG C 1 C1 FUC C 2 1555 1555 1.45
LINK O6 NAG D 1 C1 FUC D 2 1555 1555 1.43
CISPEP 1 TYR A 92 PRO A 93 0 -12.22
CISPEP 2 TYR A 212 PRO A 213 0 -0.96
CISPEP 3 HIS B 31 PRO B 32 0 3.12
CRYST1 39.828 103.898 114.829 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 0.025108 0.000000 0.000000 0.00000
SCALE2 0.000000 0.009625 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008709 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
