HEADER IMMUNE SYSTEM 16-JUL-12 4G42 TITLE STRUCTURE OF THE CHICKEN MHC CLASS I MOLECULE BF2*0401 COMPLEXED TO TITLE 2 PEPITDE P8D COMPND MOL_ID: 1; COMPND 2 MOLECULE: MHC CLASS I ALPHA CHAIN 2; COMPND 3 CHAIN: A, D; COMPND 4 FRAGMENT: UNP RESIDUES 22-291; COMPND 5 SYNONYM: MHC CLASS I GLYCOPROTEIN, MHC CLASS I MOLECULE; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: BETA-2 MICROGLOBULIN; COMPND 10 CHAIN: B, E; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: 8-MERIC PEPTIDE P8D; COMPND 14 CHAIN: C, F; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKENS; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 9 ORGANISM_COMMON: CHICKENS; SOURCE 10 ORGANISM_TAXID: 9031; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 16 ORGANISM_COMMON: CHICKENS; SOURCE 17 ORGANISM_TAXID: 9031; SOURCE 18 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN GALLUS. KEYWDS MHC I COMPLEX, NARROW BINDING GROOVE, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR J.ZHANG,Y.CHEN,J.QI,F.GAO,J.LIU,J.KAUFMAN,C.XIA,G.F.GAO REVDAT 1 21-NOV-12 4G42 0 JRNL AUTH J.ZHANG,Y.CHEN,J.QI,F.GAO,Y.LIU,J.LIU,X.ZHOU,J.KAUFMAN, JRNL AUTH 2 C.XIA,G.F.GAO JRNL TITL NARROW GROOVE AND RESTRICTED ANCHORS OF MHC CLASS I MOLECULE JRNL TITL 2 BF2*0401 PLUS PEPTIDE TRANSPORTER RESTRICTION CAN EXPLAIN JRNL TITL 3 DISEASE SUSCEPTIBILITY OF B4 CHICKENS. JRNL REF J.IMMUNOL. V. 189 4478 2012 JRNL REFN ISSN 0022-1767 JRNL PMID 23041567 JRNL DOI 10.4049/JIMMUNOL.1200885 REMARK 2 REMARK 2 RESOLUTION. 2.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 33771 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1712 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 40.6335 - 5.2477 0.99 2827 161 0.2129 0.2593 REMARK 3 2 5.2477 - 4.1666 1.00 2742 164 0.1584 0.1992 REMARK 3 3 4.1666 - 3.6403 1.00 2664 161 0.1596 0.2351 REMARK 3 4 3.6403 - 3.3077 0.99 2728 117 0.1696 0.1907 REMARK 3 5 3.3077 - 3.0707 0.99 2664 153 0.1813 0.2323 REMARK 3 6 3.0707 - 2.8897 0.99 2713 120 0.1928 0.2542 REMARK 3 7 2.8897 - 2.7450 0.99 2689 123 0.2057 0.2820 REMARK 3 8 2.7450 - 2.6255 0.99 2616 156 0.2108 0.2784 REMARK 3 9 2.6255 - 2.5245 0.98 2627 152 0.2225 0.3036 REMARK 3 10 2.5245 - 2.4374 0.98 2598 161 0.2276 0.3414 REMARK 3 11 2.4374 - 2.3612 0.98 2613 124 0.2275 0.3223 REMARK 3 12 2.3612 - 2.2937 0.94 2578 120 0.2322 0.3057 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 35.37 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.890 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.35470 REMARK 3 B22 (A**2) : 10.16790 REMARK 3 B33 (A**2) : -5.81320 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.16290 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 6292 REMARK 3 ANGLE : 0.942 8541 REMARK 3 CHIRALITY : 0.068 860 REMARK 3 PLANARITY : 0.004 1123 REMARK 3 DIHEDRAL : 17.884 2259 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4G42 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JUL-12. REMARK 100 THE RCSB ID CODE IS RCSB073711. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS VII REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33771 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.294 REMARK 200 RESOLUTION RANGE LOW (A) : 40.627 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 75.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.19600 REMARK 200 R SYM FOR SHELL (I) : 0.27900 REMARK 200 FOR SHELL : 7.500 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5% MPD, 20% PEG 6000, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 82.91600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.05400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 82.91600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.05400 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, F 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 487 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 463 LIES ON A SPECIAL POSITION. 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 -2 REMARK 465 GLU A -1 REMARK 465 PHE A 0 REMARK 465 LEU A 272 REMARK 465 MET B -2 REMARK 465 GLU B -1 REMARK 465 PHE B 0 REMARK 465 PHE B 98 REMARK 465 MET D -2 REMARK 465 GLU D -1 REMARK 465 PHE D 0 REMARK 465 MET E -2 REMARK 465 GLU E -1 REMARK 465 PHE E 0 REMARK 465 PHE E 98 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 74 CZ 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 LEU D 102 O HOH D 471 1.70 REMARK 500 O ALA D 191 O HOH D 469 1.71 REMARK 500 O GLN D 222 CB ASP D 223 1.79 REMARK 500 O GLY A 16 O HOH A 412 1.91 REMARK 500 O GLY D 221 N ASP D 223 2.00 REMARK 500 OE2 GLU A 103 O HOH A 518 2.03 REMARK 500 OD1 ASP A 104 O HOH A 492 2.08 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 OG1 THR D 39 OD2 ASP D 126 1565 2.10 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 PRO A 17 CD PRO A 17 N 0.127 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 PRO A 15 C - N - CA ANGL. DEV. = 9.3 DEGREES REMARK 500 GLY A 16 N - CA - C ANGL. DEV. = 18.9 DEGREES REMARK 500 ASP A 104 N - CA - CB ANGL. DEV. = -13.9 DEGREES REMARK 500 LEU D 2 N - CA - C ANGL. DEV. = 19.8 DEGREES REMARK 500 ASP D 104 CB - CA - C ANGL. DEV. = -12.9 DEGREES REMARK 500 GLY D 105 N - CA - C ANGL. DEV. = -17.2 DEGREES REMARK 500 ASP D 223 C - N - CA ANGL. DEV. = -15.4 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 GLU A 159 -65.89 -123.74 REMARK 500 ALA A 191 168.31 149.89 REMARK 500 ASP A 192 18.37 56.49 REMARK 500 LYS A 215 -67.31 -104.05 REMARK 500 ASP A 216 56.14 -114.13 REMARK 500 ARG A 220 79.96 -105.61 REMARK 500 GLN A 222 -18.94 -38.67 REMARK 500 ASP A 223 15.98 -140.42 REMARK 500 THR D 39 -62.21 -93.59 REMARK 500 ASP D 124 79.74 -111.45 REMARK 500 GLU D 159 -75.48 -114.90 REMARK 500 ALA D 191 -69.72 -107.09 REMARK 500 GLN D 222 23.38 -48.92 REMARK 500 ASP D 223 38.95 90.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 LEU D 2 20.3 L L OUTSIDE RANGE REMARK 500 ALA D 191 24.6 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 509 DISTANCE = 6.69 ANGSTROMS REMARK 525 HOH A 520 DISTANCE = 6.08 ANGSTROMS REMARK 525 HOH D 347 DISTANCE = 5.26 ANGSTROMS REMARK 525 HOH D 355 DISTANCE = 5.59 ANGSTROMS REMARK 525 HOH D 390 DISTANCE = 5.50 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4E0R RELATED DB: PDB REMARK 900 STRUCTURE OF THE CHICKEN MHC CLASS I MOLECULE BF2*0401 REMARK 900 RELATED ID: 4G43 RELATED DB: PDB DBREF 4G42 A 1 270 UNP O46790 O46790_CHICK 22 291 DBREF 4G42 B 1 98 UNP P21611 B2MG_CHICK 22 119 DBREF 4G42 D 1 270 UNP O46790 O46790_CHICK 22 291 DBREF 4G42 E 1 98 UNP P21611 B2MG_CHICK 22 119 DBREF 4G42 C 1 8 PDB 4G42 4G42 1 8 DBREF 4G42 F 1 8 PDB 4G42 4G42 1 8 SEQADV 4G42 MET A -2 UNP O46790 EXPRESSION TAG SEQADV 4G42 GLU A -1 UNP O46790 EXPRESSION TAG SEQADV 4G42 PHE A 0 UNP O46790 EXPRESSION TAG SEQADV 4G42 GLU A 244 UNP O46790 ASP 265 ENGINEERED MUTATION SEQADV 4G42 LYS A 271 UNP O46790 EXPRESSION TAG SEQADV 4G42 LEU A 272 UNP O46790 EXPRESSION TAG SEQADV 4G42 MET B -2 UNP P21611 EXPRESSION TAG SEQADV 4G42 GLU B -1 UNP P21611 EXPRESSION TAG SEQADV 4G42 PHE B 0 UNP P21611 EXPRESSION TAG SEQADV 4G42 MET D -2 UNP O46790 EXPRESSION TAG SEQADV 4G42 GLU D -1 UNP O46790 EXPRESSION TAG SEQADV 4G42 PHE D 0 UNP O46790 EXPRESSION TAG SEQADV 4G42 GLU D 244 UNP O46790 ASP 265 ENGINEERED MUTATION SEQADV 4G42 LYS D 271 UNP O46790 EXPRESSION TAG SEQADV 4G42 LEU D 272 UNP O46790 EXPRESSION TAG SEQADV 4G42 MET E -2 UNP P21611 EXPRESSION TAG SEQADV 4G42 GLU E -1 UNP P21611 EXPRESSION TAG SEQADV 4G42 PHE E 0 UNP P21611 EXPRESSION TAG SEQRES 1 A 275 MET GLU PHE GLU LEU HIS THR LEU ARG TYR ILE ARG THR SEQRES 2 A 275 ALA MET THR ASP PRO GLY PRO GLY GLN PRO TRP PHE VAL SEQRES 3 A 275 THR VAL GLY TYR VAL ASP GLY GLU LEU PHE VAL HIS TYR SEQRES 4 A 275 ASN SER THR ALA ARG ARG TYR VAL PRO ARG THR GLU TRP SEQRES 5 A 275 ILE ALA ALA ASN THR ASP GLN GLN TYR TRP ASP GLY GLN SEQRES 6 A 275 THR GLN ILE GLY GLN LEU ASN GLU GLN ILE ASN ARG GLU SEQRES 7 A 275 ASN LEU GLY ILE ARG GLN ARG ARG TYR ASN GLN THR GLY SEQRES 8 A 275 GLY SER HIS THR VAL GLN TRP MET PHE GLY CYS ASP ILE SEQRES 9 A 275 LEU GLU ASP GLY THR ILE ARG GLY TYR ARG GLN SER ALA SEQRES 10 A 275 TYR ASP GLY ARG ASP PHE ILE ALA LEU ASP LYS ASP MET SEQRES 11 A 275 LYS THR PHE THR ALA ALA VAL PRO GLU ALA VAL PRO THR SEQRES 12 A 275 LYS ARG LYS TRP GLU GLU GLU SER GLU PRO GLU ARG TRP SEQRES 13 A 275 LYS ASN TYR LEU GLU GLU THR CYS VAL GLU TRP LEU ARG SEQRES 14 A 275 ARG TYR VAL GLU TYR GLY LYS ALA GLU LEU GLY ARG ARG SEQRES 15 A 275 GLU ARG PRO GLU VAL ARG VAL TRP GLY LYS GLU ALA ASP SEQRES 16 A 275 GLY ILE LEU THR LEU SER CYS ARG ALA HIS GLY PHE TYR SEQRES 17 A 275 PRO ARG PRO ILE VAL VAL SER TRP LEU LYS ASP GLY ALA SEQRES 18 A 275 VAL ARG GLY GLN ASP ALA HIS SER GLY GLY ILE VAL PRO SEQRES 19 A 275 ASN GLY ASP GLY THR TYR HIS THR TRP VAL THR ILE GLU SEQRES 20 A 275 ALA GLN PRO GLY ASP GLY ASP LYS TYR GLN CYS ARG VAL SEQRES 21 A 275 GLU HIS ALA SER LEU PRO GLN PRO GLY LEU TYR SER TRP SEQRES 22 A 275 LYS LEU SEQRES 1 B 101 MET GLU PHE ASP LEU THR PRO LYS VAL GLN VAL TYR SER SEQRES 2 B 101 ARG PHE PRO ALA SER ALA GLY THR LYS ASN VAL LEU ASN SEQRES 3 B 101 CYS PHE ALA ALA GLY PHE HIS PRO PRO LYS ILE SER ILE SEQRES 4 B 101 THR LEU MET LYS ASP GLY VAL PRO MET GLU GLY ALA GLN SEQRES 5 B 101 TYR SER ASP MET SER PHE ASN ASP ASP TRP THR PHE GLN SEQRES 6 B 101 ARG LEU VAL HIS ALA ASP PHE THR PRO SER SER GLY SER SEQRES 7 B 101 THR TYR ALA CYS LYS VAL GLU HIS GLU THR LEU LYS GLU SEQRES 8 B 101 PRO GLN VAL TYR LYS TRP ASP PRO GLU PHE SEQRES 1 C 8 ILE ASP TRP PHE ASP GLY LYS ASP SEQRES 1 D 275 MET GLU PHE GLU LEU HIS THR LEU ARG TYR ILE ARG THR SEQRES 2 D 275 ALA MET THR ASP PRO GLY PRO GLY GLN PRO TRP PHE VAL SEQRES 3 D 275 THR VAL GLY TYR VAL ASP GLY GLU LEU PHE VAL HIS TYR SEQRES 4 D 275 ASN SER THR ALA ARG ARG TYR VAL PRO ARG THR GLU TRP SEQRES 5 D 275 ILE ALA ALA ASN THR ASP GLN GLN TYR TRP ASP GLY GLN SEQRES 6 D 275 THR GLN ILE GLY GLN LEU ASN GLU GLN ILE ASN ARG GLU SEQRES 7 D 275 ASN LEU GLY ILE ARG GLN ARG ARG TYR ASN GLN THR GLY SEQRES 8 D 275 GLY SER HIS THR VAL GLN TRP MET PHE GLY CYS ASP ILE SEQRES 9 D 275 LEU GLU ASP GLY THR ILE ARG GLY TYR ARG GLN SER ALA SEQRES 10 D 275 TYR ASP GLY ARG ASP PHE ILE ALA LEU ASP LYS ASP MET SEQRES 11 D 275 LYS THR PHE THR ALA ALA VAL PRO GLU ALA VAL PRO THR SEQRES 12 D 275 LYS ARG LYS TRP GLU GLU GLU SER GLU PRO GLU ARG TRP SEQRES 13 D 275 LYS ASN TYR LEU GLU GLU THR CYS VAL GLU TRP LEU ARG SEQRES 14 D 275 ARG TYR VAL GLU TYR GLY LYS ALA GLU LEU GLY ARG ARG SEQRES 15 D 275 GLU ARG PRO GLU VAL ARG VAL TRP GLY LYS GLU ALA ASP SEQRES 16 D 275 GLY ILE LEU THR LEU SER CYS ARG ALA HIS GLY PHE TYR SEQRES 17 D 275 PRO ARG PRO ILE VAL VAL SER TRP LEU LYS ASP GLY ALA SEQRES 18 D 275 VAL ARG GLY GLN ASP ALA HIS SER GLY GLY ILE VAL PRO SEQRES 19 D 275 ASN GLY ASP GLY THR TYR HIS THR TRP VAL THR ILE GLU SEQRES 20 D 275 ALA GLN PRO GLY ASP GLY ASP LYS TYR GLN CYS ARG VAL SEQRES 21 D 275 GLU HIS ALA SER LEU PRO GLN PRO GLY LEU TYR SER TRP SEQRES 22 D 275 LYS LEU SEQRES 1 E 101 MET GLU PHE ASP LEU THR PRO LYS VAL GLN VAL TYR SER SEQRES 2 E 101 ARG PHE PRO ALA SER ALA GLY THR LYS ASN VAL LEU ASN SEQRES 3 E 101 CYS PHE ALA ALA GLY PHE HIS PRO PRO LYS ILE SER ILE SEQRES 4 E 101 THR LEU MET LYS ASP GLY VAL PRO MET GLU GLY ALA GLN SEQRES 5 E 101 TYR SER ASP MET SER PHE ASN ASP ASP TRP THR PHE GLN SEQRES 6 E 101 ARG LEU VAL HIS ALA ASP PHE THR PRO SER SER GLY SER SEQRES 7 E 101 THR TYR ALA CYS LYS VAL GLU HIS GLU THR LEU LYS GLU SEQRES 8 E 101 PRO GLN VAL TYR LYS TRP ASP PRO GLU PHE SEQRES 1 F 8 ILE ASP TRP PHE ASP GLY LYS ASP FORMUL 7 HOH *536(H2 O) HELIX 1 1 THR A 47 ASN A 53 1 7 HELIX 2 2 ASP A 55 TYR A 84 1 30 HELIX 3 3 VAL A 134 GLU A 136 5 3 HELIX 4 4 ALA A 137 GLU A 147 1 11 HELIX 5 5 SER A 148 GLU A 159 1 12 HELIX 6 6 GLU A 159 GLY A 172 1 14 HELIX 7 7 GLY A 172 GLY A 177 1 6 HELIX 8 8 GLY A 248 LYS A 252 5 5 HELIX 9 9 THR D 47 ASN D 53 1 7 HELIX 10 10 ASP D 55 TYR D 84 1 30 HELIX 11 11 LYS D 125 LYS D 128 5 4 HELIX 12 12 VAL D 134 GLU D 136 5 3 HELIX 13 13 ALA D 137 GLU D 146 1 10 HELIX 14 14 SER D 148 GLU D 159 1 12 HELIX 15 15 GLU D 159 GLY D 172 1 14 HELIX 16 16 GLY D 172 ARG D 178 1 7 HELIX 17 17 ASP D 249 ASP D 251 5 3 SHEET 1 A 8 ARG A 42 PRO A 45 0 SHEET 2 A 8 GLU A 31 ASN A 37 -1 N HIS A 35 O VAL A 44 SHEET 3 A 8 PHE A 22 VAL A 28 -1 N THR A 24 O TYR A 36 SHEET 4 A 8 HIS A 3 MET A 12 -1 N ARG A 6 O TYR A 27 SHEET 5 A 8 THR A 92 ILE A 101 -1 O TRP A 95 N ARG A 9 SHEET 6 A 8 ILE A 107 TYR A 115 -1 O GLN A 112 N MET A 96 SHEET 7 A 8 ARG A 118 LEU A 123 -1 O LEU A 123 N ARG A 111 SHEET 8 A 8 PHE A 130 ALA A 132 -1 O THR A 131 N ALA A 122 SHEET 1 B 4 GLU A 183 TRP A 187 0 SHEET 2 B 4 ILE A 194 PHE A 204 -1 O SER A 198 N TRP A 187 SHEET 3 B 4 TYR A 237 ALA A 245 -1 O ILE A 243 N LEU A 197 SHEET 4 B 4 HIS A 225 SER A 226 -1 N HIS A 225 O THR A 242 SHEET 1 C 4 GLU A 190 ALA A 191 0 SHEET 2 C 4 ILE A 194 PHE A 204 -1 O ILE A 194 N ALA A 191 SHEET 3 C 4 TYR A 237 ALA A 245 -1 O ILE A 243 N LEU A 197 SHEET 4 C 4 VAL A 230 PRO A 231 -1 N VAL A 230 O HIS A 238 SHEET 1 D 3 VAL A 210 LEU A 214 0 SHEET 2 D 3 GLN A 254 GLU A 258 -1 O GLN A 254 N LEU A 214 SHEET 3 D 3 GLY A 266 SER A 269 -1 O TYR A 268 N CYS A 255 SHEET 1 E 4 LYS B 5 SER B 10 0 SHEET 2 E 4 ASN B 20 PHE B 29 -1 O ALA B 27 N LYS B 5 SHEET 3 E 4 PHE B 61 PHE B 69 -1 O ARG B 63 N ALA B 26 SHEET 4 E 4 GLN B 49 PHE B 55 -1 N SER B 51 O LEU B 64 SHEET 1 F 4 VAL B 43 PRO B 44 0 SHEET 2 F 4 SER B 35 LYS B 40 -1 N LYS B 40 O VAL B 43 SHEET 3 F 4 TYR B 77 GLU B 82 -1 O LYS B 80 N THR B 37 SHEET 4 F 4 GLN B 90 LYS B 93 -1 O GLN B 90 N VAL B 81 SHEET 1 G 8 VAL D 44 PRO D 45 0 SHEET 2 G 8 GLU D 31 ASN D 37 -1 N HIS D 35 O VAL D 44 SHEET 3 G 8 PHE D 22 VAL D 28 -1 N THR D 24 O TYR D 36 SHEET 4 G 8 HIS D 3 MET D 12 -1 N ARG D 6 O TYR D 27 SHEET 5 G 8 THR D 92 ILE D 101 -1 O PHE D 97 N TYR D 7 SHEET 6 G 8 ILE D 107 TYR D 115 -1 O GLN D 112 N MET D 96 SHEET 7 G 8 ARG D 118 ASP D 124 -1 O ARG D 118 N TYR D 115 SHEET 8 G 8 THR D 129 ALA D 132 -1 O THR D 129 N ASP D 124 SHEET 1 H 4 GLU D 183 GLU D 190 0 SHEET 2 H 4 LEU D 195 PHE D 204 -1 O SER D 198 N TRP D 187 SHEET 3 H 4 TYR D 237 ALA D 245 -1 O ILE D 243 N LEU D 197 SHEET 4 H 4 HIS D 225 SER D 226 -1 N HIS D 225 O THR D 242 SHEET 1 I 4 GLU D 183 GLU D 190 0 SHEET 2 I 4 LEU D 195 PHE D 204 -1 O SER D 198 N TRP D 187 SHEET 3 I 4 TYR D 237 ALA D 245 -1 O ILE D 243 N LEU D 197 SHEET 4 I 4 VAL D 230 PRO D 231 -1 N VAL D 230 O HIS D 238 SHEET 1 J 4 ALA D 218 VAL D 219 0 SHEET 2 J 4 ILE D 209 LYS D 215 -1 N LYS D 215 O ALA D 218 SHEET 3 J 4 TYR D 253 HIS D 259 -1 O GLN D 254 N LEU D 214 SHEET 4 J 4 GLY D 266 SER D 269 -1 O GLY D 266 N VAL D 257 SHEET 1 K 4 LYS E 5 SER E 10 0 SHEET 2 K 4 ASN E 20 PHE E 29 -1 O PHE E 25 N GLN E 7 SHEET 3 K 4 PHE E 61 PHE E 69 -1 O VAL E 65 N CYS E 24 SHEET 4 K 4 GLN E 49 TYR E 50 -1 N GLN E 49 O HIS E 66 SHEET 1 L 4 LYS E 5 SER E 10 0 SHEET 2 L 4 ASN E 20 PHE E 29 -1 O PHE E 25 N GLN E 7 SHEET 3 L 4 PHE E 61 PHE E 69 -1 O VAL E 65 N CYS E 24 SHEET 4 L 4 SER E 54 PHE E 55 -1 N SER E 54 O GLN E 62 SHEET 1 M 4 VAL E 43 PRO E 44 0 SHEET 2 M 4 SER E 35 LYS E 40 -1 N LYS E 40 O VAL E 43 SHEET 3 M 4 TYR E 77 GLU E 82 -1 O LYS E 80 N THR E 37 SHEET 4 M 4 GLN E 90 LYS E 93 -1 O TYR E 92 N CYS E 79 SSBOND 1 CYS A 99 CYS A 161 1555 1555 2.04 SSBOND 2 CYS A 199 CYS A 255 1555 1555 2.02 SSBOND 3 CYS B 24 CYS B 79 1555 1555 2.03 SSBOND 4 CYS D 99 CYS D 161 1555 1555 2.04 SSBOND 5 CYS D 199 CYS D 255 1555 1555 2.03 SSBOND 6 CYS E 24 CYS E 79 1555 1555 2.03 CISPEP 1 GLU A 1 LEU A 2 0 -0.02 CISPEP 2 PRO A 15 GLY A 16 0 -4.95 CISPEP 3 TYR A 205 PRO A 206 0 9.59 CISPEP 4 HIS B 30 PRO B 31 0 3.50 CISPEP 5 SER B 51 ASP B 52 0 4.87 CISPEP 6 ASP B 52 MET B 53 0 -3.20 CISPEP 7 PRO D 15 GLY D 16 0 -12.75 CISPEP 8 GLY D 105 THR D 106 0 -10.48 CISPEP 9 TYR D 205 PRO D 206 0 6.52 CISPEP 10 HIS E 30 PRO E 31 0 2.55 CRYST1 165.832 40.108 130.952 90.00 119.56 90.00 C 1 2 1 8 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 0.006030 0.000000 0.003420 0.00000 SCALE2 0.000000 0.024933 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008779 0.00000