HEADER VIRAL PROTEIN 03-DEC-09 3KXS TITLE CRYSTAL STRUCTURE OF HBV CAPSID MUTANT DIMER (OXY FORM), STRAIN ADYW COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAPSID PROTEIN; COMPND 3 CHAIN: F, E, C, D, A, B; COMPND 4 FRAGMENT: ASSEMBLY DOMAIN RESIDUES 1 TO 149; COMPND 5 SYNONYM: CORE PROTEIN, CORE ANTIGEN, HBCAG, P21.5; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HEPATITIS B VIRUS SUBTYPE ADYW; SOURCE 3 ORGANISM_COMMON: HBV-D; SOURCE 4 ORGANISM_TAXID: 10419; SOURCE 5 STRAIN: ADYW; SOURCE 6 GENE: C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET11C KEYWDS CORE PROTEIN, CAPSID, HEPADNAVIRUS, FOUR HELIX BUNDLE, ICOSAHEDRAL, KEYWDS 2 DIMER, CAPSID PROTEIN, DNA-BINDING, HOST CYTOPLASM, HOST-VIRUS KEYWDS 3 INTERACTION, PHOSPHOPROTEIN, RNA-BINDING, VIRION, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.PACKIANATHAN,S.P.KATEN,A.ZLOTNICK REVDAT 2 13-OCT-21 3KXS 1 SEQADV SSBOND REVDAT 1 02-FEB-10 3KXS 0 JRNL AUTH C.PACKIANATHAN,S.P.KATEN,C.E.DANN,A.ZLOTNICK JRNL TITL CONFORMATIONAL CHANGES IN THE HEPATITIS B VIRUS CORE PROTEIN JRNL TITL 2 ARE CONSISTENT WITH A ROLE FOR ALLOSTERY IN VIRUS ASSEMBLY JRNL REF J.VIROL. V. 84 1607 2010 JRNL REFN ISSN 0022-538X JRNL PMID 19939922 JRNL DOI 10.1128/JVI.02033-09 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.R.BOURNE,S.P.KATEN,M.R.FULZ,C.PACKIANATHAN,A.ZLOTNICK REMARK 1 TITL A MUTANT HEPATITIS B VIRUS CORE PROTEIN MIMICS INHIBITORS OF REMARK 1 TITL 2 ICOSAHEDRAL CAPSID SELF-ASSEMBLY REMARK 1 REF BIOCHEMISTRY V. 48 1736 2009 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 19196007 REMARK 1 DOI 10.1021/BI801814Y REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 47650 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) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2547 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) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.31 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3506 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.2780 REMARK 3 BIN FREE R VALUE SET COUNT : 199 REMARK 3 BIN FREE R VALUE : 0.3250 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6724 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 208 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : 0.02000 REMARK 3 B33 (A**2) : -0.04000 REMARK 3 B12 (A**2) : 0.01000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.294 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.231 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6936 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9517 ; 1.926 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 844 ; 5.226 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 297 ;34.046 ;22.862 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1030 ;17.267 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 46 ;23.512 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1089 ; 0.121 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5330 ; 0.015 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 4280 ; 1.120 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6963 ; 2.013 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2656 ; 2.916 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2554 ; 4.549 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3KXS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000056580. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUL-09 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 6.5 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 RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC BLUE CONFOCAL MIRROR REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 228368 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 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 : 4.500 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 41.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.57200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.340 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 1QGT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG1500, CALCIUM ACETATE, SODIUM REMARK 280 CACODYLATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.97233 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 57.94467 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: AUTHORS STATE THAT THE MUTANT IS AN ASSEMBLY DEFICIENT REMARK 300 DIMER OF CORE PROTEIN. THE WT IS ALSO A DIMER IN SOLUTION BUT CAN REMARK 300 BE ASSEMBLED INTO AN ICOSAHEDRON (PDB ACCESSION 2G33). 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: 3830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: F, E 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: 3780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 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 350 REMARK 350 BIOMOLECULE: 3 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: 3890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 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 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 LEU F 143 REMARK 465 LEU C 143 REMARK 465 THR D 142 REMARK 465 LEU D 143 REMARK 465 SER A 141 REMARK 465 THR A 142 REMARK 465 LEU A 143 REMARK 465 LEU B 143 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 ARG C 82 CG CD NE CZ NH1 NH2 REMARK 470 ARG D 82 CG CD NE CZ NH1 NH2 REMARK 470 ASP D 83 CG OD1 OD2 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 ASP D 83 O LEU D 84 1.79 REMARK 500 O SER D 81 N LEU D 84 2.10 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 NH2 ARG E 127 OG SER A 81 3544 0.72 REMARK 500 CZ ARG E 127 OG SER A 81 3544 1.77 REMARK 500 NH2 ARG E 127 CB SER A 81 3544 2.11 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 F 135 C - N - CD ANGL. DEV. = -12.6 DEGREES REMARK 500 PRO D 79 C - N - CD ANGL. DEV. = -19.5 DEGREES REMARK 500 PRO B 20 C - N - CD ANGL. DEV. = -19.3 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 F 22 -14.23 -49.05 REMARK 500 CYS F 48 -53.17 70.93 REMARK 500 TRP F 125 -70.34 -45.79 REMARK 500 PRO F 130 34.42 -50.89 REMARK 500 PRO F 135 -23.18 -30.73 REMARK 500 ASN F 136 64.16 -49.29 REMARK 500 ALA E 11 -169.02 -126.86 REMARK 500 CYS E 48 -52.28 69.69 REMARK 500 ASN E 92 -93.25 -122.31 REMARK 500 ALA E 132 -148.73 -69.76 REMARK 500 ARG E 133 92.66 66.51 REMARK 500 PRO E 134 174.47 -41.77 REMARK 500 ILE C 126 1.70 -61.19 REMARK 500 ARG C 133 130.25 -36.15 REMARK 500 SER C 141 72.43 -156.50 REMARK 500 ASP D 2 -68.79 -95.81 REMARK 500 ILE D 3 103.31 69.42 REMARK 500 SER D 26 172.00 -54.15 REMARK 500 ASP D 78 -80.22 -12.83 REMARK 500 PRO D 79 -24.06 37.14 REMARK 500 ALA D 80 25.44 87.35 REMARK 500 SER D 81 -74.19 -92.74 REMARK 500 ARG D 82 -57.72 -22.84 REMARK 500 LEU D 84 -144.59 -45.26 REMARK 500 VAL D 85 -72.97 44.24 REMARK 500 ASN D 92 -82.31 -120.49 REMARK 500 PRO D 138 171.55 -53.24 REMARK 500 LEU A 19 111.20 95.24 REMARK 500 SER A 44 -179.53 -68.92 REMARK 500 CYS A 48 -34.48 -35.75 REMARK 500 ASN A 75 -160.46 -108.76 REMARK 500 LEU A 76 -14.53 104.67 REMARK 500 GLU A 77 57.20 38.93 REMARK 500 SER A 81 -53.70 111.09 REMARK 500 ASN A 92 -79.26 -113.35 REMARK 500 PRO A 129 134.94 -33.81 REMARK 500 ALA A 132 42.18 -95.07 REMARK 500 PRO A 135 9.01 -52.78 REMARK 500 ALA A 137 -138.25 -59.48 REMARK 500 ILE A 139 151.59 62.00 REMARK 500 ALA B 11 -163.24 -116.54 REMARK 500 LEU B 19 106.29 -56.18 REMARK 500 SER B 21 8.46 -43.27 REMARK 500 ASP B 22 11.80 -146.08 REMARK 500 CYS B 48 -53.68 67.03 REMARK 500 GLU B 77 158.59 165.76 REMARK 500 ASP B 78 45.29 -169.13 REMARK 500 PRO B 79 46.31 -60.23 REMARK 500 ALA B 80 25.94 39.20 REMARK 500 SER B 81 31.90 -96.55 REMARK 500 REMARK 500 THIS ENTRY HAS 53 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2G33 RELATED DB: PDB REMARK 900 T=4 CAPSID OF 120 ASSEMBLY DOMAIN DIMERS REMARK 900 RELATED ID: 2G34 RELATED DB: PDB REMARK 900 T=4 CAPSID OF 120 ASSEMBLY DOMAIN DIMERS COMPLEXED WITH THE REMARK 900 ASSEMBLY EFFECTOR HAP1 DBREF 3KXS F 1 143 UNP P03147 CAPSD_HBVD1 1 143 DBREF 3KXS E 1 143 UNP P03147 CAPSD_HBVD1 1 143 DBREF 3KXS C 1 143 UNP P03147 CAPSD_HBVD1 1 143 DBREF 3KXS D 1 143 UNP P03147 CAPSD_HBVD1 1 143 DBREF 3KXS A 1 143 UNP P03147 CAPSD_HBVD1 1 143 DBREF 3KXS B 1 143 UNP P03147 CAPSD_HBVD1 1 143 SEQADV 3KXS ALA F 132 UNP P03147 TYR 132 ENGINEERED MUTATION SEQADV 3KXS ALA E 132 UNP P03147 TYR 132 ENGINEERED MUTATION SEQADV 3KXS ALA C 132 UNP P03147 TYR 132 ENGINEERED MUTATION SEQADV 3KXS ALA D 132 UNP P03147 TYR 132 ENGINEERED MUTATION SEQADV 3KXS ALA A 132 UNP P03147 TYR 132 ENGINEERED MUTATION SEQADV 3KXS ALA B 132 UNP P03147 TYR 132 ENGINEERED MUTATION SEQRES 1 F 143 MET ASP ILE ASP PRO TYR LYS GLU PHE GLY ALA THR VAL SEQRES 2 F 143 GLU LEU LEU SER PHE LEU PRO SER ASP PHE PHE PRO SER SEQRES 3 F 143 VAL ARG ASP LEU LEU ASP THR ALA ALA ALA LEU TYR ARG SEQRES 4 F 143 ASP ALA LEU GLU SER PRO GLU HIS CYS SER PRO HIS HIS SEQRES 5 F 143 THR ALA LEU ARG GLN ALA ILE LEU CYS TRP GLY ASP LEU SEQRES 6 F 143 MET THR LEU ALA THR TRP VAL GLY THR ASN LEU GLU ASP SEQRES 7 F 143 PRO ALA SER ARG ASP LEU VAL VAL SER TYR VAL ASN THR SEQRES 8 F 143 ASN VAL GLY LEU LYS PHE ARG GLN LEU LEU TRP PHE HIS SEQRES 9 F 143 ILE SER CYS LEU THR PHE GLY ARG GLU THR VAL LEU GLU SEQRES 10 F 143 TYR LEU VAL SER PHE GLY VAL TRP ILE ARG THR PRO PRO SEQRES 11 F 143 ALA ALA ARG PRO PRO ASN ALA PRO ILE LEU SER THR LEU SEQRES 1 E 143 MET ASP ILE ASP PRO TYR LYS GLU PHE GLY ALA THR VAL SEQRES 2 E 143 GLU LEU LEU SER PHE LEU PRO SER ASP PHE PHE PRO SER SEQRES 3 E 143 VAL ARG ASP LEU LEU ASP THR ALA ALA ALA LEU TYR ARG SEQRES 4 E 143 ASP ALA LEU GLU SER PRO GLU HIS CYS SER PRO HIS HIS SEQRES 5 E 143 THR ALA LEU ARG GLN ALA ILE LEU CYS TRP GLY ASP LEU SEQRES 6 E 143 MET THR LEU ALA THR TRP VAL GLY THR ASN LEU GLU ASP SEQRES 7 E 143 PRO ALA SER ARG ASP LEU VAL VAL SER TYR VAL ASN THR SEQRES 8 E 143 ASN VAL GLY LEU LYS PHE ARG GLN LEU LEU TRP PHE HIS SEQRES 9 E 143 ILE SER CYS LEU THR PHE GLY ARG GLU THR VAL LEU GLU SEQRES 10 E 143 TYR LEU VAL SER PHE GLY VAL TRP ILE ARG THR PRO PRO SEQRES 11 E 143 ALA ALA ARG PRO PRO ASN ALA PRO ILE LEU SER THR LEU SEQRES 1 C 143 MET ASP ILE ASP PRO TYR LYS GLU PHE GLY ALA THR VAL SEQRES 2 C 143 GLU LEU LEU SER PHE LEU PRO SER ASP PHE PHE PRO SER SEQRES 3 C 143 VAL ARG ASP LEU LEU ASP THR ALA ALA ALA LEU TYR ARG SEQRES 4 C 143 ASP ALA LEU GLU SER PRO GLU HIS CYS SER PRO HIS HIS SEQRES 5 C 143 THR ALA LEU ARG GLN ALA ILE LEU CYS TRP GLY ASP LEU SEQRES 6 C 143 MET THR LEU ALA THR TRP VAL GLY THR ASN LEU GLU ASP SEQRES 7 C 143 PRO ALA SER ARG ASP LEU VAL VAL SER TYR VAL ASN THR SEQRES 8 C 143 ASN VAL GLY LEU LYS PHE ARG GLN LEU LEU TRP PHE HIS SEQRES 9 C 143 ILE SER CYS LEU THR PHE GLY ARG GLU THR VAL LEU GLU SEQRES 10 C 143 TYR LEU VAL SER PHE GLY VAL TRP ILE ARG THR PRO PRO SEQRES 11 C 143 ALA ALA ARG PRO PRO ASN ALA PRO ILE LEU SER THR LEU SEQRES 1 D 143 MET ASP ILE ASP PRO TYR LYS GLU PHE GLY ALA THR VAL SEQRES 2 D 143 GLU LEU LEU SER PHE LEU PRO SER ASP PHE PHE PRO SER SEQRES 3 D 143 VAL ARG ASP LEU LEU ASP THR ALA ALA ALA LEU TYR ARG SEQRES 4 D 143 ASP ALA LEU GLU SER PRO GLU HIS CYS SER PRO HIS HIS SEQRES 5 D 143 THR ALA LEU ARG GLN ALA ILE LEU CYS TRP GLY ASP LEU SEQRES 6 D 143 MET THR LEU ALA THR TRP VAL GLY THR ASN LEU GLU ASP SEQRES 7 D 143 PRO ALA SER ARG ASP LEU VAL VAL SER TYR VAL ASN THR SEQRES 8 D 143 ASN VAL GLY LEU LYS PHE ARG GLN LEU LEU TRP PHE HIS SEQRES 9 D 143 ILE SER CYS LEU THR PHE GLY ARG GLU THR VAL LEU GLU SEQRES 10 D 143 TYR LEU VAL SER PHE GLY VAL TRP ILE ARG THR PRO PRO SEQRES 11 D 143 ALA ALA ARG PRO PRO ASN ALA PRO ILE LEU SER THR LEU SEQRES 1 A 143 MET ASP ILE ASP PRO TYR LYS GLU PHE GLY ALA THR VAL SEQRES 2 A 143 GLU LEU LEU SER PHE LEU PRO SER ASP PHE PHE PRO SER SEQRES 3 A 143 VAL ARG ASP LEU LEU ASP THR ALA ALA ALA LEU TYR ARG SEQRES 4 A 143 ASP ALA LEU GLU SER PRO GLU HIS CYS SER PRO HIS HIS SEQRES 5 A 143 THR ALA LEU ARG GLN ALA ILE LEU CYS TRP GLY ASP LEU SEQRES 6 A 143 MET THR LEU ALA THR TRP VAL GLY THR ASN LEU GLU ASP SEQRES 7 A 143 PRO ALA SER ARG ASP LEU VAL VAL SER TYR VAL ASN THR SEQRES 8 A 143 ASN VAL GLY LEU LYS PHE ARG GLN LEU LEU TRP PHE HIS SEQRES 9 A 143 ILE SER CYS LEU THR PHE GLY ARG GLU THR VAL LEU GLU SEQRES 10 A 143 TYR LEU VAL SER PHE GLY VAL TRP ILE ARG THR PRO PRO SEQRES 11 A 143 ALA ALA ARG PRO PRO ASN ALA PRO ILE LEU SER THR LEU SEQRES 1 B 143 MET ASP ILE ASP PRO TYR LYS GLU PHE GLY ALA THR VAL SEQRES 2 B 143 GLU LEU LEU SER PHE LEU PRO SER ASP PHE PHE PRO SER SEQRES 3 B 143 VAL ARG ASP LEU LEU ASP THR ALA ALA ALA LEU TYR ARG SEQRES 4 B 143 ASP ALA LEU GLU SER PRO GLU HIS CYS SER PRO HIS HIS SEQRES 5 B 143 THR ALA LEU ARG GLN ALA ILE LEU CYS TRP GLY ASP LEU SEQRES 6 B 143 MET THR LEU ALA THR TRP VAL GLY THR ASN LEU GLU ASP SEQRES 7 B 143 PRO ALA SER ARG ASP LEU VAL VAL SER TYR VAL ASN THR SEQRES 8 B 143 ASN VAL GLY LEU LYS PHE ARG GLN LEU LEU TRP PHE HIS SEQRES 9 B 143 ILE SER CYS LEU THR PHE GLY ARG GLU THR VAL LEU GLU SEQRES 10 B 143 TYR LEU VAL SER PHE GLY VAL TRP ILE ARG THR PRO PRO SEQRES 11 B 143 ALA ALA ARG PRO PRO ASN ALA PRO ILE LEU SER THR LEU FORMUL 7 HOH *208(H2 O) HELIX 1 1 TYR F 6 GLY F 10 5 5 HELIX 2 2 THR F 12 PHE F 18 1 7 HELIX 3 3 PRO F 20 PHE F 24 5 5 HELIX 4 4 SER F 26 SER F 44 1 19 HELIX 5 5 SER F 49 GLU F 77 1 29 HELIX 6 6 ASP F 78 ARG F 82 5 5 HELIX 7 7 ASP F 83 GLY F 111 1 29 HELIX 8 8 GLY F 111 ARG F 127 1 17 HELIX 9 9 TYR E 6 GLY E 10 5 5 HELIX 10 10 THR E 12 PHE E 18 1 7 HELIX 11 11 LEU E 19 PHE E 24 5 6 HELIX 12 12 SER E 26 SER E 44 1 19 HELIX 13 13 SER E 49 ASN E 75 1 27 HELIX 14 14 ASP E 78 ASN E 92 1 15 HELIX 15 15 ASN E 92 GLY E 111 1 20 HELIX 16 16 GLY E 111 ARG E 127 1 17 HELIX 17 17 TYR C 6 GLY C 10 5 5 HELIX 18 18 THR C 12 SER C 17 1 6 HELIX 19 19 PHE C 18 LEU C 19 5 2 HELIX 20 20 PRO C 20 PHE C 24 5 5 HELIX 21 21 SER C 26 SER C 44 1 19 HELIX 22 22 SER C 49 THR C 74 1 26 HELIX 23 23 ASP C 78 GLY C 111 1 34 HELIX 24 24 GLY C 111 ILE C 126 1 16 HELIX 25 25 TYR D 6 GLY D 10 5 5 HELIX 26 26 THR D 12 PHE D 18 1 7 HELIX 27 27 PRO D 20 PHE D 24 5 5 HELIX 28 28 SER D 26 SER D 44 1 19 HELIX 29 29 SER D 49 GLY D 73 1 25 HELIX 30 30 ARG D 82 ASN D 92 1 11 HELIX 31 31 ASN D 92 GLY D 111 1 20 HELIX 32 32 GLY D 111 THR D 128 1 18 HELIX 33 33 PRO D 129 ARG D 133 5 5 HELIX 34 34 TYR A 6 GLY A 10 5 5 HELIX 35 35 THR A 12 PHE A 18 1 7 HELIX 36 36 PRO A 20 PHE A 24 5 5 HELIX 37 37 SER A 26 TYR A 38 1 13 HELIX 38 38 TYR A 38 SER A 44 1 7 HELIX 39 39 SER A 49 ASN A 75 1 27 HELIX 40 40 SER A 81 ASN A 92 1 12 HELIX 41 41 ASN A 92 GLY A 111 1 20 HELIX 42 42 GLY A 111 ILE A 126 1 16 HELIX 43 43 TYR B 6 GLY B 10 5 5 HELIX 44 44 THR B 12 SER B 17 1 6 HELIX 45 45 SER B 26 GLU B 43 1 18 HELIX 46 46 SER B 49 LEU B 76 1 28 HELIX 47 47 ASP B 83 GLY B 111 1 29 HELIX 48 48 GLY B 111 THR B 128 1 18 HELIX 49 49 PRO B 129 ARG B 133 5 5 SSBOND 1 CYS F 61 CYS E 61 1555 1555 2.05 SSBOND 2 CYS C 61 CYS D 61 1555 1555 2.06 SSBOND 3 CYS A 61 CYS B 61 1555 1555 2.11 CRYST1 104.162 104.162 86.917 90.00 90.00 120.00 P 31 18 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 0.009600 0.005543 0.000000 0.00000 SCALE2 0.000000 0.011086 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011505 0.00000 MASTER 424 0 0 49 0 0 0 6 0 0 0 66 END