HEADER HYDROLASE 22-JUN-09 3HYF TITLE CRYSTAL STRUCTURE OF HIV-1 RNASE H P15 WITH ENGINEERED E. COLI LOOP TITLE 2 AND ACTIVE SITE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: REVERSE TRANSCRIPTASE/RNASEH; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.26.4; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1, ESCHERICHIA SOURCE 3 COLI; SOURCE 4 ORGANISM_TAXID: 11676, 83333; SOURCE 5 GENE: POL, REVERSE TRANSCRIPTASE (AMINO ACIDS 427-560); SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET30B KEYWDS RNASE H, HIV-1, HYDROLASE, DI-VALENT METAL NUCLEIC ACID CLEAVAGE KEYWDS 2 MECHANISM, DI-VALENT METAL COORDINATION, ASPARTYL PROTEASE, DNA KEYWDS 3 INTEGRATION, DNA RECOMBINATION, ENDONUCLEASE, MULTIFUNCTIONAL KEYWDS 4 ENZYME, NUCLEASE, NUCLEOTIDYLTRANSFERASE, PROTEASE, RNA-DIRECTED DNA KEYWDS 5 POLYMERASE, TRANSFERASE, MAGNESIUM, METAL-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR E.B.LANSDON,T.A.KIRSCHBERG REVDAT 6 13-MAR-24 3HYF 1 SOURCE REVDAT 5 06-SEP-23 3HYF 1 REMARK SEQADV LINK REVDAT 4 16-AUG-17 3HYF 1 SOURCE REMARK REVDAT 3 16-NOV-11 3HYF 1 HETATM REVDAT 2 13-JUL-11 3HYF 1 VERSN REVDAT 1 20-OCT-09 3HYF 0 JRNL AUTH T.A.KIRSCHBERG,M.BALAKRISHNAN,N.H.SQUIRES,T.BARNES, JRNL AUTH 2 K.M.BRENDZA,X.CHEN,E.J.EISENBERG,W.JIN,N.KUTTY,S.LEAVITT, JRNL AUTH 3 A.LICLICAN,Q.LIU,X.LIU,J.MAK,J.K.PERRY,M.WANG,W.J.WATKINS, JRNL AUTH 4 E.B.LANSDON JRNL TITL RNASE H ACTIVE SITE INHIBITORS OF HUMAN IMMUNODEFICIENCY JRNL TITL 2 VIRUS TYPE 1 REVERSE TRANSCRIPTASE: DESIGN, BIOCHEMICAL JRNL TITL 3 ACTIVITY, AND STRUCTURAL INFORMATION. JRNL REF J.MED.CHEM. V. 52 5781 2009 JRNL REFN ISSN 0022-2623 JRNL PMID 19791799 JRNL DOI 10.1021/JM900597Q REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNX 2005 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN,ACCELRYS REMARK 3 : SOFTWARE INC.(BADGER,BERARD,KUMAR,SZALMA, REMARK 3 : YIP,DZAKULA) REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 78272.720 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 22030 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1050 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.2350 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.2330 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1096 REMARK 3 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : 0.0080 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 22881 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3192 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE : 0.2180 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 168 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1135 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 189 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.19000 REMARK 3 B22 (A**2) : -6.18000 REMARK 3 B33 (A**2) : -2.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.13 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.10 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 0.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.620 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 5.540 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 7.150 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 9.930 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 11.210; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 70.57 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 : PROTEIN_REP.P REMARK 3 PARAMETER FILE 2 : ON1.PAR REMARK 3 PARAMETER FILE 3 : WATER_REP.PAR REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ON1.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3HYF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000053735. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-DEC-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL, CYLINDRICALLY REMARK 200 BENT, SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26856 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 29.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 37.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.34700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB CODE 1HRH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0M MGSO4, 100MM SODIUM ACETATE PH REMARK 280 4.6, 5MM MANGANESE CHLORIDE, 5MM TCEP, 1.5MM INHIBITOR, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y,-Z REMARK 290 8555 X,-Y,-Z+1/2 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 19.85850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.66700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.16300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.66700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.85850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.16300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 19.85850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.16300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 56.66700 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.16300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 19.85850 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 56.66700 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 A 116 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 606 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 608 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 609 LIES ON A SPECIAL POSITION. 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 91 REMARK 465 THR A 92 REMARK 465 ALA A 93 REMARK 465 ASP A 94 REMARK 465 LYS A 95 REMARK 465 LYS A 96 REMARK 465 PHE A 561 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 NE1 TRP A 85 NE1 TRP A 85 7555 1.94 REMARK 500 O HOH A 176 O HOH A 176 6565 2.09 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 558 -79.29 -47.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 601 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 443 OD1 REMARK 620 2 GLU A 478 OE1 88.6 REMARK 620 3 ASP A 498 OD2 100.7 124.4 REMARK 620 4 ON1 A 701 O4 170.8 83.3 87.5 REMARK 620 5 ON1 A 701 O1 93.3 119.3 114.8 87.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 602 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 443 OD2 REMARK 620 2 ASP A 549 OD2 98.9 REMARK 620 3 HOH A 603 O 92.3 93.1 REMARK 620 4 HOH A 604 O 91.8 89.5 174.8 REMARK 620 5 ON1 A 701 O1 101.2 159.3 91.3 84.8 REMARK 620 6 ON1 A 701 O2 178.5 82.0 88.8 87.0 77.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 650 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 698 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 699 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ON1 A 701 DBREF 3HYF A 427 506 UNP Q72547 Q72547_9HIV1 427 506 DBREF 3HYF A 79 102 UNP P0A7Y4 RNH_ECOLI 79 102 DBREF 3HYF A 517 561 UNP Q72547 Q72547_9HIV1 517 561 SEQADV 3HYF MET A 426 UNP Q72547 INITIATING METHIONINE SEQRES 1 A 150 MET TYR GLN LEU GLU LYS GLU PRO ILE VAL GLY ALA GLU SEQRES 2 A 150 THR PHE TYR VAL ASP GLY ALA ALA ASN ARG GLU THR LYS SEQRES 3 A 150 LEU GLY LYS ALA GLY TYR VAL THR ASN ARG GLY ARG GLN SEQRES 4 A 150 LYS VAL VAL THR LEU THR ASP THR THR ASN GLN LYS THR SEQRES 5 A 150 GLU LEU GLN ALA ILE TYR LEU ALA LEU GLN ASP SER GLY SEQRES 6 A 150 LEU GLU VAL ASN ILE VAL THR ASP SER GLN TYR ALA LEU SEQRES 7 A 150 GLY ILE ILE THR GLN TRP ILE HIS ASN TRP LYS LYS ARG SEQRES 8 A 150 GLY TRP LYS THR ALA ASP LYS LYS PRO VAL LYS ASN VAL SEQRES 9 A 150 ASP LEU VAL ASN GLN ILE ILE GLU GLN LEU ILE LYS LYS SEQRES 10 A 150 GLU LYS VAL TYR LEU ALA TRP VAL PRO ALA HIS LYS GLY SEQRES 11 A 150 ILE GLY GLY ASN GLU GLN VAL ASP LYS LEU VAL SER ALA SEQRES 12 A 150 GLY ILE ARG LYS VAL LEU PHE HET MN A 601 1 HET MN A 602 1 HET ACT A 650 4 HET GOL A 698 6 HET GOL A 699 6 HET ON1 A 701 20 HETNAM MN MANGANESE (II) ION HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETNAM ON1 2-(3,4-DICHLOROBENZYL)-5,6-DIHYDROXYPYRIMIDINE-4- HETNAM 2 ON1 CARBOXYLIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 MN 2(MN 2+) FORMUL 4 ACT C2 H3 O2 1- FORMUL 5 GOL 2(C3 H8 O3) FORMUL 7 ON1 C12 H8 CL2 N2 O4 FORMUL 8 HOH *189(H2 O) HELIX 1 1 THR A 473 SER A 489 1 17 HELIX 2 2 SER A 499 ARG A 88 1 18 HELIX 3 3 ASN A 100 ILE A 526 1 13 HELIX 4 4 ILE A 542 ALA A 554 1 13 SHEET 1 A 5 GLN A 464 LEU A 469 0 SHEET 2 A 5 GLY A 453 THR A 459 -1 N GLY A 453 O LEU A 469 SHEET 3 A 5 GLU A 438 ALA A 446 -1 N TYR A 441 O VAL A 458 SHEET 4 A 5 GLU A 492 THR A 497 1 O VAL A 496 N PHE A 440 SHEET 5 A 5 LYS A 530 TRP A 535 1 O TYR A 532 N ILE A 495 LINK OD1 ASP A 443 MN MN A 601 1555 1555 2.09 LINK OD2 ASP A 443 MN MN A 602 1555 1555 2.08 LINK OE1 GLU A 478 MN MN A 601 1555 1555 2.11 LINK OD2 ASP A 498 MN MN A 601 1555 1555 2.06 LINK OD2 ASP A 549 MN MN A 602 1555 1555 2.14 LINK MN MN A 601 O4 ON1 A 701 1555 1555 2.22 LINK MN MN A 601 O1 ON1 A 701 1555 1555 2.06 LINK MN MN A 602 O HOH A 603 1555 1555 2.16 LINK MN MN A 602 O HOH A 604 1555 1555 2.18 LINK MN MN A 602 O1 ON1 A 701 1555 1555 2.19 LINK MN MN A 602 O2 ON1 A 701 1555 1555 2.17 SITE 1 AC1 5 ASP A 443 GLU A 478 ASP A 498 MN A 602 SITE 2 AC1 5 ON1 A 701 SITE 1 AC2 6 ASP A 443 ASP A 549 MN A 601 HOH A 603 SITE 2 AC2 6 HOH A 604 ON1 A 701 SITE 1 AC3 4 HOH A 166 TYR A 441 GLY A 544 GLN A 547 SITE 1 AC4 6 HOH A 10 HOH A 33 HOH A 180 HOH A 184 SITE 2 AC4 6 ARG A 461 GLY A 490 SITE 1 AC5 5 HOH A 182 ARG A 448 THR A 473 ASN A 474 SITE 2 AC5 5 GLN A 475 SITE 1 AC6 16 HOH A 4 HOH A 7 HOH A 15 HOH A 41 SITE 2 AC6 16 ASP A 443 GLU A 478 ASP A 498 GLN A 500 SITE 3 AC6 16 ALA A 538 HIS A 539 ASP A 549 ARG A 557 SITE 4 AC6 16 MN A 601 MN A 602 HOH A 603 HOH A 604 CRYST1 39.717 90.326 113.334 90.00 90.00 90.00 I 21 21 21 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 0.025178 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011071 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008823 0.00000