10 20 30 40 50 60 70 80 3KXS - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER VIRAL PROTEIN 03-DEC-09 3KXS
TITLE CRYSTAL STRUCTURE OF HBV CAPSID MUTANT DIMER (OXY FORM), TITLE 2 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, KEYWDS 2 ICOSAHEDRAL, DIMER, CAPSID PROTEIN, DNA-BINDING, HOST KEYWDS 3 CYTOPLASM, HOST-VIRUS INTERACTION, PHOSPHOPROTEIN, RNA- KEYWDS 4 BINDING, VIRION
EXPDTA X-RAY DIFFRACTION
AUTHOR C.PACKIANATHAN,S.P.KATEN,A.ZLOTNICK
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 JRNL TITL 2 CORE PROTEIN ARE CONSISTENT WITH A ROLE FOR JRNL TITL 3 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, REMARK 1 AUTH 2 A.ZLOTNICK REMARK 1 TITL A MUTANT HEPATITIS B VIRUS CORE PROTEIN MIMICS REMARK 1 TITL 2 INHIBITORS OF 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 5.5.0066 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON 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 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2656 ; 2.916 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2554 ; 4.549 ; 4.500 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. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-DEC-09. REMARK 100 THE RCSB ID CODE IS RCSB056580.
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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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 REMARK 300 CAN 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: 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 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
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 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 SEQADV 3KXS ALA E 132 UNP P03147 TYR 132 ENGINEERED SEQADV 3KXS ALA C 132 UNP P03147 TYR 132 ENGINEERED SEQADV 3KXS ALA D 132 UNP P03147 TYR 132 ENGINEERED SEQADV 3KXS ALA A 132 UNP P03147 TYR 132 ENGINEERED SEQADV 3KXS ALA B 132 UNP P03147 TYR 132 ENGINEERED
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 E 61 CYS F 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