HEADER IMMUNE SYSTEM 02-JAN-02 1KPV TITLE HIGH RESOLUTION CRYSTAL STRUCTURE OF THE MHC CLASS I COMPLEX H- TITLE 2 2KB/SEV9 CAVEAT 1KPV NAG C 2 HAS WRONG CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EXTRACELLULAR DOMAIN, SEQUENCE DATABASE RESIDUES 22-295, COMPND 5 NUMBERED 1-274; COMPND 6 SYNONYM: MHC CLASS I H-2KB HEAVY CHAIN; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: BETA-2-MICROGLOBULIN; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: SEQUENCE DATABASE RESIDUES 21-119, NUMBERED 1-99; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: NUCLEOCAPSID PROTEIN; COMPND 15 CHAIN: P; COMPND 16 FRAGMENT: SEQUENCE DATABASE RESIDUES 324-332, NUMBERED 1-9; COMPND 17 SYNONYM: SEV9, NUCLEOPROTEIN FRAGMENT; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: DROSOPHILA MELANOGASTER; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FRUIT FLY; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7227; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PRMHA-3; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 12 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 13 ORGANISM_TAXID: 10090; SOURCE 14 EXPRESSION_SYSTEM: DROSOPHILA MELANOGASTER; SOURCE 15 EXPRESSION_SYSTEM_COMMON: FRUIT FLY; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 7227; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_VECTOR: PRMHA-3; SOURCE 19 MOL_ID: 3; SOURCE 20 SYNTHETIC: YES; SOURCE 21 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE SOURCE 22 OF THE PEPTIDE IS FOUND NATURALLY IN SENDAI VIRUS. KEYWDS MAJOR HISTOCOMPATIBILITY COMPLEX, PEPTIDE-MHC, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR M.G.RUDOLPH,I.A.WILSON REVDAT 7 16-OCT-24 1KPV 1 REMARK REVDAT 6 16-AUG-23 1KPV 1 HETSYN LINK REVDAT 5 29-JUL-20 1KPV 1 CAVEAT COMPND REMARK HETNAM REVDAT 5 2 1 LINK SITE ATOM REVDAT 4 24-JUL-19 1KPV 1 REMARK LINK REVDAT 3 13-JUL-11 1KPV 1 VERSN REVDAT 2 24-FEB-09 1KPV 1 VERSN REVDAT 1 10-JUN-03 1KPV 0 JRNL AUTH M.G.RUDOLPH,I.A.WILSON JRNL TITL HIGH RESOLUTION CRYSTAL STRUCTURE OF H-2KB/VSV8 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.H.FREMONT,M.MATSUMURA,E.A.STURA,P.A.PETERSON,I.A.WILSON REMARK 1 TITL CRYSTAL STRUCTURES OF TWO VIRAL PEPTIDES IN COMPLEX WITH REMARK 1 TITL 2 MURINE MHC CLASS I H-2KB REMARK 1 REF SCIENCE V. 257 919 1992 REMARK 1 REFN ISSN 0036-8075 REMARK 2 REMARK 2 RESOLUTION. 1.71 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 54406 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) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2890 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) : 1.71 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.75 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3614 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2740 REMARK 3 BIN FREE R VALUE SET COUNT : 186 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3112 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 72 REMARK 3 SOLVENT ATOMS : 343 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.74000 REMARK 3 B22 (A**2) : 1.34000 REMARK 3 B33 (A**2) : -0.61000 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): 0.098 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.092 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.091 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.857 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3301 ; 0.017 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2842 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4489 ; 1.784 ; 1.961 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6628 ; 2.559 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 378 ; 4.734 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 589 ;17.040 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 464 ; 0.153 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3603 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 682 ; 0.006 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 609 ; 0.222 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2674 ; 0.210 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 5 ; 0.411 ; 0.500 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 368 ; 0.169 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.036 ; 0.500 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): 13 ; 0.155 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 41 ; 0.179 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 16 ; 0.229 ; 0.500 REMARK 3 SYMMETRY H-BOND OTHERS (A): 1 ; 0.190 ; 0.500 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): 1903 ; 1.088 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3081 ; 1.989 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1398 ; 3.054 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1408 ; 5.076 ; 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 : NULL 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 1KPV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JAN-02. REMARK 100 THE DEPOSITION ID IS D_1000015210. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-NOV-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60060 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 32.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05600 REMARK 200 FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.59100 REMARK 200 FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 2VAB CHAINS A AND B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: K/NA PHOSPHATE, MPD, PH 6.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 68.14350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.17100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 68.14350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.17100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, P, 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: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 14440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -130.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, P, 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 BIOMT1 2 -1.000000 0.000000 0.000000 136.28700 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 88.34200 REMARK 350 BIOMT3 2 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 ILE B 1 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 GLU A 32 O 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 SG CYS A 121 O HOH A 1039 2.03 REMARK 500 O PRO A 195 O HOH A 907 2.12 REMARK 500 O HOH B 723 O HOH B 768 2.15 REMARK 500 OE2 GLU B 69 O HOH B 772 2.17 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 ASP A 197 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP B 53 CB - CG - OD2 ANGL. DEV. = 5.9 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 29 -129.83 54.49 REMARK 500 ILE A 225 -34.87 -33.42 REMARK 500 ASN P 5 48.25 74.42 REMARK 500 TYR P 6 106.84 -58.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2VAB RELATED DB: PDB REMARK 900 THIS STRUCTURE IS A REDETERMINATION OF 2VAB TO HIGH RESOLUTION REMARK 900 RELATED ID: 1KPU RELATED DB: PDB REMARK 900 HIGH RESOLUTION CRYSTAL STRUCTURE OF THE MHC CLASS I COMPLEX H-2KB/ REMARK 900 VSV8 DBREF 1KPV A 1 274 UNP P01901 HA1B_MOUSE 22 295 DBREF 1KPV B 1 99 UNP P01887 B2MG_MOUSE 21 119 DBREF 1KPV P 1 9 GB 534831 AAB60593 324 332 SEQRES 1 A 274 GLY PRO HIS SER LEU ARG TYR PHE VAL THR ALA VAL SER SEQRES 2 A 274 ARG PRO GLY LEU GLY GLU PRO ARG TYR MET GLU VAL GLY SEQRES 3 A 274 TYR VAL ASP ASP THR GLU PHE VAL ARG PHE ASP SER ASP SEQRES 4 A 274 ALA GLU ASN PRO ARG TYR GLU PRO ARG ALA ARG TRP MET SEQRES 5 A 274 GLU GLN GLU GLY PRO GLU TYR TRP GLU ARG GLU THR GLN SEQRES 6 A 274 LYS ALA LYS GLY ASN GLU GLN SER PHE ARG VAL ASP LEU SEQRES 7 A 274 ARG THR LEU LEU GLY TYR TYR ASN GLN SER LYS GLY GLY SEQRES 8 A 274 SER HIS THR ILE GLN VAL ILE SER GLY CYS GLU VAL GLY SEQRES 9 A 274 SER ASP GLY ARG LEU LEU ARG GLY TYR GLN GLN TYR ALA SEQRES 10 A 274 TYR ASP GLY CYS ASP TYR ILE ALA LEU ASN GLU ASP LEU SEQRES 11 A 274 LYS THR TRP THR ALA ALA ASP MET ALA ALA LEU ILE THR SEQRES 12 A 274 LYS HIS LYS TRP GLU GLN ALA GLY GLU ALA GLU ARG LEU SEQRES 13 A 274 ARG ALA TYR LEU GLU GLY THR CYS VAL GLU TRP LEU ARG SEQRES 14 A 274 ARG TYR LEU LYS ASN GLY ASN ALA THR LEU LEU ARG THR SEQRES 15 A 274 ASP SER PRO LYS ALA HIS VAL THR HIS HIS SER ARG PRO SEQRES 16 A 274 GLU ASP LYS VAL THR LEU ARG CYS TRP ALA LEU GLY PHE SEQRES 17 A 274 TYR PRO ALA ASP ILE THR LEU THR TRP GLN LEU ASN GLY SEQRES 18 A 274 GLU GLU LEU ILE GLN ASP MET GLU LEU VAL GLU THR ARG SEQRES 19 A 274 PRO ALA GLY ASP GLY THR PHE GLN LYS TRP ALA SER VAL SEQRES 20 A 274 VAL VAL PRO LEU GLY LYS GLU GLN TYR TYR THR CYS HIS SEQRES 21 A 274 VAL TYR HIS GLN GLY LEU PRO GLU PRO LEU THR LEU ARG SEQRES 22 A 274 TRP 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 ASP SER MET ALA GLU PRO LYS SEQRES 8 B 99 THR VAL TYR TRP ASP ARG ASP MET SEQRES 1 P 9 PHE ALA PRO GLY ASN TYR PRO ALA LEU MODRES 1KPV ASN A 176 ASN GLYCOSYLATION SITE HET NAG C 1 14 HET NAG C 2 14 HET FUC C 3 10 HET PO4 A 801 5 HET PO4 A 802 5 HET MPD A 702 8 HET MPD B 701 8 HET MPD B 703 8 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM PO4 PHOSPHATE ION HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL 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 FORMUL 4 NAG 2(C8 H15 N O6) FORMUL 4 FUC C6 H12 O5 FORMUL 5 PO4 2(O4 P 3-) FORMUL 7 MPD 3(C6 H14 O2) FORMUL 10 HOH *343(H2 O) HELIX 1 1 ALA A 49 GLU A 55 5 7 HELIX 2 2 GLY A 56 ASN A 86 1 31 HELIX 3 3 ASP A 137 GLY A 151 1 15 HELIX 4 4 GLY A 151 GLY A 162 1 12 HELIX 5 5 GLY A 162 GLY A 175 1 14 HELIX 6 6 GLY A 175 LEU A 180 1 6 HELIX 7 7 ILE A 225 MET A 228 5 4 HELIX 8 8 LYS A 253 TYR A 257 5 5 SHEET 1 A 8 GLU A 46 PRO A 47 0 SHEET 2 A 8 THR A 31 ASP A 37 -1 N ARG A 35 O GLU A 46 SHEET 3 A 8 ARG A 21 VAL A 28 -1 N GLU A 24 O PHE A 36 SHEET 4 A 8 HIS A 3 VAL A 12 -1 N PHE A 8 O VAL A 25 SHEET 5 A 8 THR A 94 VAL A 103 -1 O VAL A 97 N VAL A 9 SHEET 6 A 8 LEU A 109 TYR A 118 -1 O LEU A 110 N GLU A 102 SHEET 7 A 8 CYS A 121 LEU A 126 -1 O ILE A 124 N TYR A 116 SHEET 8 A 8 TRP A 133 ALA A 135 -1 O THR A 134 N ALA A 125 SHEET 1 B 4 LYS A 186 SER A 193 0 SHEET 2 B 4 LYS A 198 PHE A 208 -1 O TRP A 204 N HIS A 188 SHEET 3 B 4 PHE A 241 PRO A 250 -1 O VAL A 249 N VAL A 199 SHEET 4 B 4 GLU A 229 LEU A 230 -1 N GLU A 229 O SER A 246 SHEET 1 C 4 LYS A 186 SER A 193 0 SHEET 2 C 4 LYS A 198 PHE A 208 -1 O TRP A 204 N HIS A 188 SHEET 3 C 4 PHE A 241 PRO A 250 -1 O VAL A 249 N VAL A 199 SHEET 4 C 4 ARG A 234 PRO A 235 -1 N ARG A 234 O GLN A 242 SHEET 1 D 4 GLU A 222 GLU A 223 0 SHEET 2 D 4 THR A 214 LEU A 219 -1 N LEU A 219 O GLU A 222 SHEET 3 D 4 THR A 258 TYR A 262 -1 O HIS A 260 N THR A 216 SHEET 4 D 4 LEU A 270 LEU A 272 -1 O LEU A 272 N CYS A 259 SHEET 1 E 4 GLN B 6 SER B 11 0 SHEET 2 E 4 ASN B 21 PHE B 30 -1 O THR B 28 N GLN B 6 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 PHE B 56 -1 N SER B 52 O LEU B 65 SHEET 1 F 4 LYS B 44 LYS B 45 0 SHEET 2 F 4 GLU B 36 LYS B 41 -1 N LYS B 41 O LYS B 44 SHEET 3 F 4 TYR B 78 LYS B 83 -1 O ALA B 79 N LEU B 40 SHEET 4 F 4 LYS B 91 TYR B 94 -1 O VAL B 93 N CYS B 80 SSBOND 1 CYS A 101 CYS A 164 1555 1555 2.13 SSBOND 2 CYS A 203 CYS A 259 1555 1555 2.02 SSBOND 3 CYS B 25 CYS B 80 1555 1555 2.04 LINK ND2 ASN A 176 C1 NAG C 1 1555 1555 1.45 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.47 LINK O6 NAG C 1 C1 FUC C 3 1555 1555 1.43 CISPEP 1 TYR A 209 PRO A 210 0 -3.42 CISPEP 2 HIS B 31 PRO B 32 0 2.83 CRYST1 136.287 88.342 45.322 90.00 90.00 90.00 P 21 21 2 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 0.007337 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011320 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022064 0.00000