PDB Short entry for 1HAR HEADER VIRAL PROTEIN, TRANSFERASE 28-OCT-94 1HAR TITLE 2.2 ANGSTROMS RESOLUTION STRUCTURE OF THE AMINO-TERMINAL HALF OF HIV-1 TITLE 2 REVERSE TRANSCRIPTASE (FINGERS AND PALM SUBDOMAINS) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 REVERSE TRANSCRIPTASE (FINGERS AND PALM SUBDOMAINS); COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.49; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PRT216.ET (DERIVATIVE OF PET) KEYWDS REVERSE TRANSCRIPTASE, VIRAL PROTEIN, TRANSFERASE, DNA POLYMERASE, KEYWDS 2 FINGERS-PALM SUBDOMAINS, N-TERMINAL HALF EXPDTA X-RAY DIFFRACTION AUTHOR T.UNGE,S.KNIGHT,B.STRANDBERG REVDAT 4 07-FEB-24 1HAR 1 SEQADV REVDAT 3 24-FEB-09 1HAR 1 VERSN REVDAT 2 01-APR-03 1HAR 1 JRNL REVDAT 1 20-APR-95 1HAR 0 JRNL AUTH T.UNGE,S.KNIGHT,R.BHIKHABHAI,S.LOVGREN,Z.DAUTER,K.WILSON, JRNL AUTH 2 B.STRANDBERG JRNL TITL 2.2 A RESOLUTION STRUCTURE OF THE AMINO-TERMINAL HALF OF JRNL TITL 2 HIV-1 REVERSE TRANSCRIPTASE (FINGERS AND PALM SUBDOMAINS). JRNL REF STRUCTURE V. 2 953 1994 JRNL REFN ISSN 0969-2126 JRNL PMID 7532533 JRNL DOI 10.1016/S0969-2126(94)00097-2 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 14650 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1542 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 90 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1HAR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000173751. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL 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 : 14650 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 15.85000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 23.77500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 7.92500 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 LYS A 64 REMARK 465 LYS A 65 REMARK 465 LYS A 66 REMARK 465 ASP A 67 REMARK 465 SER A 68 REMARK 465 THR A 69 REMARK 465 LYS A 70 REMARK 465 GLN A 91 REMARK 465 LEU A 92 REMARK 465 GLY A 93 REMARK 465 ILE A 94 REMARK 465 PRO A 95 REMARK 465 HIS A 96 REMARK 465 PRO A 97 REMARK 465 ALA A 98 REMARK 465 GLY A 99 REMARK 465 LEU A 100 REMARK 465 LYS A 101 REMARK 465 LYS A 102 REMARK 465 LYS A 103 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 SER A 134 OG REMARK 470 ILE A 135 CG1 CG2 CD1 REMARK 470 ASN A 136 CG OD1 ND2 REMARK 470 ASN A 137 CG OD1 ND2 REMARK 470 GLU A 138 CG CD OE1 OE2 REMARK 470 THR A 139 OG1 CG2 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 PRO A 4 38.99 -78.86 REMARK 500 ASN A 137 14.22 58.99 REMARK 500 GLU A 138 -87.41 -65.22 REMARK 500 ASP A 185 -19.24 81.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: ACT REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: NULL DBREF 1HAR A 1 216 UNP Q8UTX6 Q8UTX6_9HIV1 168 383 SEQADV 1HAR ALA A 22 UNP Q8UTX6 LYS 189 CONFLICT SEQADV 1HAR ALA A 28 UNP Q8UTX6 GLU 195 CONFLICT SEQADV 1HAR ALA A 29 UNP Q8UTX6 GLU 196 CONFLICT SEQADV 1HAR ALA A 32 UNP Q8UTX6 LYS 199 CONFLICT SEQADV 1HAR ALA A 36 UNP Q8UTX6 GLU 203 CONFLICT SEQADV 1HAR ALA A 72 UNP Q8UTX6 ARG 239 CONFLICT SEQADV 1HAR ALA A 169 UNP Q8UTX6 GLU 336 CONFLICT SEQADV 1HAR ALA A 173 UNP Q8UTX6 LYS 340 CONFLICT SEQADV 1HAR ALA A 174 UNP Q8UTX6 GLN 341 CONFLICT SEQADV 1HAR ALA A 194 UNP Q8UTX6 GLU 361 CONFLICT SEQADV 1HAR ALA A 197 UNP Q8UTX6 GLN 364 CONFLICT SEQRES 1 A 216 PRO ILE SER PRO ILE GLU THR VAL PRO VAL LYS LEU LYS SEQRES 2 A 216 PRO GLY MET ASP GLY PRO LYS VAL ALA GLN TRP PRO LEU SEQRES 3 A 216 THR ALA ALA LYS ILE ALA ALA LEU VAL ALA ILE CYS THR SEQRES 4 A 216 GLU MET GLU LYS GLU GLY LYS ILE SER LYS ILE GLY PRO SEQRES 5 A 216 GLU ASN PRO TYR ASN THR PRO VAL PHE ALA ILE LYS LYS SEQRES 6 A 216 LYS ASP SER THR LYS TRP ALA LYS LEU VAL ASP PHE ARG SEQRES 7 A 216 GLU LEU ASN LYS ARG THR GLN ASP PHE TRP GLU VAL GLN SEQRES 8 A 216 LEU GLY ILE PRO HIS PRO ALA GLY LEU LYS LYS LYS LYS SEQRES 9 A 216 SER VAL THR VAL LEU ASP VAL GLY ASP ALA TYR PHE SER SEQRES 10 A 216 VAL PRO LEU ASP GLU ASP PHE ARG LYS TYR THR ALA PHE SEQRES 11 A 216 THR ILE PRO SER ILE ASN ASN GLU THR PRO GLY ILE ARG SEQRES 12 A 216 TYR GLN TYR ASN VAL LEU PRO GLN GLY TRP LYS GLY SER SEQRES 13 A 216 PRO ALA ILE PHE GLN SER SER MET THR LYS ILE LEU ALA SEQRES 14 A 216 PRO PHE LYS ALA ALA ASN PRO ASP ILE VAL ILE TYR GLN SEQRES 15 A 216 TYR MET ASP ASP LEU TYR VAL GLY SER ASP LEU ALA ILE SEQRES 16 A 216 GLY ALA HIS ARG THR LYS ILE GLU GLU LEU ARG GLN HIS SEQRES 17 A 216 LEU LEU ARG TRP GLY LEU THR THR FORMUL 2 HOH *90(H2 O) HELIX 1 1 ALA A 28 LYS A 43 1 16 HELIX 2 2 ARG A 78 ARG A 83 1 6 HELIX 3 3 GLY A 112 SER A 117 5 6 HELIX 4 4 ARG A 125 THR A 128 5 4 HELIX 5 5 ILE A 135 ASN A 137 5 3 HELIX 6 6 SER A 156 ALA A 174 1 19 HELIX 7 7 ILE A 195 TRP A 212 1 18 SHEET 1 A 3 ILE A 47 LYS A 49 0 SHEET 2 A 3 ILE A 142 TYR A 146 -1 N GLN A 145 O SER A 48 SHEET 3 A 3 PHE A 130 ILE A 132 -1 N ILE A 132 O ILE A 142 SHEET 1 B 2 VAL A 60 ILE A 63 0 SHEET 2 B 2 ALA A 72 VAL A 75 -1 N LEU A 74 O PHE A 61 SHEET 1 C 3 SER A 105 ASP A 110 0 SHEET 2 C 3 ASP A 186 SER A 191 -1 N SER A 191 O SER A 105 SHEET 3 C 3 ILE A 178 TYR A 183 -1 N TYR A 183 O ASP A 186 SITE 1 ACT 3 ASP A 110 ASP A 185 ASP A 186 CRYST1 98.200 98.200 31.700 90.00 90.00 90.00 P 43 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 0.010183 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010183 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031546 0.00000