PDB Short entry for 2WLV HEADER VIRAL PROTEIN 26-JUN-09 2WLV TITLE STRUCTURE OF THE N-TERMINAL CAPSID DOMAIN OF HIV-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAG POLYPROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN, RESIDUES 99-242; COMPND 5 SYNONYM: HIV-2 CAPSID,; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: GAG POLYPROTEIN; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: N-TERMINAL DOMAIN, RESIDUES 99-242; COMPND 11 SYNONYM: HIV-2 CAPSID,; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 2 (ISOLATE SOURCE 3 D194); SOURCE 4 ORGANISM_TAXID: 11713; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 2 (ISOLATE SOURCE 9 D194); SOURCE 10 ORGANISM_TAXID: 11713; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS VIRAL PROTEIN, RNA-BINDING, CAPSID PROTEIN, VIRAL NUCLEOPROTEIN, KEYWDS 2 HIV, AIDS, HIV-2, HIV-1 EXPDTA X-RAY DIFFRACTION AUTHOR A.J.PRICE,F.MARZETTA,M.LAMMERS,L.M.J.YLINEN,T.SCHALLER,S.J.WILSON, AUTHOR 2 G.J.TOWERS,L.C.JAMES REVDAT 5 12-MAR-14 2WLV 1 SOURCE REVDAT 4 24-APR-13 2WLV 1 HEADER COMPND SOURCE KEYWDS REVDAT 4 2 AUTHOR JRNL REMARK VERSN REVDAT 4 3 SEQADV SEQRES CRYST1 ATOM REVDAT 4 4 ANISOU HETATM MASTER REVDAT 3 06-JUL-11 2WLV 1 JRNL REMARK FORMUL REVDAT 2 29-SEP-09 2WLV 1 JRNL REVDAT 1 22-SEP-09 2WLV 0 JRNL AUTH A.J.PRICE,F.MARZETTA,M.LAMMERS,L.M.J.YLINEN,T.SCHALLER, JRNL AUTH 2 S.J.WILSON,G.J.TOWERS,L.C.JAMES JRNL TITL ACTIVE SITE REMODELLING SWITCHES HIV SPECIFICITY OF JRNL TITL 2 ANTIRETROVIRAL TRIMCYP JRNL REF NAT.STRUCT.MOL.BIOL. V. 16 1036 2009 JRNL REFN ISSN 1545-9993 JRNL PMID 19767750 JRNL DOI 10.1038/NSMB.1667 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0088 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) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 88.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.79 REMARK 3 NUMBER OF REFLECTIONS : 107428 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) : 0.15456 REMARK 3 R VALUE (WORKING SET) : 0.15295 REMARK 3 FREE R VALUE : 0.18444 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 5669 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) : 1.248 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.280 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7816 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.47 REMARK 3 BIN R VALUE (WORKING SET) : 0.244 REMARK 3 BIN FREE R VALUE SET COUNT : 435 REMARK 3 BIN FREE R VALUE : 0.285 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2278 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 675 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.3 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.659 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.33 REMARK 3 B22 (A**2) : -0.59 REMARK 3 B33 (A**2) : 0.26 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.038 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.040 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.026 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.309 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.965 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2520 ; 0.031 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1745 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3458 ; 2.429 ; 1.943 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4256 ; 1.318 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 322 ; 6.584 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 128 ;31.629 ;24.219 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 419 ;14.713 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;21.366 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 362 ; 0.159 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2906 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 500 ; 0.003 ; 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): 1539 ; 2.744 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 611 ; 1.655 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2530 ; 3.674 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 981 ; 4.713 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 925 ; 6.587 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 4265 ; 2.668 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 675 ;13.540 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4185 ; 6.781 ; 3.000 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 : BABINET MODEL WITH 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 2WLV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-APR-13. REMARK 100 THE PDBE ID CODE IS EBI-40217. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 113327 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.20 REMARK 200 RESOLUTION RANGE LOW (A) : 34.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.9 REMARK 200 R MERGE (I) : 0.05 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.90 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 47.76000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.90750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 47.76000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.90750 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 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: 1530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.2 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2038 LIES ON A SPECIAL POSITION. 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 NH1B ARG A 17 O HOH A 2060 2.17 REMARK 500 NH2B ARG A 17 O HOH A 2060 2.18 REMARK 500 OE2A GLU A 27 O HOH A 2102 2.08 REMARK 500 OE2B GLU A 78 O HOH A 2245 2.12 REMARK 500 O GLY A 92 O HOH A 2266 2.02 REMARK 500 CB GLN A 93 O HOH A 2266 1.98 REMARK 500 OE1 GLU A 96 O HOH A 2283 2.03 REMARK 500 OE1 GLU A 111 O HOH A 2276 2.20 REMARK 500 CZ B ARG A 142 O HOH A 2355 2.05 REMARK 500 NH1B ARG A 142 O HOH A 2355 1.63 REMARK 500 NH2B ARG A 142 O HOH A 2355 1.97 REMARK 500 C LYS B 29 O HOH B 2102 1.91 REMARK 500 NZ LYS B 29 O HOH B 2097 1.83 REMARK 500 N LYS B 30 O HOH B 2102 1.78 REMARK 500 CG1 VAL B 58 O HOH B 2169 1.89 REMARK 500 SD MET B 65 O HOH B 2169 2.10 REMARK 500 OE1 GLU B 74 O HOH B 2205 1.85 REMARK 500 OE1 GLN B 114 O HOH B 2262 2.19 REMARK 500 OE1A GLN B 134 O HOH B 2300 2.02 REMARK 500 CZ B ARG B 142 O HOH B 2313 2.14 REMARK 500 NH1B ARG B 142 O HOH B 2313 1.81 REMARK 500 NH2B ARG B 142 O HOH B 2313 1.90 REMARK 500 O HOH A 2021 O HOH A 2058 0.95 REMARK 500 O HOH A 2022 O HOH A 2057 1.97 REMARK 500 O HOH A 2023 O HOH A 2024 1.80 REMARK 500 O HOH A 2029 O HOH A 2039 2.11 REMARK 500 O HOH A 2033 O HOH A 2105 2.16 REMARK 500 O HOH A 2038 O HOH A 2127 1.51 REMARK 500 O HOH A 2044 O HOH A 2045 1.60 REMARK 500 O HOH A 2047 O HOH A 2048 0.74 REMARK 500 O HOH A 2050 O HOH A 2051 0.81 REMARK 500 O HOH A 2053 O HOH A 2164 1.92 REMARK 500 O HOH A 2057 O HOH A 2059 0.87 REMARK 500 O HOH A 2058 O HOH A 2059 1.93 REMARK 500 O HOH A 2065 O HOH A 2178 2.06 REMARK 500 O HOH A 2067 O HOH A 2197 1.66 REMARK 500 O HOH A 2073 O HOH A 2074 1.90 REMARK 500 O HOH A 2077 O HOH A 2222 2.05 REMARK 500 O HOH A 2080 O HOH A 2081 1.11 REMARK 500 O HOH A 2081 O HOH A 2104 1.75 REMARK 500 O HOH A 2093 O HOH A 2237 2.16 REMARK 500 O HOH A 2094 O HOH A 2350 1.79 REMARK 500 O HOH A 2094 O HOH A 2175 1.15 REMARK 500 O HOH A 2099 O HOH A 2100 1.05 REMARK 500 O HOH A 2101 O HOH A 2115 1.44 REMARK 500 O HOH A 2110 O HOH A 2254 2.18 REMARK 500 O HOH A 2130 O HOH A 2275 1.40 REMARK 500 O HOH A 2136 O HOH A 2137 1.25 REMARK 500 O HOH A 2140 O HOH A 2292 2.08 REMARK 500 O HOH A 2140 O HOH A 2143 0.94 REMARK 500 REMARK 500 THIS ENTRY HAS 134 CLOSE CONTACTS REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O GLY A 92 O HOH A 2203 3445 1.91 REMARK 500 O A ARG A 142 O HOH A 2205 2555 2.04 REMARK 500 O B ARG A 142 O HOH A 2205 2555 2.06 REMARK 500 O HOH A 2038 O HOH A 2127 2555 1.51 REMARK 500 O HOH A 2055 O HOH A 2257 3455 2.09 REMARK 500 O HOH A 2070 O HOH A 2253 3455 1.65 REMARK 500 O HOH A 2123 O HOH A 2124 2555 1.89 REMARK 500 O HOH A 2124 O HOH A 2124 2555 0.73 REMARK 500 O HOH A 2148 O HOH A 2321 3455 1.93 REMARK 500 O HOH A 2189 O HOH A 2323 3455 0.86 REMARK 500 O HOH A 2192 O HOH A 2284 3455 1.96 REMARK 500 O HOH A 2192 O HOH A 2322 3455 2.13 REMARK 500 O HOH A 2203 O HOH A 2267 3455 1.91 REMARK 500 O HOH A 2211 O HOH A 2267 3455 1.86 REMARK 500 O HOH A 2213 O HOH A 2320 3455 2.17 REMARK 500 O HOH A 2217 O HOH A 2225 2555 2.13 REMARK 500 O HOH B 2068 O HOH B 2307 2545 2.10 REMARK 500 O HOH B 2069 O HOH B 2195 2545 1.56 REMARK 500 O HOH B 2185 O HOH B 2187 2545 1.54 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 LYS A 30 CB LYS A 30 CG -0.213 REMARK 500 GLN A 40 CD GLN A 40 NE2 0.164 REMARK 500 GLU A 44 CD GLU A 44 OE1 0.079 REMARK 500 GLU A 44 CG GLU A 44 CD 0.108 REMARK 500 TYR A 49 CE2 TYR A 49 CZ -0.089 REMARK 500 GLY A 92 CA GLY A 92 C 0.105 REMARK 500 GLY A 92 C GLY A 92 O 0.121 REMARK 500 GLY A 92 N GLY A 92 CA 0.095 REMARK 500 TYR A 144 CA TYR A 144 C 0.176 REMARK 500 TYR A 144 C TYR A 144 O 0.296 REMARK 500 GLU B 34 CG A GLU B 34 CD A 0.165 REMARK 500 TYR B 144 CA TYR B 144 C 0.185 REMARK 500 TYR B 144 C TYR B 144 O 0.124 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 A 84 C - N - CA ANGL. DEV. = 10.1 DEGREES REMARK 500 PRO A 86 C - N - CA ANGL. DEV. = 19.2 DEGREES REMARK 500 PRO A 86 C - N - CD ANGL. DEV. = -22.7 DEGREES REMARK 500 ARG A 130 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 142 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 142 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 TYR A 144 CA - C - O ANGL. DEV. = -26.9 DEGREES REMARK 500 TYR B 49 CB - CG - CD1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ASP B 60 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 TYR B 144 CA - C - O ANGL. DEV. = -20.4 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 LYS A 30 77.31 68.90 REMARK 500 ILE A 85 -82.79 154.59 REMARK 500 VAL B 5 -82.56 -114.29 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 ILE A 85 PRO A 86 -44.00 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 LYS B 24 -11.05 REMARK 500 GLN B 28 12.07 REMARK 500 LYS B 29 10.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WLW RELATED DB: PDB REMARK 900 STRUCTURE OF THE N-TERMINAL CAPSID DOMAIN OF HIV-2 DBREF 2WLV A 1 144 UNP Q76929 Q76929_9HIV2 99 242 DBREF 2WLV B 1 144 UNP Q76929 Q76929_9HIV2 99 242 SEQADV 2WLV THR A 8 UNP Q76929 ASN 106 CONFLICT SEQADV 2WLV GLU A 110 UNP Q76929 ASP 208 CONFLICT SEQADV 2WLV THR B 8 UNP Q76929 ASN 106 CONFLICT SEQADV 2WLV GLN B 27 UNP Q76929 GLU 125 CONFLICT SEQADV 2WLV GLN B 28 UNP Q76929 GLU 126 CONFLICT SEQADV 2WLV GLU B 110 UNP Q76929 ASP 208 CONFLICT SEQRES 1 A 144 PRO VAL GLN HIS VAL GLY GLY THR TYR THR HIS ILE PRO SEQRES 2 A 144 LEU SER PRO ARG THR LEU ASN ALA TRP VAL LYS LEU VAL SEQRES 3 A 144 GLU GLU LYS LYS PHE GLY ALA GLU VAL VAL PRO GLY PHE SEQRES 4 A 144 GLN ALA LEU SER GLU GLY CYS THR PRO TYR ASP ILE ASN SEQRES 5 A 144 GLN MET LEU ASN CYS VAL GLY ASP HIS GLN ALA ALA MET SEQRES 6 A 144 GLN ILE ILE ARG GLU ILE ILE ASN GLU GLU ALA ALA GLU SEQRES 7 A 144 TRP ASP VAL GLN HIS PRO ILE PRO GLY PRO LEU PRO ALA SEQRES 8 A 144 GLY GLN LEU ARG GLU PRO ARG GLY SER ASP ILE ALA GLY SEQRES 9 A 144 THR THR SER THR VAL GLU GLU GLN ILE GLN TRP MET PHE SEQRES 10 A 144 ARG PRO GLN ASN PRO VAL PRO VAL GLY ASN ILE TYR ARG SEQRES 11 A 144 ARG TRP ILE GLN ILE GLY LEU GLN LYS CYS VAL ARG MET SEQRES 12 A 144 TYR SEQRES 1 B 144 PRO VAL GLN HIS VAL GLY GLY THR TYR THR HIS ILE PRO SEQRES 2 B 144 LEU SER PRO ARG THR LEU ASN ALA TRP VAL LYS LEU VAL SEQRES 3 B 144 GLN GLN LYS LYS PHE GLY ALA GLU VAL VAL PRO GLY PHE SEQRES 4 B 144 GLN ALA LEU SER GLU GLY CYS THR PRO TYR ASP ILE ASN SEQRES 5 B 144 GLN MET LEU ASN CYS VAL GLY ASP HIS GLN ALA ALA MET SEQRES 6 B 144 GLN ILE ILE ARG GLU ILE ILE ASN GLU GLU ALA ALA GLU SEQRES 7 B 144 TRP ASP VAL GLN HIS PRO ILE PRO GLY PRO LEU PRO ALA SEQRES 8 B 144 GLY GLN LEU ARG GLU PRO ARG GLY SER ASP ILE ALA GLY SEQRES 9 B 144 THR THR SER THR VAL GLU GLU GLN ILE GLN TRP MET PHE SEQRES 10 B 144 ARG PRO GLN ASN PRO VAL PRO VAL GLY ASN ILE TYR ARG SEQRES 11 B 144 ARG TRP ILE GLN ILE GLY LEU GLN LYS CYS VAL ARG MET SEQRES 12 B 144 TYR FORMUL 3 HOH *675(H2 O) HELIX 1 1 SER A 15 LYS A 30 1 16 HELIX 2 2 GLU A 34 SER A 43 1 10 HELIX 3 3 THR A 47 CYS A 57 1 11 HELIX 4 4 HIS A 61 GLN A 82 1 22 HELIX 5 5 ARG A 98 ALA A 103 1 6 HELIX 6 6 THR A 108 ARG A 118 1 11 HELIX 7 7 PRO A 124 TYR A 144 1 21 HELIX 8 8 SER B 15 LYS B 29 1 15 HELIX 9 9 GLU B 34 SER B 43 1 10 HELIX 10 10 THR B 47 GLY B 59 1 13 HELIX 11 11 HIS B 61 HIS B 83 1 23 HELIX 12 12 ARG B 98 ALA B 103 1 6 HELIX 13 13 THR B 108 ARG B 118 1 11 HELIX 14 14 PRO B 124 TYR B 144 1 21 SHEET 1 AA 2 VAL A 2 VAL A 5 0 SHEET 2 AA 2 THR A 8 HIS A 11 -1 O THR A 8 N VAL A 5 SHEET 1 BA 2 VAL B 2 HIS B 4 0 SHEET 2 BA 2 TYR B 9 HIS B 11 -1 O THR B 10 N GLN B 3 CISPEP 1 GLY A 87 PRO A 88 0 -7.69 CISPEP 2 GLY B 87 PRO B 88 0 -26.20 CRYST1 95.520 47.815 88.570 90.00 90.00 90.00 P 21 21 2 8 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 0.010469 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020914 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011291 0.00000