PDB Short entry for 1RDH HEADER HYDROLASE(ENDORIBONUCLEASE) 05-MAR-93 1RDH TITLE CRYSTALLOGRAPHIC ANALYSES OF AN ACTIVE HIV-1 RIBONUCLEASE H DOMAIN TITLE 2 SHOW STRUCTURAL FEATURES THAT DISTINGUISH IT FROM THE INACTIVE FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 REVERSE TRANSCRIPTASE (RIBONUCLEASE H DOMAIN); COMPND 3 CHAIN: A, B; 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 KEYWDS HYDROLASE(ENDORIBONUCLEASE) EXPDTA X-RAY DIFFRACTION MDLTYP CA ATOMS ONLY, CHAIN A, B AUTHOR B.C.FINZEL,D.CHATTOPADHYAY,H.M.EINSPAHR REVDAT 4 14-FEB-24 1RDH 1 REMARK REVDAT 3 29-NOV-17 1RDH 1 HELIX REVDAT 2 24-FEB-09 1RDH 1 VERSN REVDAT 1 31-MAY-94 1RDH 0 JRNL AUTH D.CHATTOPADHYAY,B.C.FINZEL,S.H.MUNSON,D.B.EVANS,S.K.SHARMA, JRNL AUTH 2 N.A.STRAKALAITUS,D.P.BRUNNER,F.M.ECKENRODE,Z.DAUTER, JRNL AUTH 3 C.BETZEL,H.M.EINSPAHR JRNL TITL CRYSTALLOGRAPHIC ANALYSES OF AN ACTIVE HIV-1 RIBONUCLEASE H JRNL TITL 2 DOMAIN SHOW STRUCTURAL FEATURES THAT DISTINGUISH IT FROM THE JRNL TITL 3 INACTIVE FORM. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 49 423 1993 JRNL REFN ISSN 0907-4449 JRNL PMID 15299518 JRNL DOI 10.1107/S0907444993002409 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.F.DAVIES II,Z.HOSTOMSKA,Z.HOSTOMSKY,S.R.JORDAN, REMARK 1 AUTH 2 D.A.MATTHEWS REMARK 1 TITL CRYSTAL STRUCTURE OF THE RIBONUCLEASE H DOMAIN OF HIV-1 REMARK 1 TITL 2 REVERSE TRANSCRIPTASE REMARK 1 REF SCIENCE V. 252 88 1991 REMARK 1 REFN ISSN 0036-8075 REMARK 1 REFERENCE 2 REMARK 1 AUTH D.B.EVANS,K.BRAWN,M.R.DEIBEL JUNIOR,W.G.TARPLEY,S.K.SHARMA REMARK 1 TITL A RECOMBINANT RIBONUCLEASE H DOMAIN OF HIV-1 REVERSE REMARK 1 TITL 2 TRANSCRIPTASE THAT IS ENZYMATICALLY ACTIVE REMARK 1 REF J.BIOL.CHEM. V. 266 20583 1991 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 8147 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 + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 254 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.026 ; 0.030 REMARK 3 ANGLE DISTANCE (A) : 0.052 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.054 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.018 ; 0.030 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.383 ; 0.300 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.229 ; 0.400 REMARK 3 MULTIPLE TORSION (A) : 0.264 ; 0.400 REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : 0.249 ; 0.400 REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 2.500 ; 3.000 REMARK 3 STAGGERED (DEGREES) : 10.800; 5.000 REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.995 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.699 ; 3.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.763 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.899 ; 4.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1RDH 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_1000176033. 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 : NULL 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 (%) : NULL 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 37.97333 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 75.94667 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: THERE ARE TWO MOLECULES IN THE ASYMMETRIC UNIT. THEY HAVE REMARK 300 BEEN ASSIGNED CHAIN INDICATORS *A* AND *B*. THE RESIDUE REMARK 300 NUMBERING IS BASED ON THE REVERSE TRANSCRIPTASE SEQUENCE. 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A 415 REMARK 465 PRO A 416 REMARK 465 ILE A 417 REMARK 465 HIS A 418 REMARK 465 ASP A 419 REMARK 465 HIS A 420 REMARK 465 ASP A 421 REMARK 465 HIS A 422 REMARK 465 PRO A 423 REMARK 465 PHE A 424 REMARK 465 HIS A 425 REMARK 465 GLY A 426 REMARK 465 HIS A 539 REMARK 465 LYS A 540 REMARK 465 GLY A 541 REMARK 465 ARG A 557 REMARK 465 LYS A 558 REMARK 465 ILE A 559 REMARK 465 LEU A 560 REMARK 465 MET B 415 REMARK 465 PRO B 416 REMARK 465 ILE B 417 REMARK 465 HIS B 418 REMARK 465 ASP B 419 REMARK 465 HIS B 420 REMARK 465 ASP B 421 REMARK 465 HIS B 422 REMARK 465 PRO B 423 REMARK 465 PHE B 424 REMARK 465 HIS B 425 REMARK 465 GLY B 426 REMARK 465 HIS B 539 REMARK 465 LYS B 540 REMARK 465 GLY B 541 REMARK 465 ARG B 557 REMARK 465 LYS B 558 REMARK 465 ILE B 559 REMARK 465 LEU B 560 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS RECOMBINANT VERSION OF THE HIV-1 RNASE H DOMAIN WAS REMARK 999 PREPARED WITH AN N-TERMINAL SEQUENCE TO SIMPLIFY ISOLATION. REMARK 999 THIS SEQUENCE MET-PRO-ILE-HIS-ASP-HIS-ASP-HIS-PRO-PHE-HIS REMARK 999 -GLY PRECEDING TYR 427 IS COMPLETELY DISORDERED IN THE REMARK 999 CRYSTAL AND NOT INCLUDED IN THIS ENTRY. DBREF 1RDH A 427 560 UNP P03366 POL_HV1B1 594 727 DBREF 1RDH B 427 560 UNP P03366 POL_HV1B1 594 727 SEQRES 1 A 146 MET PRO ILE HIS ASP HIS ASP HIS PRO PHE HIS GLY TYR SEQRES 2 A 146 GLN LEU GLU LYS GLU PRO ILE VAL GLY ALA GLU THR PHE SEQRES 3 A 146 TYR VAL ASP GLY ALA ALA ASN ARG GLU THR LYS LEU GLY SEQRES 4 A 146 LYS ALA GLY TYR VAL THR ASN LYS GLY ARG GLN LYS VAL SEQRES 5 A 146 VAL PRO LEU THR ASN THR THR ASN GLN LYS THR GLU LEU SEQRES 6 A 146 GLN ALA ILE TYR LEU ALA LEU GLN ASP SER GLY LEU GLU SEQRES 7 A 146 VAL ASN ILE VAL THR ASP SER GLN TYR ALA LEU GLY ILE SEQRES 8 A 146 ILE GLN ALA GLN PRO ASP LYS SER GLU SER GLU LEU VAL SEQRES 9 A 146 ASN GLN ILE ILE GLU GLN LEU ILE LYS LYS GLU LYS VAL SEQRES 10 A 146 TYR LEU ALA TRP VAL PRO ALA HIS LYS GLY ILE GLY GLY SEQRES 11 A 146 ASN GLU GLN VAL ASP LYS LEU VAL SER ALA GLY ILE ARG SEQRES 12 A 146 LYS ILE LEU SEQRES 1 B 146 MET PRO ILE HIS ASP HIS ASP HIS PRO PHE HIS GLY TYR SEQRES 2 B 146 GLN LEU GLU LYS GLU PRO ILE VAL GLY ALA GLU THR PHE SEQRES 3 B 146 TYR VAL ASP GLY ALA ALA ASN ARG GLU THR LYS LEU GLY SEQRES 4 B 146 LYS ALA GLY TYR VAL THR ASN LYS GLY ARG GLN LYS VAL SEQRES 5 B 146 VAL PRO LEU THR ASN THR THR ASN GLN LYS THR GLU LEU SEQRES 6 B 146 GLN ALA ILE TYR LEU ALA LEU GLN ASP SER GLY LEU GLU SEQRES 7 B 146 VAL ASN ILE VAL THR ASP SER GLN TYR ALA LEU GLY ILE SEQRES 8 B 146 ILE GLN ALA GLN PRO ASP LYS SER GLU SER GLU LEU VAL SEQRES 9 B 146 ASN GLN ILE ILE GLU GLN LEU ILE LYS LYS GLU LYS VAL SEQRES 10 B 146 TYR LEU ALA TRP VAL PRO ALA HIS LYS GLY ILE GLY GLY SEQRES 11 B 146 ASN GLU GLN VAL ASP LYS LEU VAL SER ALA GLY ILE ARG SEQRES 12 B 146 LYS ILE LEU HELIX 1 AA THR A 473 ASP A 488 1 16 HELIX 2 BA SER A 499 GLN A 509 1 11 HELIX 3 DA SER A 515 LYS A 528 1 14 HELIX 4 EA GLY A 544 SER A 553 1 10 HELIX 5 AB THR B 473 ASP B 488 1 16 HELIX 6 BB SER B 499 GLN B 509 1 11 HELIX 7 DB SER B 515 LYS B 528 1 14 HELIX 8 EB GLY B 543 SER B 553 1 11 SHEET 1 IA 5 ARG A 463 LEU A 469 0 SHEET 2 IA 5 LEU A 452 THR A 459 -1 SHEET 3 IA 5 GLU A 438 ASN A 447 -1 SHEET 4 IA 5 LEU A 491 THR A 497 1 SHEET 5 IA 5 LYS A 530 VAL A 536 1 SHEET 1 IB 5 ARG B 463 LEU B 469 0 SHEET 2 IB 5 LEU B 452 THR B 459 -1 SHEET 3 IB 5 GLU B 438 ASN B 447 -1 SHEET 4 IB 5 LEU B 491 THR B 497 1 SHEET 5 IB 5 LYS B 530 VAL B 536 1 CRYST1 52.030 52.030 113.920 90.00 90.00 120.00 P 31 6 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 0.019220 0.011096 0.000000 0.00000 SCALE2 0.000000 0.022193 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008778 0.00000