HEADER IMMUNE SYSTEM 16-MAY-12 4F7M
TITLE CRYSTAL STRUCTURE OF HLA-A*2402 COMPLEXED WITH A NEWLY IDENTIFIED
TITLE 2 PEPTIDE FROM 2009 H1N1 PA (649-658)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-24 ALPHA CHAIN;
COMPND 3 CHAIN: A, D;
COMPND 4 FRAGMENT: UNP RESIDUES 25-298;
COMPND 5 SYNONYM: AW-24, HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-9 ALPHA
COMPND 6 CHAIN, MHC CLASS I ANTIGEN A*24;
COMPND 7 ENGINEERED: YES;
COMPND 8 MOL_ID: 2;
COMPND 9 MOLECULE: BETA-2-MICROGLOBULIN;
COMPND 10 CHAIN: B, E;
COMPND 11 FRAGMENT: UNP RESIDUES 21-119;
COMPND 12 SYNONYM: BETA-2-MICROGLOBULIN FORM PI 5.3;
COMPND 13 ENGINEERED: YES;
COMPND 14 MOL_ID: 3;
COMPND 15 MOLECULE: PA POLYMERASE SUBUNIT;
COMPND 16 CHAIN: C, F;
COMPND 17 FRAGMENT: UNP RESIDUES 649-658;
COMPND 18 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: HLA-A, HLAA;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 MOL_ID: 2;
SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 10 ORGANISM_COMMON: HUMAN;
SOURCE 11 ORGANISM_TAXID: 9606;
SOURCE 12 GENE: B2M, CDABP0092, HDCMA22P;
SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 15 MOL_ID: 3;
SOURCE 16 SYNTHETIC: YES;
SOURCE 17 ORGANISM_SCIENTIFIC: INFLUENZA A VIRUS H3N2;
SOURCE 18 ORGANISM_TAXID: 41857;
SOURCE 19 OTHER_DETAILS: IN VITRO SYNTHESIZED PEPTIDE FROM INFLUENZA A VIRUS
SOURCE 20 POLYMERASE
KEYWDS HLA-A*2402, INFLUENZA A VIRUS, 2009 H1N1, HLA-A3 SUPERTYPE, IMMUNE
KEYWDS 2 SYSTEM
EXPDTA X-RAY DIFFRACTION
AUTHOR J.LIU,S.ZHANG,S.TAN,Y.YI,B.WU,F.ZHU,H.WANG,J.QI,F.G.GEORGE
REVDAT 3 13-SEP-23 4F7M 1 SEQADV
REVDAT 2 05-DEC-12 4F7M 1 JRNL
REVDAT 1 10-OCT-12 4F7M 0
JRNL AUTH J.LIU,S.ZHANG,S.TAN,Y.YI,B.WU,B.CAO,F.ZHU,C.WANG,H.WANG,
JRNL AUTH 2 J.QI,G.F.GAO
JRNL TITL CROSS-ALLELE CYTOTOXIC T LYMPHOCYTE RESPONSES AGAINST 2009
JRNL TITL 2 PANDEMIC H1N1 INFLUENZA A VIRUS AMONG HLA-A24 AND HLA-A3
JRNL TITL 3 SUPERTYPE-POSITIVE INDIVIDUALS.
JRNL REF J.VIROL. V. 86 13281 2012
JRNL REFN ISSN 0022-538X
JRNL PMID 23015716
JRNL DOI 10.1128/JVI.01841-12
REMARK 2
REMARK 2 RESOLUTION. 2.40 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2)
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.67
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.150
REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9
REMARK 3 NUMBER OF REFLECTIONS : 31150
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.242
REMARK 3 R VALUE (WORKING SET) : 0.239
REMARK 3 FREE R VALUE : 0.289
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080
REMARK 3 FREE R VALUE TEST SET COUNT : 1581
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 40.6764 - 5.3416 0.99 2885 180 0.2411 0.2542
REMARK 3 2 5.3416 - 4.2413 0.99 2852 142 0.1868 0.2327
REMARK 3 3 4.2413 - 3.7055 0.98 2807 149 0.2026 0.2480
REMARK 3 4 3.7055 - 3.3669 0.98 2832 143 0.2196 0.2769
REMARK 3 5 3.3669 - 3.1257 0.97 2770 145 0.2384 0.2980
REMARK 3 6 3.1257 - 2.9415 0.95 2720 145 0.2590 0.2953
REMARK 3 7 2.9415 - 2.7942 0.93 2653 132 0.2602 0.3158
REMARK 3 8 2.7942 - 2.6726 0.92 2624 137 0.2667 0.3469
REMARK 3 9 2.6726 - 2.5697 0.90 2578 122 0.2700 0.3385
REMARK 3 10 2.5697 - 2.4810 0.89 2544 140 0.2728 0.3680
REMARK 3 11 2.4810 - 2.4035 0.83 2304 146 0.2740 0.3306
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 : 0.34
REMARK 3 B_SOL : 24.26
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.330
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.690
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) : 5.57930
REMARK 3 B22 (A**2) : -1.84670
REMARK 3 B33 (A**2) : -3.73260
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 3.64860
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 : 0.004 6448
REMARK 3 ANGLE : 0.708 8732
REMARK 3 CHIRALITY : 0.050 885
REMARK 3 PLANARITY : 0.003 1154
REMARK 3 DIHEDRAL : 18.366 2346
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 1
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: ALL
REMARK 3 ORIGIN FOR THE GROUP (A): 4.3064 -6.7243 -21.5987
REMARK 3 T TENSOR
REMARK 3 T11: 0.0505 T22: 0.0383
REMARK 3 T33: 0.0428 T12: 0.0024
REMARK 3 T13: 0.0058 T23: 0.0050
REMARK 3 L TENSOR
REMARK 3 L11: 0.0754 L22: 0.0724
REMARK 3 L33: 0.0329 L12: 0.0343
REMARK 3 L13: -0.0149 L23: 0.0084
REMARK 3 S TENSOR
REMARK 3 S11: -0.0042 S12: 0.0244 S13: 0.0293
REMARK 3 S21: -0.0080 S22: 0.0052 S23: 0.0133
REMARK 3 S31: -0.0027 S32: 0.0009 S33: 0.0000
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 4F7M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAY-12.
REMARK 100 THE DEPOSITION ID IS D_1000072556.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 13-NOV-10
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
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 : SI 111 CHANNEL
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 : 33004
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : 4.100
REMARK 200 R MERGE (I) : 0.18000
REMARK 200 R SYM (I) : 0.18000
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.0600
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8
REMARK 200 DATA REDUNDANCY IN SHELL : 3.80
REMARK 200 R MERGE FOR SHELL (I) : 0.48300
REMARK 200 R SYM FOR SHELL (I) : 0.48300
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.380
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: 3I6L
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 48.68
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM NITRATE AND 20% (W/V)
REMARK 280 POLYETHYLENE GLYCOL 3,350, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,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 33.54600
REMARK 290 SMTRY3 2 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: 4210 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 19060 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 4210 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 19120 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 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 0
REMARK 465 MET B 0
REMARK 465 MET D 0
REMARK 465 MET E 0
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 HOH B 158 O HOH B 167 1.80
REMARK 500 O THR A 134 O HOH A 421 1.81
REMARK 500 O HOH D 361 O HOH D 407 1.81
REMARK 500 O GLU B 77 O HOH B 183 1.82
REMARK 500 SD MET D 189 O HOH D 372 1.82
REMARK 500 OG SER B 88 O HOH B 166 1.82
REMARK 500 O HOH D 343 O HOH D 371 1.84
REMARK 500 O HOH A 362 O HOH A 373 1.84
REMARK 500 O HOH E 136 O HOH E 141 1.84
REMARK 500 OH TYR D 257 O HOH D 390 1.84
REMARK 500 O HOH D 367 O HOH D 396 1.84
REMARK 500 O HOH A 317 O HOH A 427 1.87
REMARK 500 OH TYR A 257 O HOH A 419 1.87
REMARK 500 O ARG E 12 O HOH E 160 1.87
REMARK 500 OG1 THR B 68 O HOH B 180 1.89
REMARK 500 CB THR B 68 O HOH B 180 1.90
REMARK 500 O HOH B 112 O HOH B 143 1.90
REMARK 500 O HOH A 406 O HOH A 415 1.90
REMARK 500 O HOH D 349 O HOH D 364 1.91
REMARK 500 NE1 TRP A 244 O HOH A 397 1.91
REMARK 500 NH1 ARG D 75 O HOH D 350 1.92
REMARK 500 O LEU A 110 O HOH A 423 1.93
REMARK 500 C LEU A 110 O HOH A 423 1.93
REMARK 500 N ARG E 3 O HOH E 145 1.93
REMARK 500 O GLU D 222 O HOH D 374 1.94
REMARK 500 O HOH A 375 O HOH A 376 1.94
REMARK 500 OH TYR D 257 O HOH D 383 1.94
REMARK 500 N GLU A 229 O HOH A 394 1.94
REMARK 500 O HOH B 105 O HOH B 114 1.95
REMARK 500 C THR A 228 O HOH A 394 1.95
REMARK 500 O HIS E 31 O HOH E 145 1.95
REMARK 500 NH2 ARG D 75 O HOH D 350 1.96
REMARK 500 O HOH B 184 O HOH B 185 1.96
REMARK 500 O HOH A 386 O HOH A 407 1.96
REMARK 500 O HOH D 376 O HOH D 380 1.96
REMARK 500 O ARG D 21 O HOH D 312 1.96
REMARK 500 CB GLU D 58 O HOH D 380 1.97
REMARK 500 O HOH D 383 O HOH D 390 1.98
REMARK 500 O HOH A 328 O HOH A 340 1.99
REMARK 500 O HOH D 381 O HOH D 391 1.99
REMARK 500 O HOH A 388 O HOH B 154 2.00
REMARK 500 OD1 ASP D 227 O HOH D 370 2.00
REMARK 500 N ASN B 42 O HOH B 183 2.01
REMARK 500 O ASP A 227 O HOH A 394 2.01
REMARK 500 O HOH B 170 O HOH B 174 2.01
REMARK 500 O MET B 99 O HOH A 397 2.02
REMARK 500 O HOH D 316 O HOH D 360 2.03
REMARK 500 O HOH D 325 O HOH E 160 2.03
REMARK 500 O HOH D 326 O HOH D 368 2.04
REMARK 500 N ILE A 194 O HOH A 353 2.05
REMARK 500
REMARK 500 THIS ENTRY HAS 83 CLOSE CONTACTS
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 430 O HOH B 186 2545 1.85
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 -132.99 53.75
REMARK 500 LEU A 110 -31.64 -142.65
REMARK 500 HIS A 114 91.80 -171.56
REMARK 500 PRO A 210 -176.78 -69.89
REMARK 500 ASP A 220 -5.58 59.84
REMARK 500 GLN A 226 28.07 -74.86
REMARK 500 ASP A 227 -7.01 -143.70
REMARK 500 PRO B 32 -175.39 -69.04
REMARK 500 GLU B 47 -74.79 -74.74
REMARK 500 TRP B 60 -11.53 85.94
REMARK 500 GLU C 8 75.88 89.05
REMARK 500 ASP D 29 -130.25 52.14
REMARK 500 LEU D 110 -58.53 -129.38
REMARK 500 HIS D 114 90.12 -165.44
REMARK 500 TYR D 123 -64.76 -109.44
REMARK 500 PRO D 210 -177.15 -68.47
REMARK 500 ASP D 220 -2.51 64.80
REMARK 500 GLN D 224 55.64 -99.98
REMARK 500 GLN D 226 29.23 -74.22
REMARK 500 ASP D 227 -1.17 -145.58
REMARK 500 GLU E 47 -81.85 -66.68
REMARK 500 SER E 57 -168.22 -100.83
REMARK 500 TRP E 60 -13.48 78.93
REMARK 500 GLU F 8 66.78 84.59
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN C OF PA POLYMERASE
REMARK 800 SUBUNIT
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN F OF PA POLYMERASE
REMARK 800 SUBUNIT
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3I6L RELATED DB: PDB
REMARK 900 USED AS MODEL FOR MOLECULAR REPLACEMENT
REMARK 900 RELATED ID: 4F7P RELATED DB: PDB
REMARK 900 RELATED ID: 4F7T RELATED DB: PDB
REMARK 900 RELATED ID: 4F7Q RELATED DB: PDB
DBREF 4F7M A 1 274 UNP P05534 1A24_HUMAN 25 298
DBREF 4F7M B 1 99 UNP P61769 B2MG_HUMAN 21 119
DBREF 4F7M C 1 10 UNP Q9YXL3 Q9YXL3_9INFA 649 658
DBREF 4F7M D 1 274 UNP P05534 1A24_HUMAN 25 298
DBREF 4F7M E 1 99 UNP P61769 B2MG_HUMAN 21 119
DBREF 4F7M F 1 10 UNP Q9YXL3 Q9YXL3_9INFA 649 658
SEQADV 4F7M MET A 0 UNP P05534 INITIATING METHIONINE
SEQADV 4F7M MET B 0 UNP P61769 INITIATING METHIONINE
SEQADV 4F7M MET D 0 UNP P05534 INITIATING METHIONINE
SEQADV 4F7M MET E 0 UNP P61769 INITIATING METHIONINE
SEQRES 1 A 275 MET GLY SER HIS SER MET ARG TYR PHE SER THR SER VAL
SEQRES 2 A 275 SER ARG PRO GLY ARG GLY GLU PRO ARG PHE ILE ALA VAL
SEQRES 3 A 275 GLY TYR VAL ASP ASP THR GLN PHE VAL ARG PHE ASP SER
SEQRES 4 A 275 ASP ALA ALA SER GLN ARG MET GLU PRO ARG ALA PRO TRP
SEQRES 5 A 275 ILE GLU GLN GLU GLY PRO GLU TYR TRP ASP GLU GLU THR
SEQRES 6 A 275 GLY LYS VAL LYS ALA HIS SER GLN THR ASP ARG GLU ASN
SEQRES 7 A 275 LEU ARG ILE ALA LEU ARG TYR TYR ASN GLN SER GLU ALA
SEQRES 8 A 275 GLY SER HIS THR LEU GLN MET MET PHE GLY CYS ASP VAL
SEQRES 9 A 275 GLY SER ASP GLY ARG PHE LEU ARG GLY TYR HIS GLN TYR
SEQRES 10 A 275 ALA TYR ASP GLY LYS ASP TYR ILE ALA LEU LYS GLU ASP
SEQRES 11 A 275 LEU ARG SER TRP THR ALA ALA ASP MET ALA ALA GLN ILE
SEQRES 12 A 275 THR LYS ARG LYS TRP GLU ALA ALA HIS VAL ALA GLU GLN
SEQRES 13 A 275 GLN ARG ALA TYR LEU GLU GLY THR CYS VAL ASP GLY LEU
SEQRES 14 A 275 ARG ARG TYR LEU GLU ASN GLY LYS GLU THR LEU GLN ARG
SEQRES 15 A 275 THR ASP PRO PRO LYS THR HIS MET THR HIS HIS PRO ILE
SEQRES 16 A 275 SER ASP HIS GLU ALA THR LEU ARG CYS TRP ALA LEU GLY
SEQRES 17 A 275 PHE TYR PRO ALA GLU ILE THR LEU THR TRP GLN ARG ASP
SEQRES 18 A 275 GLY GLU ASP GLN THR GLN ASP THR GLU LEU VAL GLU THR
SEQRES 19 A 275 ARG PRO ALA GLY ASP GLY THR PHE GLN LYS TRP ALA ALA
SEQRES 20 A 275 VAL VAL VAL PRO SER GLY GLU GLU GLN ARG TYR THR CYS
SEQRES 21 A 275 HIS VAL GLN HIS GLU GLY LEU PRO LYS PRO LEU THR LEU
SEQRES 22 A 275 ARG TRP
SEQRES 1 B 100 MET ILE GLN ARG THR PRO LYS ILE GLN VAL TYR SER ARG
SEQRES 2 B 100 HIS PRO ALA GLU ASN GLY LYS SER ASN PHE LEU ASN CYS
SEQRES 3 B 100 TYR VAL SER GLY PHE HIS PRO SER ASP ILE GLU VAL ASP
SEQRES 4 B 100 LEU LEU LYS ASN GLY GLU ARG ILE GLU LYS VAL GLU HIS
SEQRES 5 B 100 SER ASP LEU SER PHE SER LYS ASP TRP SER PHE TYR LEU
SEQRES 6 B 100 LEU TYR TYR THR GLU PHE THR PRO THR GLU LYS ASP GLU
SEQRES 7 B 100 TYR ALA CYS ARG VAL ASN HIS VAL THR LEU SER GLN PRO
SEQRES 8 B 100 LYS ILE VAL LYS TRP ASP ARG ASP MET
SEQRES 1 C 10 LEU TYR ALA SER PRO GLN LEU GLU GLY PHE
SEQRES 1 D 275 MET GLY SER HIS SER MET ARG TYR PHE SER THR SER VAL
SEQRES 2 D 275 SER ARG PRO GLY ARG GLY GLU PRO ARG PHE ILE ALA VAL
SEQRES 3 D 275 GLY TYR VAL ASP ASP THR GLN PHE VAL ARG PHE ASP SER
SEQRES 4 D 275 ASP ALA ALA SER GLN ARG MET GLU PRO ARG ALA PRO TRP
SEQRES 5 D 275 ILE GLU GLN GLU GLY PRO GLU TYR TRP ASP GLU GLU THR
SEQRES 6 D 275 GLY LYS VAL LYS ALA HIS SER GLN THR ASP ARG GLU ASN
SEQRES 7 D 275 LEU ARG ILE ALA LEU ARG TYR TYR ASN GLN SER GLU ALA
SEQRES 8 D 275 GLY SER HIS THR LEU GLN MET MET PHE GLY CYS ASP VAL
SEQRES 9 D 275 GLY SER ASP GLY ARG PHE LEU ARG GLY TYR HIS GLN TYR
SEQRES 10 D 275 ALA TYR ASP GLY LYS ASP TYR ILE ALA LEU LYS GLU ASP
SEQRES 11 D 275 LEU ARG SER TRP THR ALA ALA ASP MET ALA ALA GLN ILE
SEQRES 12 D 275 THR LYS ARG LYS TRP GLU ALA ALA HIS VAL ALA GLU GLN
SEQRES 13 D 275 GLN ARG ALA TYR LEU GLU GLY THR CYS VAL ASP GLY LEU
SEQRES 14 D 275 ARG ARG TYR LEU GLU ASN GLY LYS GLU THR LEU GLN ARG
SEQRES 15 D 275 THR ASP PRO PRO LYS THR HIS MET THR HIS HIS PRO ILE
SEQRES 16 D 275 SER ASP HIS GLU ALA THR LEU ARG CYS TRP ALA LEU GLY
SEQRES 17 D 275 PHE TYR PRO ALA GLU ILE THR LEU THR TRP GLN ARG ASP
SEQRES 18 D 275 GLY GLU ASP GLN THR GLN ASP THR GLU LEU VAL GLU THR
SEQRES 19 D 275 ARG PRO ALA GLY ASP GLY THR PHE GLN LYS TRP ALA ALA
SEQRES 20 D 275 VAL VAL VAL PRO SER GLY GLU GLU GLN ARG TYR THR CYS
SEQRES 21 D 275 HIS VAL GLN HIS GLU GLY LEU PRO LYS PRO LEU THR LEU
SEQRES 22 D 275 ARG TRP
SEQRES 1 E 100 MET ILE GLN ARG THR PRO LYS ILE GLN VAL TYR SER ARG
SEQRES 2 E 100 HIS PRO ALA GLU ASN GLY LYS SER ASN PHE LEU ASN CYS
SEQRES 3 E 100 TYR VAL SER GLY PHE HIS PRO SER ASP ILE GLU VAL ASP
SEQRES 4 E 100 LEU LEU LYS ASN GLY GLU ARG ILE GLU LYS VAL GLU HIS
SEQRES 5 E 100 SER ASP LEU SER PHE SER LYS ASP TRP SER PHE TYR LEU
SEQRES 6 E 100 LEU TYR TYR THR GLU PHE THR PRO THR GLU LYS ASP GLU
SEQRES 7 E 100 TYR ALA CYS ARG VAL ASN HIS VAL THR LEU SER GLN PRO
SEQRES 8 E 100 LYS ILE VAL LYS TRP ASP ARG ASP MET
SEQRES 1 F 10 LEU TYR ALA SER PRO GLN LEU GLU GLY PHE
FORMUL 7 HOH *402(H2 O)
HELIX 1 1 ALA A 49 GLU A 53 5 5
HELIX 2 2 GLY A 56 ASN A 86 1 31
HELIX 3 3 ASP A 137 ALA A 150 1 14
HELIX 4 4 HIS A 151 GLY A 162 1 12
HELIX 5 5 GLY A 162 GLY A 175 1 14
HELIX 6 6 GLY A 175 GLN A 180 1 6
HELIX 7 7 GLU A 253 GLN A 255 5 3
HELIX 8 8 ALA D 49 GLU D 53 5 5
HELIX 9 9 GLY D 56 ASN D 86 1 31
HELIX 10 10 ALA D 139 ALA D 150 1 12
HELIX 11 11 HIS D 151 GLY D 162 1 12
HELIX 12 12 GLY D 162 GLY D 175 1 14
HELIX 13 13 GLY D 175 GLN D 180 1 6
HELIX 14 14 GLU D 253 GLN D 255 5 3
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 ALA A 24 O PHE A 36
SHEET 4 A 8 HIS A 3 VAL A 12 -1 N ARG A 6 O TYR A 27
SHEET 5 A 8 THR A 94 VAL A 103 -1 O LEU A 95 N SER A 11
SHEET 6 A 8 PHE A 109 TYR A 118 -1 O ALA A 117 N GLN A 96
SHEET 7 A 8 LYS 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 HIS A 192 0
SHEET 2 B 4 GLU A 198 PHE A 208 -1 O THR A 200 N HIS A 192
SHEET 3 B 4 PHE A 241 PRO A 250 -1 O ALA A 245 N CYS A 203
SHEET 4 B 4 THR A 228 LEU A 230 -1 N GLU A 229 O ALA A 246
SHEET 1 C 4 LYS A 186 HIS A 192 0
SHEET 2 C 4 GLU A 198 PHE A 208 -1 O THR A 200 N HIS A 192
SHEET 3 C 4 PHE A 241 PRO A 250 -1 O ALA A 245 N CYS A 203
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 ASP A 223 0
SHEET 2 D 4 THR A 214 ARG A 219 -1 N ARG A 219 O GLU A 222
SHEET 3 D 4 TYR A 257 GLN A 262 -1 O HIS A 260 N THR A 216
SHEET 4 D 4 LEU A 270 ARG A 273 -1 O LEU A 272 N CYS A 259
SHEET 1 E 4 LYS B 6 SER B 11 0
SHEET 2 E 4 ASN B 21 PHE B 30 -1 O SER B 28 N LYS B 6
SHEET 3 E 4 PHE B 62 PHE B 70 -1 O PHE B 70 N ASN B 21
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 SER B 28 N LYS B 6
SHEET 3 F 4 PHE B 62 PHE B 70 -1 O PHE B 70 N ASN B 21
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 VAL B 93 N CYS B 80
SHEET 1 H 8 GLU D 46 PRO D 47 0
SHEET 2 H 8 THR D 31 ASP D 37 -1 N ARG D 35 O GLU D 46
SHEET 3 H 8 ARG D 21 VAL D 28 -1 N VAL D 28 O THR D 31
SHEET 4 H 8 HIS D 3 VAL D 12 -1 N ARG D 6 O TYR D 27
SHEET 5 H 8 THR D 94 VAL D 103 -1 O LEU D 95 N SER D 11
SHEET 6 H 8 PHE D 109 TYR D 118 -1 O ARG D 111 N ASP D 102
SHEET 7 H 8 LYS D 121 LEU D 126 -1 O ILE D 124 N TYR D 116
SHEET 8 H 8 TRP D 133 ALA D 135 -1 O THR D 134 N ALA D 125
SHEET 1 I 4 LYS D 186 PRO D 193 0
SHEET 2 I 4 GLU D 198 PHE D 208 -1 O LEU D 206 N LYS D 186
SHEET 3 I 4 PHE D 241 PRO D 250 -1 O ALA D 245 N CYS D 203
SHEET 4 I 4 THR D 228 LEU D 230 -1 N GLU D 229 O ALA D 246
SHEET 1 J 4 LYS D 186 PRO D 193 0
SHEET 2 J 4 GLU D 198 PHE D 208 -1 O LEU D 206 N LYS D 186
SHEET 3 J 4 PHE D 241 PRO D 250 -1 O ALA D 245 N CYS D 203
SHEET 4 J 4 ARG D 234 PRO D 235 -1 N ARG D 234 O GLN D 242
SHEET 1 K 4 GLU D 222 ASP D 223 0
SHEET 2 K 4 THR D 214 ARG D 219 -1 N ARG D 219 O GLU D 222
SHEET 3 K 4 TYR D 257 GLN D 262 -1 O HIS D 260 N THR D 216
SHEET 4 K 4 LEU D 270 ARG D 273 -1 O LEU D 272 N CYS D 259
SHEET 1 L 4 LYS E 6 SER E 11 0
SHEET 2 L 4 ASN E 21 PHE E 30 -1 O ASN E 24 N TYR E 10
SHEET 3 L 4 PHE E 62 PHE E 70 -1 O THR E 68 N LEU E 23
SHEET 4 L 4 GLU E 50 HIS E 51 -1 N GLU E 50 O TYR E 67
SHEET 1 M 4 LYS E 6 SER E 11 0
SHEET 2 M 4 ASN E 21 PHE E 30 -1 O ASN E 24 N TYR E 10
SHEET 3 M 4 PHE E 62 PHE E 70 -1 O THR E 68 N LEU E 23
SHEET 4 M 4 SER E 55 PHE E 56 -1 N SER E 55 O TYR E 63
SHEET 1 N 4 GLU E 44 ARG E 45 0
SHEET 2 N 4 GLU E 36 LYS E 41 -1 N LYS E 41 O GLU E 44
SHEET 3 N 4 TYR E 78 ASN E 83 -1 O ARG E 81 N ASP E 38
SHEET 4 N 4 LYS E 91 LYS E 94 -1 O VAL E 93 N CYS E 80
SSBOND 1 CYS A 101 CYS A 164 1555 1555 2.04
SSBOND 2 CYS A 203 CYS A 259 1555 1555 2.03
SSBOND 3 CYS B 25 CYS B 80 1555 1555 2.03
SSBOND 4 CYS D 101 CYS D 164 1555 1555 2.04
SSBOND 5 CYS D 203 CYS D 259 1555 1555 2.03
SSBOND 6 CYS E 25 CYS E 80 1555 1555 2.03
CISPEP 1 TYR A 209 PRO A 210 0 1.88
CISPEP 2 HIS B 31 PRO B 32 0 1.70
CISPEP 3 TYR D 209 PRO D 210 0 3.79
CISPEP 4 HIS E 31 PRO E 32 0 3.69
SITE 1 AC1 28 TYR A 7 TYR A 59 GLU A 63 LYS A 66
SITE 2 AC1 28 VAL A 67 HIS A 70 THR A 73 ASN A 77
SITE 3 AC1 28 ILE A 80 TYR A 84 PHE A 99 TYR A 116
SITE 4 AC1 28 TYR A 123 THR A 143 LYS A 146 TRP A 147
SITE 5 AC1 28 VAL A 152 GLN A 156 TYR A 159 THR A 163
SITE 6 AC1 28 GLY A 167 ARG A 170 TYR A 171 HOH A 340
SITE 7 AC1 28 HOH C 101 HOH C 102 HOH C 103 HOH C 105
SITE 1 AC2 23 TYR D 7 TYR D 59 GLU D 63 LYS D 66
SITE 2 AC2 23 HIS D 70 THR D 73 ASN D 77 ILE D 80
SITE 3 AC2 23 TYR D 84 PHE D 99 TYR D 123 THR D 143
SITE 4 AC2 23 LYS D 146 TRP D 147 VAL D 152 GLN D 156
SITE 5 AC2 23 TYR D 159 THR D 163 GLY D 167 ARG D 170
SITE 6 AC2 23 TYR D 171 HOH F 101 HOH F 102
CRYST1 74.272 67.092 87.668 90.00 101.30 90.00 P 1 21 1 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 0.013464 0.000000 0.002691 0.00000
SCALE2 0.000000 0.014905 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011632 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
