HEADER DNA BINDING PROTEIN/DNA 22-JAN-11 3QFQ TITLE ASYMMETRIC ASSEMBLY OF MERKEL CELL POLYOMAVIRUS LARGE T-ANTIGEN ORIGIN TITLE 2 BINDING DOMAINS AT THE VIRAL ORIGIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: LARGE T ANTIGEN; COMPND 3 CHAIN: A, B, E; COMPND 4 FRAGMENT: ORIGIN BINDING DOMAIN (UNP RESIDUES 308-433); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (26-MER); COMPND 8 CHAIN: W; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: MERKEL CELL VIRUS ORIGIN SITE 1/2 (WATSON STRAND); COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (26-MER); COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES; COMPND 15 OTHER_DETAILS: MERKEL CELL VIRUS ORIGIN SITE 1/2 (CRICK STRAND) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MERKEL CELL POLYOMAVIRUS; SOURCE 3 ORGANISM_TAXID: 493803; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-15B; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 OTHER_DETAILS: SYNTHESIZED; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 OTHER_DETAILS: SYNTHESIZED KEYWDS ORIGIN BINDING DOMAIN, PROTEIN-DNA COMPLEX, REPLICATION, DNA BINDING KEYWDS 2 PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.J.HARRISON,G.MEINKE,A.BOHM REVDAT 3 13-SEP-23 3QFQ 1 SEQADV REVDAT 2 15-JUN-11 3QFQ 1 JRNL REVDAT 1 27-APR-11 3QFQ 0 JRNL AUTH C.J.HARRISON,G.MEINKE,H.J.KWUN,H.ROGALIN,P.J.PHELAN, JRNL AUTH 2 P.A.BULLOCK,Y.CHANG,P.S.MOORE,A.BOHM JRNL TITL ASYMMETRIC ASSEMBLY OF MERKEL CELL POLYOMAVIRUS LARGE JRNL TITL 2 T-ANTIGEN ORIGIN BINDING DOMAINS AT THE VIRAL ORIGIN. JRNL REF J.MOL.BIOL. V. 409 529 2011 JRNL REFN ISSN 0022-2836 JRNL PMID 21501625 JRNL DOI 10.1016/J.JMB.2011.03.051 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) 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 : LS_WUNIT_K1 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 75.7 REMARK 3 NUMBER OF REFLECTIONS : 12396 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.760 REMARK 3 FREE R VALUE TEST SET COUNT : 590 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 38.1599 - 4.6015 0.98 3979 197 0.1775 0.2470 REMARK 3 2 4.6015 - 3.6533 0.75 2769 131 0.2304 0.2931 REMARK 3 3 3.6533 - 3.1918 0.55 1988 105 0.2718 0.3185 REMARK 3 4 3.1918 - 2.9001 0.80 3070 157 0.3793 0.4167 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.06 REMARK 3 K_SOL : 0.22 REMARK 3 B_SOL : 25.41 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.730 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) : -17.41170 REMARK 3 B22 (A**2) : -37.94250 REMARK 3 B33 (A**2) : 55.35420 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 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 : 0.003 3969 REMARK 3 ANGLE : 0.710 5613 REMARK 3 CHIRALITY : 0.040 642 REMARK 3 PLANARITY : 0.002 534 REMARK 3 DIHEDRAL : 17.368 1485 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A) REMARK 3 ORIGIN FOR THE GROUP (A): 37.6880 -57.3728 -34.9444 REMARK 3 T TENSOR REMARK 3 T11: 0.1436 T22: 0.3327 REMARK 3 T33: 0.1075 T12: -0.0464 REMARK 3 T13: 0.0470 T23: 0.0077 REMARK 3 L TENSOR REMARK 3 L11: 4.4780 L22: 4.4325 REMARK 3 L33: 1.9187 L12: -0.7074 REMARK 3 L13: -0.6384 L23: 2.7408 REMARK 3 S TENSOR REMARK 3 S11: -0.3562 S12: 0.7156 S13: -0.1081 REMARK 3 S21: -0.0071 S22: 0.1568 S23: 0.1141 REMARK 3 S31: -0.0164 S32: -0.2082 S33: 0.0002 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN B) REMARK 3 ORIGIN FOR THE GROUP (A): 23.4875 3.7913 -4.4397 REMARK 3 T TENSOR REMARK 3 T11: 0.5634 T22: 0.4889 REMARK 3 T33: 0.3574 T12: -0.0014 REMARK 3 T13: -0.1306 T23: 0.1502 REMARK 3 L TENSOR REMARK 3 L11: 1.8270 L22: 3.0942 REMARK 3 L33: 3.0137 L12: 0.4368 REMARK 3 L13: 0.4842 L23: 1.2096 REMARK 3 S TENSOR REMARK 3 S11: -0.0742 S12: -0.4863 S13: 0.0110 REMARK 3 S21: 0.6998 S22: 0.1197 S23: -0.0715 REMARK 3 S31: -0.6797 S32: 0.0041 S33: 0.0002 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN E) REMARK 3 ORIGIN FOR THE GROUP (A): 25.0295 -29.7798 -1.3244 REMARK 3 T TENSOR REMARK 3 T11: 0.4702 T22: 0.4676 REMARK 3 T33: 0.5158 T12: 0.0967 REMARK 3 T13: -0.0701 T23: -0.0557 REMARK 3 L TENSOR REMARK 3 L11: 0.7648 L22: 2.0569 REMARK 3 L33: 2.7737 L12: -0.9738 REMARK 3 L13: -0.2691 L23: -1.0784 REMARK 3 S TENSOR REMARK 3 S11: -0.5251 S12: -0.3049 S13: 0.1700 REMARK 3 S21: 1.0339 S22: -0.0906 S23: -0.5637 REMARK 3 S31: 0.2626 S32: 0.2258 S33: 0.0002 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN R) REMARK 3 ORIGIN FOR THE GROUP (A): 22.9423 -30.5577 -24.0542 REMARK 3 T TENSOR REMARK 3 T11: 0.5193 T22: 0.4638 REMARK 3 T33: 0.9117 T12: 0.0182 REMARK 3 T13: -0.1126 T23: 0.0469 REMARK 3 L TENSOR REMARK 3 L11: 1.0253 L22: 2.0840 REMARK 3 L33: 0.6869 L12: -1.4454 REMARK 3 L13: -1.0173 L23: 1.3641 REMARK 3 S TENSOR REMARK 3 S11: 0.2083 S12: 0.1250 S13: -0.2151 REMARK 3 S21: 0.0769 S22: -0.6267 S23: 0.9125 REMARK 3 S31: -0.1846 S32: -0.1603 S33: 0.0012 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN W) REMARK 3 ORIGIN FOR THE GROUP (A): 21.9547 -26.7515 -23.0761 REMARK 3 T TENSOR REMARK 3 T11: 0.5671 T22: 0.5004 REMARK 3 T33: 0.5388 T12: -0.0127 REMARK 3 T13: 0.0794 T23: -0.0112 REMARK 3 L TENSOR REMARK 3 L11: 2.4104 L22: 2.0197 REMARK 3 L33: 1.0272 L12: -1.7062 REMARK 3 L13: 0.0683 L23: 0.9686 REMARK 3 S TENSOR REMARK 3 S11: 0.1833 S12: 0.2047 S13: 0.1407 REMARK 3 S21: -0.5493 S22: -0.6276 S23: -0.5609 REMARK 3 S31: -0.0654 S32: -0.0439 S33: 0.0003 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 3QFQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1000063587. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.075 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15228 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 44.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.8 REMARK 200 DATA REDUNDANCY : 13.00 REMARK 200 R MERGE (I) : 0.13100 REMARK 200 R SYM (I) : 0.13100 REMARK 200 FOR THE DATA SET : 10.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.06 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 13.80 REMARK 200 R MERGE FOR SHELL (I) : 0.68800 REMARK 200 R SYM FOR SHELL (I) : 0.68800 REMARK 200 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 2NTC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19-21% PEG 3350, 0.2M LITHIUM ACETATE, REMARK 280 50 MM TRIS PH 7.1, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277K 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 40.20000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 85.67000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 40.20000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 85.67000 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 THREE T-ANTIGEN ORIGIN BINDING REMARK 300 DOMAIN MOLECULES BOUND TO A DNA TARGET THAT CONTAINS FOUR POTENTIAL REMARK 300 BINDING SITES 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: PENTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, E, W, 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 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 299 REMARK 465 GLY A 300 REMARK 465 HIS A 301 REMARK 465 HIS A 302 REMARK 465 HIS A 303 REMARK 465 HIS A 304 REMARK 465 HIS A 305 REMARK 465 HIS A 306 REMARK 465 GLY A 307 REMARK 465 GLU A 308 REMARK 465 ASN A 428 REMARK 465 TYR A 429 REMARK 465 GLU A 430 REMARK 465 PHE A 431 REMARK 465 GLN A 432 REMARK 465 GLU A 433 REMARK 465 MET B 299 REMARK 465 GLY B 300 REMARK 465 HIS B 301 REMARK 465 HIS B 302 REMARK 465 HIS B 303 REMARK 465 HIS B 304 REMARK 465 HIS B 305 REMARK 465 HIS B 306 REMARK 465 GLY B 307 REMARK 465 GLU B 308 REMARK 465 TYR B 429 REMARK 465 GLU B 430 REMARK 465 PHE B 431 REMARK 465 GLN B 432 REMARK 465 GLU B 433 REMARK 465 MET E 299 REMARK 465 GLY E 300 REMARK 465 HIS E 301 REMARK 465 HIS E 302 REMARK 465 HIS E 303 REMARK 465 HIS E 304 REMARK 465 HIS E 305 REMARK 465 HIS E 306 REMARK 465 GLY E 307 REMARK 465 GLU E 308 REMARK 465 THR E 309 REMARK 465 PRO E 310 REMARK 465 ASN E 428 REMARK 465 TYR E 429 REMARK 465 GLU E 430 REMARK 465 PHE E 431 REMARK 465 GLN E 432 REMARK 465 GLU E 433 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 THR A 309 OG1 CG2 REMARK 470 PRO A 312 CG CD REMARK 470 THR A 340 OG1 CG2 REMARK 470 THR A 341 OG1 CG2 REMARK 470 LYS A 344 CG CD CE NZ REMARK 470 ILE A 346 CG1 CG2 CD1 REMARK 470 LYS A 351 CG CD CE NZ REMARK 470 ILE A 352 CD1 REMARK 470 LYS A 356 CG CD CE NZ REMARK 470 CYS A 365 SG REMARK 470 LEU A 367 CG CD1 CD2 REMARK 470 LEU A 376 CG CD1 CD2 REMARK 470 LYS A 385 CG CD CE NZ REMARK 470 ILE A 394 CG1 CG2 CD1 REMARK 470 LYS A 414 CG CD CE NZ REMARK 470 LYS A 418 CG CD CE NZ REMARK 470 LEU A 427 CG CD1 CD2 REMARK 470 THR B 309 OG1 CG2 REMARK 470 ILE B 346 CG1 CG2 CD1 REMARK 470 LYS B 351 CG CD CE NZ REMARK 470 ILE B 352 CD1 REMARK 470 LYS B 356 CG CD CE NZ REMARK 470 GLU B 366 CG CD OE1 OE2 REMARK 470 LEU B 367 CG CD1 CD2 REMARK 470 LYS B 385 CG CD CE NZ REMARK 470 CYS B 392 SG REMARK 470 THR B 393 OG1 CG2 REMARK 470 ILE B 394 CG1 CG2 CD1 REMARK 470 LYS B 400 CG CD CE NZ REMARK 470 LYS B 414 CG CD CE NZ REMARK 470 PRO B 415 CG CD REMARK 470 LYS B 418 CG CD CE NZ REMARK 470 GLN B 421 CG CD OE1 NE2 REMARK 470 LEU B 426 CG CD1 CD2 REMARK 470 LEU B 427 CG CD1 CD2 REMARK 470 ASN B 428 CG OD1 ND2 REMARK 470 ILE E 346 CG1 CG2 CD1 REMARK 470 ILE E 352 CD1 REMARK 470 LYS E 356 CG CD CE NZ REMARK 470 LEU E 367 CG CD1 CD2 REMARK 470 LYS E 385 CE NZ REMARK 470 THR E 393 OG1 CG2 REMARK 470 ILE E 394 CG1 CG2 CD1 REMARK 470 SER E 395 CB OG REMARK 470 LYS E 414 CG CD CE NZ REMARK 470 LYS E 418 CG CD CE NZ REMARK 470 ASN E 423 CG OD1 ND2 REMARK 470 LEU E 426 CG CD1 CD2 REMARK 470 LEU E 427 CG CD1 CD2 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 ILE E 338 CD1 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 B 415 N - CA - CB ANGL. DEV. = 7.3 DEGREES REMARK 500 DC W 22 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DC C 21 O4' - C1' - N1 ANGL. DEV. = 1.9 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 314 145.41 76.44 REMARK 500 LEU A 319 10.58 -150.54 REMARK 500 SER A 320 31.06 -78.59 REMARK 500 SER A 334 -45.05 -132.33 REMARK 500 THR A 340 -139.05 -107.16 REMARK 500 GLU A 353 -9.17 -59.15 REMARK 500 ASP A 358 -60.10 -90.89 REMARK 500 CYS A 365 -118.97 -87.60 REMARK 500 GLU A 366 -64.97 -124.29 REMARK 500 THR A 393 29.31 45.52 REMARK 500 ILE A 394 -171.62 -175.01 REMARK 500 SER A 395 -145.61 68.38 REMARK 500 LYS A 418 139.28 -175.25 REMARK 500 GLN A 421 130.87 -170.88 REMARK 500 VAL B 311 -52.70 139.33 REMARK 500 PRO B 312 -103.30 -107.14 REMARK 500 THR B 313 -51.85 -129.52 REMARK 500 HIS B 325 58.13 -106.88 REMARK 500 TYR B 328 43.35 -107.31 REMARK 500 GLU B 353 33.00 -75.08 REMARK 500 LYS B 356 87.59 50.38 REMARK 500 CYS B 369 107.87 -169.39 REMARK 500 CYS B 392 91.39 -63.94 REMARK 500 LYS B 414 -133.23 -74.27 REMARK 500 LYS B 418 -156.37 -123.95 REMARK 500 LEU B 419 -107.42 -124.80 REMARK 500 LEU B 420 -83.06 79.45 REMARK 500 GLN B 421 -108.46 43.23 REMARK 500 GLU B 422 -143.43 -80.71 REMARK 500 ASN B 423 -54.04 -160.31 REMARK 500 PRO B 425 -99.60 -88.03 REMARK 500 ASP E 314 141.17 70.23 REMARK 500 HIS E 325 53.26 -103.82 REMARK 500 GLU E 353 3.18 -68.60 REMARK 500 THR E 393 -37.24 -149.00 REMARK 500 LYS E 404 74.20 -102.72 REMARK 500 PRO E 415 -59.01 -25.89 REMARK 500 LYS E 424 148.96 87.74 REMARK 500 PRO E 425 -102.03 -61.19 REMARK 500 LEU E 426 -127.26 -140.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLN B 421 GLU B 422 -138.07 REMARK 500 REMARK 500 REMARK: NULL DBREF 3QFQ A 308 433 UNP E2IPT4 E2IPT4_9POLY 230 355 DBREF 3QFQ B 308 433 UNP E2IPT4 E2IPT4_9POLY 230 355 DBREF 3QFQ E 308 433 UNP E2IPT4 E2IPT4_9POLY 230 355 DBREF 3QFQ W 1 26 PDB 3QFQ 3QFQ 1 26 DBREF 3QFQ C 1 26 PDB 3QFQ 3QFQ 1 26 SEQADV 3QFQ MET A 299 UNP E2IPT4 EXPRESSION TAG SEQADV 3QFQ GLY A 300 UNP E2IPT4 EXPRESSION TAG SEQADV 3QFQ HIS A 301 UNP E2IPT4 EXPRESSION TAG SEQADV 3QFQ HIS A 302 UNP E2IPT4 EXPRESSION TAG SEQADV 3QFQ HIS A 303 UNP E2IPT4 EXPRESSION TAG SEQADV 3QFQ HIS A 304 UNP E2IPT4 EXPRESSION TAG SEQADV 3QFQ HIS A 305 UNP E2IPT4 EXPRESSION TAG SEQADV 3QFQ HIS A 306 UNP E2IPT4 EXPRESSION TAG SEQADV 3QFQ GLY A 307 UNP E2IPT4 EXPRESSION TAG SEQADV 3QFQ MET B 299 UNP E2IPT4 EXPRESSION TAG SEQADV 3QFQ GLY B 300 UNP E2IPT4 EXPRESSION TAG SEQADV 3QFQ HIS B 301 UNP E2IPT4 EXPRESSION TAG SEQADV 3QFQ HIS B 302 UNP E2IPT4 EXPRESSION TAG SEQADV 3QFQ HIS B 303 UNP E2IPT4 EXPRESSION TAG SEQADV 3QFQ HIS B 304 UNP E2IPT4 EXPRESSION TAG SEQADV 3QFQ HIS B 305 UNP E2IPT4 EXPRESSION TAG SEQADV 3QFQ HIS B 306 UNP E2IPT4 EXPRESSION TAG SEQADV 3QFQ GLY B 307 UNP E2IPT4 EXPRESSION TAG SEQADV 3QFQ MET E 299 UNP E2IPT4 EXPRESSION TAG SEQADV 3QFQ GLY E 300 UNP E2IPT4 EXPRESSION TAG SEQADV 3QFQ HIS E 301 UNP E2IPT4 EXPRESSION TAG SEQADV 3QFQ HIS E 302 UNP E2IPT4 EXPRESSION TAG SEQADV 3QFQ HIS E 303 UNP E2IPT4 EXPRESSION TAG SEQADV 3QFQ HIS E 304 UNP E2IPT4 EXPRESSION TAG SEQADV 3QFQ HIS E 305 UNP E2IPT4 EXPRESSION TAG SEQADV 3QFQ HIS E 306 UNP E2IPT4 EXPRESSION TAG SEQADV 3QFQ GLY E 307 UNP E2IPT4 EXPRESSION TAG SEQRES 1 A 135 MET GLY HIS HIS HIS HIS HIS HIS GLY GLU THR PRO VAL SEQRES 2 A 135 PRO THR ASP PHE PRO ILE ASP LEU SER ASP TYR LEU SER SEQRES 3 A 135 HIS ALA VAL TYR SER ASN LYS THR VAL SER CYS PHE ALA SEQRES 4 A 135 ILE TYR THR THR SER ASP LYS ALA ILE GLU LEU TYR ASP SEQRES 5 A 135 LYS ILE GLU LYS PHE LYS VAL ASP PHE LYS SER ARG HIS SEQRES 6 A 135 ALA CYS GLU LEU GLY CYS ILE LEU LEU PHE ILE THR LEU SEQRES 7 A 135 SER LYS HIS ARG VAL SER ALA ILE LYS ASN PHE CYS SER SEQRES 8 A 135 THR PHE CYS THR ILE SER PHE LEU ILE CYS LYS GLY VAL SEQRES 9 A 135 ASN LYS MET PRO GLU MET TYR ASN ASN LEU CYS LYS PRO SEQRES 10 A 135 PRO TYR LYS LEU LEU GLN GLU ASN LYS PRO LEU LEU ASN SEQRES 11 A 135 TYR GLU PHE GLN GLU SEQRES 1 B 135 MET GLY HIS HIS HIS HIS HIS HIS GLY GLU THR PRO VAL SEQRES 2 B 135 PRO THR ASP PHE PRO ILE ASP LEU SER ASP TYR LEU SER SEQRES 3 B 135 HIS ALA VAL TYR SER ASN LYS THR VAL SER CYS PHE ALA SEQRES 4 B 135 ILE TYR THR THR SER ASP LYS ALA ILE GLU LEU TYR ASP SEQRES 5 B 135 LYS ILE GLU LYS PHE LYS VAL ASP PHE LYS SER ARG HIS SEQRES 6 B 135 ALA CYS GLU LEU GLY CYS ILE LEU LEU PHE ILE THR LEU SEQRES 7 B 135 SER LYS HIS ARG VAL SER ALA ILE LYS ASN PHE CYS SER SEQRES 8 B 135 THR PHE CYS THR ILE SER PHE LEU ILE CYS LYS GLY VAL SEQRES 9 B 135 ASN LYS MET PRO GLU MET TYR ASN ASN LEU CYS LYS PRO SEQRES 10 B 135 PRO TYR LYS LEU LEU GLN GLU ASN LYS PRO LEU LEU ASN SEQRES 11 B 135 TYR GLU PHE GLN GLU SEQRES 1 E 135 MET GLY HIS HIS HIS HIS HIS HIS GLY GLU THR PRO VAL SEQRES 2 E 135 PRO THR ASP PHE PRO ILE ASP LEU SER ASP TYR LEU SER SEQRES 3 E 135 HIS ALA VAL TYR SER ASN LYS THR VAL SER CYS PHE ALA SEQRES 4 E 135 ILE TYR THR THR SER ASP LYS ALA ILE GLU LEU TYR ASP SEQRES 5 E 135 LYS ILE GLU LYS PHE LYS VAL ASP PHE LYS SER ARG HIS SEQRES 6 E 135 ALA CYS GLU LEU GLY CYS ILE LEU LEU PHE ILE THR LEU SEQRES 7 E 135 SER LYS HIS ARG VAL SER ALA ILE LYS ASN PHE CYS SER SEQRES 8 E 135 THR PHE CYS THR ILE SER PHE LEU ILE CYS LYS GLY VAL SEQRES 9 E 135 ASN LYS MET PRO GLU MET TYR ASN ASN LEU CYS LYS PRO SEQRES 10 E 135 PRO TYR LYS LEU LEU GLN GLU ASN LYS PRO LEU LEU ASN SEQRES 11 E 135 TYR GLU PHE GLN GLU SEQRES 1 W 26 DG DC DA DG DA DG DG DC DT DT DG DG DG SEQRES 2 W 26 DG DC DT DC DC DT DA DG DC DC DT DC DC SEQRES 1 C 26 DC DG DG DA DG DG DC DT DA DG DG DA DG SEQRES 2 C 26 DC DC DC DC DA DA DG DC DC DT DC DT DG FORMUL 6 HOH *14(H2 O) HELIX 1 1 PRO A 316 SER A 320 5 5 HELIX 2 2 THR A 341 ILE A 352 1 12 HELIX 3 3 GLU A 353 PHE A 355 5 3 HELIX 4 4 ARG A 380 CYS A 388 1 9 HELIX 5 5 LYS A 404 LEU A 412 1 9 HELIX 6 6 PRO B 316 SER B 320 5 5 HELIX 7 7 THR B 341 ILE B 352 1 12 HELIX 8 8 ARG B 380 SER B 389 1 10 HELIX 9 9 THR B 390 CYS B 392 5 3 HELIX 10 10 LYS B 404 LEU B 412 1 9 HELIX 11 11 PRO E 316 SER E 320 5 5 HELIX 12 12 THR E 341 LYS E 351 1 11 HELIX 13 13 ILE E 352 PHE E 355 5 4 HELIX 14 14 ARG E 380 SER E 389 1 10 HELIX 15 15 LYS E 404 LEU E 412 1 9 SHEET 1 A 5 CYS A 399 GLY A 401 0 SHEET 2 A 5 VAL A 333 ILE A 338 -1 N ALA A 337 O LYS A 400 SHEET 3 A 5 CYS A 369 HIS A 379 -1 O LEU A 371 N ILE A 338 SHEET 4 A 5 VAL A 357 ALA A 364 -1 N SER A 361 O LEU A 372 SHEET 5 A 5 LEU A 419 GLU A 422 -1 O GLN A 421 N ARG A 362 SHEET 1 B 4 VAL B 357 ARG B 362 0 SHEET 2 B 4 CYS B 369 HIS B 379 -1 O ILE B 374 N PHE B 359 SHEET 3 B 4 VAL B 333 THR B 340 -1 N PHE B 336 O PHE B 373 SHEET 4 B 4 ILE B 398 GLY B 401 -1 O LYS B 400 N ALA B 337 SHEET 1 C 5 ILE E 398 GLY E 401 0 SHEET 2 C 5 VAL E 333 THR E 340 -1 N ALA E 337 O LYS E 400 SHEET 3 C 5 CYS E 369 HIS E 379 -1 O PHE E 373 N PHE E 336 SHEET 4 C 5 VAL E 357 HIS E 363 -1 N PHE E 359 O ILE E 374 SHEET 5 C 5 LEU E 419 ASN E 423 -1 O GLN E 421 N ARG E 362 CISPEP 1 VAL B 311 PRO B 312 0 -2.46 CRYST1 80.400 171.340 51.280 90.00 90.00 90.00 P 21 21 2 12 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 0.012438 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005836 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019501 0.00000