HEADER VIRAL PROTEIN/INHIBITOR 11-FEB-14 4OYD TITLE CRYSTAL STRUCTURE OF A COMPUTATIONALLY DESIGNED INHIBITOR OF AN TITLE 2 EPSTEIN-BARR VIRAL BCL-2 PROTEIN CAVEAT 4OYD RESIDUE B LYS 22 AND RESIDUE B GLN 23 ARE CONNECTED BY C-N CAVEAT 2 4OYD BOND OF 1.61 ANGSTROMS THAT IS LONGER THAN NORMAL COMPND MOL_ID: 1; COMPND 2 MOLECULE: APOPTOSIS REGULATOR BHRF1; COMPND 3 CHAIN: A, C; COMPND 4 SYNONYM: EARLY ANTIGEN PROTEIN R,EA-R,NUCLEAR ANTIGEN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: COMPUTATIONALLY DESIGNED INHIBITOR; COMPND 8 CHAIN: B, D; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EPSTEIN-BARR VIRUS; SOURCE 3 ORGANISM_COMMON: HHV-4; SOURCE 4 ORGANISM_TAXID: 82830; SOURCE 5 STRAIN: AG876; SOURCE 6 GENE: BHRF1; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS INHIBITOR, COMPLEX, APOPTOSIS, VIRAL PROTEIN-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.SHEN,E.PROCKO,D.BAKER,B.STODDARD REVDAT 4 27-DEC-23 4OYD 1 REMARK REVDAT 3 01-NOV-17 4OYD 1 SOURCE REMARK REVDAT 2 14-JAN-15 4OYD 1 CAVEAT DBREF REVDAT 1 09-JUL-14 4OYD 0 JRNL AUTH E.PROCKO,G.Y.BERGUIG,B.W.SHEN,Y.SONG,S.FRAYO,A.J.CONVERTINE, JRNL AUTH 2 D.MARGINEANTU,G.BOOTH,B.E.CORREIA,Y.CHENG,W.R.SCHIEF, JRNL AUTH 3 D.M.HOCKENBERY,O.W.PRESS,B.L.STODDARD,P.S.STAYTON,D.BAKER JRNL TITL A COMPUTATIONALLY DESIGNED INHIBITOR OF AN EPSTEIN-BARR JRNL TITL 2 VIRAL BCL-2 PROTEIN INDUCES APOPTOSIS IN INFECTED CELLS. JRNL REF CELL V. 157 1644 2014 JRNL REFN ISSN 1097-4172 JRNL PMID 24949974 JRNL DOI 10.1016/J.CELL.2014.04.034 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 82.5 REMARK 3 NUMBER OF REFLECTIONS : 46840 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) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2487 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 876 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 20.94 REMARK 3 BIN R VALUE (WORKING SET) : 0.2070 REMARK 3 BIN FREE R VALUE SET COUNT : 46 REMARK 3 BIN FREE R VALUE : 0.3280 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4473 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 165 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -8.77000 REMARK 3 B22 (A**2) : 8.02000 REMARK 3 B33 (A**2) : 0.75000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -3.76000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.025 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.024 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.050 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.321 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4815 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4670 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6518 ; 1.857 ; 1.968 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10752 ; 1.340 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 599 ; 5.426 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 248 ;33.264 ;23.548 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 931 ;16.924 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 52 ;17.335 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 710 ; 0.123 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5508 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1128 ; 0.005 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2318 ; 1.636 ; 1.578 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2317 ; 1.635 ; 1.578 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2928 ; 2.502 ; 2.345 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2929 ; 2.502 ; 2.346 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2497 ; 2.441 ; 1.963 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2497 ; 2.438 ; 1.963 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3586 ; 3.913 ; 2.817 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5753 ; 5.604 ;12.963 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5754 ; 5.604 ;12.964 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 2 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 1 156 C 1 156 8276 0.16 0.05 REMARK 3 2 B 1 117 D 1 117 7354 0.09 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 156 REMARK 3 ORIGIN FOR THE GROUP (A): 10.3283 23.7130 -35.5962 REMARK 3 T TENSOR REMARK 3 T11: 0.0090 T22: 0.0621 REMARK 3 T33: 0.0148 T12: 0.0046 REMARK 3 T13: 0.0041 T23: -0.0079 REMARK 3 L TENSOR REMARK 3 L11: 2.3642 L22: 1.3162 REMARK 3 L33: 1.9850 L12: -0.0065 REMARK 3 L13: -0.1916 L23: 0.0751 REMARK 3 S TENSOR REMARK 3 S11: -0.0216 S12: -0.0440 S13: -0.1114 REMARK 3 S21: -0.0255 S22: 0.0118 S23: -0.1009 REMARK 3 S31: 0.1253 S32: 0.1363 S33: 0.0098 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 117 REMARK 3 ORIGIN FOR THE GROUP (A): -4.1705 37.6208 -28.5331 REMARK 3 T TENSOR REMARK 3 T11: 0.0676 T22: 0.0897 REMARK 3 T33: 0.0669 T12: 0.0225 REMARK 3 T13: 0.0231 T23: 0.0115 REMARK 3 L TENSOR REMARK 3 L11: 2.8787 L22: 3.0109 REMARK 3 L33: 1.8481 L12: 1.2396 REMARK 3 L13: 0.2098 L23: 0.2957 REMARK 3 S TENSOR REMARK 3 S11: 0.0496 S12: -0.0722 S13: 0.3852 REMARK 3 S21: 0.1084 S22: -0.0245 S23: 0.0730 REMARK 3 S31: -0.2790 S32: 0.0799 S33: -0.0250 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 158 REMARK 3 ORIGIN FOR THE GROUP (A): -23.0508 28.8432 -7.7564 REMARK 3 T TENSOR REMARK 3 T11: 0.0066 T22: 0.0289 REMARK 3 T33: 0.0097 T12: 0.0088 REMARK 3 T13: -0.0050 T23: 0.0031 REMARK 3 L TENSOR REMARK 3 L11: 2.5088 L22: 1.6504 REMARK 3 L33: 1.7705 L12: 0.1246 REMARK 3 L13: -0.0182 L23: -0.0158 REMARK 3 S TENSOR REMARK 3 S11: -0.0334 S12: -0.0004 S13: 0.0616 REMARK 3 S21: -0.0635 S22: 0.0203 S23: 0.1151 REMARK 3 S31: -0.0692 S32: -0.1299 S33: 0.0131 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1 D 117 REMARK 3 ORIGIN FOR THE GROUP (A): -8.7138 15.2771 -0.5725 REMARK 3 T TENSOR REMARK 3 T11: 0.0283 T22: 0.0399 REMARK 3 T33: 0.0102 T12: 0.0250 REMARK 3 T13: -0.0060 T23: -0.0015 REMARK 3 L TENSOR REMARK 3 L11: 2.4136 L22: 3.4200 REMARK 3 L33: 0.9425 L12: 2.1685 REMARK 3 L13: -0.7040 L23: -0.6975 REMARK 3 S TENSOR REMARK 3 S11: 0.0311 S12: -0.0192 S13: -0.1172 REMARK 3 S21: 0.1028 S22: -0.0199 S23: -0.0786 REMARK 3 S31: 0.0912 S32: 0.0539 S33: -0.0112 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 201 A 236 REMARK 3 RESIDUE RANGE : B 201 B 223 REMARK 3 RESIDUE RANGE : C 201 C 250 REMARK 3 RESIDUE RANGE : D 301 D 344 REMARK 3 ORIGIN FOR THE GROUP (A): -10.1454 23.7188 -13.6685 REMARK 3 T TENSOR REMARK 3 T11: 0.0841 T22: 0.1171 REMARK 3 T33: 0.0991 T12: -0.0012 REMARK 3 T13: 0.0083 T23: 0.0076 REMARK 3 L TENSOR REMARK 3 L11: 0.1566 L22: 0.0587 REMARK 3 L33: 0.3740 L12: 0.0096 REMARK 3 L13: -0.1493 L23: -0.0461 REMARK 3 S TENSOR REMARK 3 S11: 0.0198 S12: -0.0187 S13: -0.0136 REMARK 3 S21: 0.0033 S22: -0.0078 S23: 0.0153 REMARK 3 S31: 0.0041 S32: -0.0097 S33: -0.0119 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 201 D 201 REMARK 3 ORIGIN FOR THE GROUP (A): -31.3864 -5.8970 8.4614 REMARK 3 T TENSOR REMARK 3 T11: 0.0421 T22: 0.0870 REMARK 3 T33: 0.0775 T12: -0.0020 REMARK 3 T13: -0.0310 T23: -0.0093 REMARK 3 L TENSOR REMARK 3 L11: 12.6096 L22: 120.5920 REMARK 3 L33: 42.2039 L12: 23.6357 REMARK 3 L13: -3.3933 L23: -62.4854 REMARK 3 S TENSOR REMARK 3 S11: 0.0330 S12: -0.1344 S13: -0.0137 REMARK 3 S21: 0.9805 S22: -0.6132 S23: -0.8066 REMARK 3 S31: -0.6865 S32: 0.3023 S33: 0.5803 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4OYD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1000200246. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46840 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 39.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09900 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) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.24900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.470 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: PHYSICALLY TWINNED. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG8000, MAGNESIUM CHLORIDE, TRISHCL, REMARK 280 PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 56.93450 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 300 REMARK: GELFILTRATION REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASN A 157 REMARK 465 ILE A 158 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 NH1 ARG A 60 O HOH A 221 1.90 REMARK 500 OE1 GLU A 67 O HOH A 226 1.91 REMARK 500 OD1 ASN C 157 NH2 ARG D 65 2.17 REMARK 500 O GLY A 23 O HOH A 201 2.19 REMARK 500 OE1 GLU A 43 O HOH A 202 2.19 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 ALA B 14 C GLU B 15 N 0.141 REMARK 500 LYS B 22 C GLN B 23 N 0.273 REMARK 500 LYS B 22 C GLN B 23 N 0.273 REMARK 500 GLU C 63 CD GLU C 63 OE1 0.092 REMARK 500 TYR D 61 CE1 TYR D 61 CZ -0.088 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 GLN B 23 C - N - CA ANGL. DEV. = -15.9 DEGREES REMARK 500 GLN B 23 C - N - CA ANGL. DEV. = -15.9 DEGREES REMARK 500 LEU C 81 CA - CB - CG ANGL. DEV. = 14.3 DEGREES REMARK 500 ARG D 101 NE - CZ - NH2 ANGL. DEV. = -4.5 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 GLN C 119 27.80 48.06 REMARK 500 ASP C 156 32.29 -77.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ALA B 14 -12.45 REMARK 500 ALA B 14 -12.65 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 residue EDO D 201 DBREF 4OYD A 2 158 UNP P0C6Z1 EAR_EBVA8 2 158 DBREF 4OYD B 1 117 PDB 4OYD 4OYD 1 117 DBREF 4OYD C 2 158 UNP P0C6Z1 EAR_EBVA8 2 158 DBREF 4OYD D 1 117 PDB 4OYD 4OYD 1 117 SEQADV 4OYD SER A 1 UNP P0C6Z1 EXPRESSION TAG SEQADV 4OYD SER C 1 UNP P0C6Z1 EXPRESSION TAG SEQRES 1 A 158 SER ALA TYR SER THR ARG GLU ILE LEU LEU ALA LEU CYS SEQRES 2 A 158 ILE ARG ASP SER ARG VAL HIS GLY ASN GLY THR LEU HIS SEQRES 3 A 158 PRO VAL LEU GLU LEU ALA ALA ARG GLU THR PRO LEU ARG SEQRES 4 A 158 LEU SER PRO GLU ASP THR VAL VAL LEU ARG TYR HIS VAL SEQRES 5 A 158 LEU LEU GLU GLU ILE ILE GLU ARG ASN SER GLU THR PHE SEQRES 6 A 158 THR GLU THR TRP ASN ARG PHE ILE THR HIS THR GLU HIS SEQRES 7 A 158 VAL ASP LEU ASP PHE ASN SER VAL PHE LEU GLU ILE PHE SEQRES 8 A 158 HIS ARG GLY ASP PRO SER LEU GLY ARG ALA LEU ALA TRP SEQRES 9 A 158 MET ALA TRP CYS MET HIS ALA CYS ARG THR LEU CYS CYS SEQRES 10 A 158 ASN GLN SER THR PRO TYR TYR VAL VAL ASP LEU SER VAL SEQRES 11 A 158 ARG GLY MET LEU GLU ALA SER GLU GLY LEU ASP GLY TRP SEQRES 12 A 158 ILE HIS GLN GLN GLY GLY TRP SER THR LEU ILE GLU ASP SEQRES 13 A 158 ASN ILE SEQRES 1 B 117 ALA ASP PRO LYS LYS VAL LEU ASP LYS ALA LYS ASP GLN SEQRES 2 B 117 ALA GLU ASN ARG VAL ARG GLU LEU LYS GLN LYS LEU GLU SEQRES 3 B 117 GLU LEU TYR LYS GLU ALA ARG LYS LEU ASP LEU THR GLN SEQRES 4 B 117 GLU MET ARG ARG LYS LEU GLU LEU ARG TYR ILE ALA ALA SEQRES 5 B 117 MET LEU MET ALA ILE GLY ASP ILE TYR ASN ALA ILE ARG SEQRES 6 B 117 GLN ALA LYS GLN GLU ALA ASP LYS LEU LYS LYS ALA GLY SEQRES 7 B 117 LEU VAL ASN SER GLN GLN LEU ASP GLU LEU LYS ARG ARG SEQRES 8 B 117 LEU GLU GLU LEU LYS GLU GLU ALA SER ARG LYS ALA ARG SEQRES 9 B 117 ASP TYR GLY ARG GLU PHE GLN LEU LYS LEU GLU TYR GLY SEQRES 1 C 158 SER ALA TYR SER THR ARG GLU ILE LEU LEU ALA LEU CYS SEQRES 2 C 158 ILE ARG ASP SER ARG VAL HIS GLY ASN GLY THR LEU HIS SEQRES 3 C 158 PRO VAL LEU GLU LEU ALA ALA ARG GLU THR PRO LEU ARG SEQRES 4 C 158 LEU SER PRO GLU ASP THR VAL VAL LEU ARG TYR HIS VAL SEQRES 5 C 158 LEU LEU GLU GLU ILE ILE GLU ARG ASN SER GLU THR PHE SEQRES 6 C 158 THR GLU THR TRP ASN ARG PHE ILE THR HIS THR GLU HIS SEQRES 7 C 158 VAL ASP LEU ASP PHE ASN SER VAL PHE LEU GLU ILE PHE SEQRES 8 C 158 HIS ARG GLY ASP PRO SER LEU GLY ARG ALA LEU ALA TRP SEQRES 9 C 158 MET ALA TRP CYS MET HIS ALA CYS ARG THR LEU CYS CYS SEQRES 10 C 158 ASN GLN SER THR PRO TYR TYR VAL VAL ASP LEU SER VAL SEQRES 11 C 158 ARG GLY MET LEU GLU ALA SER GLU GLY LEU ASP GLY TRP SEQRES 12 C 158 ILE HIS GLN GLN GLY GLY TRP SER THR LEU ILE GLU ASP SEQRES 13 C 158 ASN ILE SEQRES 1 D 117 ALA ASP PRO LYS LYS VAL LEU ASP LYS ALA LYS ASP GLN SEQRES 2 D 117 ALA GLU ASN ARG VAL ARG GLU LEU LYS GLN LYS LEU GLU SEQRES 3 D 117 GLU LEU TYR LYS GLU ALA ARG LYS LEU ASP LEU THR GLN SEQRES 4 D 117 GLU MET ARG ARG LYS LEU GLU LEU ARG TYR ILE ALA ALA SEQRES 5 D 117 MET LEU MET ALA ILE GLY ASP ILE TYR ASN ALA ILE ARG SEQRES 6 D 117 GLN ALA LYS GLN GLU ALA ASP LYS LEU LYS LYS ALA GLY SEQRES 7 D 117 LEU VAL ASN SER GLN GLN LEU ASP GLU LEU LYS ARG ARG SEQRES 8 D 117 LEU GLU GLU LEU LYS GLU GLU ALA SER ARG LYS ALA ARG SEQRES 9 D 117 ASP TYR GLY ARG GLU PHE GLN LEU LYS LEU GLU TYR GLY HET EDO D 201 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 EDO C2 H6 O2 FORMUL 6 HOH *165(H2 O) HELIX 1 AA1 SER A 4 ARG A 18 1 15 HELIX 2 AA2 HIS A 26 THR A 36 1 11 HELIX 3 AA3 ASP A 44 ASN A 61 1 18 HELIX 4 AA4 ASN A 61 THR A 74 1 14 HELIX 5 AA5 HIS A 78 HIS A 92 1 15 HELIX 6 AA6 SER A 97 ASN A 118 1 22 HELIX 7 AA7 PRO A 122 GLU A 138 1 17 HELIX 8 AA8 LEU A 140 GLN A 147 1 8 HELIX 9 AA9 GLY A 148 ILE A 154 1 7 HELIX 10 AB1 ASP B 2 ARG B 33 1 32 HELIX 11 AB2 THR B 38 ALA B 77 1 40 HELIX 12 AB3 ASN B 81 GLY B 117 1 37 HELIX 13 AB4 SER C 4 VAL C 19 1 16 HELIX 14 AB5 HIS C 26 THR C 36 1 11 HELIX 15 AB6 ASP C 44 ASN C 61 1 18 HELIX 16 AB7 ASN C 61 THR C 74 1 14 HELIX 17 AB8 HIS C 78 HIS C 92 1 15 HELIX 18 AB9 SER C 97 ASN C 118 1 22 HELIX 19 AC1 PRO C 122 GLU C 138 1 17 HELIX 20 AC2 LEU C 140 GLN C 147 1 8 HELIX 21 AC3 GLY C 148 ILE C 154 1 7 HELIX 22 AC4 GLU C 155 ILE C 158 5 4 HELIX 23 AC5 ASP D 2 ARG D 33 1 32 HELIX 24 AC6 THR D 38 ALA D 77 1 40 HELIX 25 AC7 ASN D 81 GLY D 117 1 37 CISPEP 1 THR A 36 PRO A 37 0 -10.47 CISPEP 2 THR C 36 PRO C 37 0 -8.34 SITE 1 AC1 2 ASN D 81 SER D 82 CRYST1 52.103 113.869 55.670 90.00 90.03 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 0.019193 0.000000 0.000010 0.00000 SCALE2 0.000000 0.008782 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017963 0.00000