HEADER TRANSCRIPTION REGULATION 13-MAR-98 1TAC TITLE HIV-1 TAT CYS-, NMR, 10 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: TAT PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRANSACTIVATING REGULATORY PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 VARIANT: ZAIRE 2; SOURCE 5 CELL_LINE: BL21; SOURCE 6 GENE: TATCYS-; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PET; SOURCE 11 EXPRESSION_SYSTEM_VECTOR: PTK3; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: BL21; SOURCE 13 EXPRESSION_SYSTEM_GENE: TATCYS- KEYWDS TRANSCRIPTION REGULATION, HIV-1, TRANSACTIVATION, RNA BINDING EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR P.ROESCH,M.BOEHM,H.STICHT REVDAT 3 03-NOV-21 1TAC 1 REMARK SEQADV REVDAT 2 24-FEB-09 1TAC 1 VERSN REVDAT 1 23-MAR-99 1TAC 0 JRNL AUTH M.BOEHM,H.STICHT,G.SEIDEL,P.ROESCH JRNL TITL SOLUTION STRUCTURE OF HIV-1 TAT PROTEIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.BAYER,M.KRAFT,A.EJCHART,M.WESTENDORP,R.FRANK,P.ROSCH REMARK 1 TITL STRUCTURAL STUDIES OF HIV-1 TAT PROTEIN REMARK 1 REF J.MOL.BIOL. V. 247 529 1995 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DESCRIPTION OF THE STRATEGY USED FOR REMARK 3 NMR STRUCTURE CALCULATION AND REFINEMENT: NOE CROSS-PEAKS WERE REMARK 3 DIVIDED INTO THREE CATEGORIES AND ASSIGNED DISTANCE RANGES REMARK 3 ACCORDING TO THEIR INTENSITY: STRONG (<0.29 NM); MEDIUM (<0.42 REMARK 3 NM); WEAK (<0.57 NM). PEAK INTENSITIES WERE ESTIMATED FROM THE REMARK 3 NUMBER OF CONTOURS IN NOESY SPECTRUM. 23 3JHNA COUPLING REMARK 3 CONSTANTS WERE EXTRACTED FROM DQF-COSY SPECTRUM, AND CONVERTED REMARK 3 TO PHI-ANGLES ACCORDING THE KARPLUS EQUATION. THE STRUCTURE REMARK 3 CALCULATIONS USED MODIFIED AB INITIO SIMULATED ANNEALING (SA. REMARK 3 INP) AND REFINEMENT (REFINE. INP) PROTOCOLS FROM THE X-PLOR REMARK 3 PROGRAM PACKAGE WHICH INCLUDED FLOATING ASSIGNMENT OF PROCHIRAL REMARK 3 GROUPS, REDUCED PRESENTATION FOR NON-BOND INTERACTIONS FOR PART REMARK 3 OF THE CALCULATION, REFINEMENT AGAINST CONFORMATIONAL DATABASE REMARK 3 AND DIRECT REFINEMENT AGAINST 3JHNA COUPLING CONSTANTS. IN EACH REMARK 3 ROUND OF STRUCTURE CALCULATION, 100 STRUCTURES WERE CALCULATED REMARK 3 FROM TEMPLATES WITH RANDOM BACKBONE TORSION ANGLES. IN THE REMARK 3 CONFORMATIONAL SEARCH PHASE 60 PS OF MOLECULAR DYNAMICS WERE REMARK 3 SIMULATED AT 2000 K. THE REFINEMENT COMPRISED A TWO-PHASE REMARK 3 COOLING PROCEDURE TREATING THE NON-BONDED INTERACTIONS BETWEEN REMARK 3 ALL ATOMS BY A REPULSIVE ('REPEL') POTENTIAL. IN THE FIRST REMARK 3 REFINEMENT STAGE, THE SYSTEM WAS COOLED FROM 2000 K TO 1000 K REMARK 3 WITHIN 135 PS, CONCOMITANTLY INCREASING THE FORCE CONSTANTS TO REMARK 3 THEIR FINAL VALUES. IN THE NEXT STAGE OF THE CALCULATION THE REMARK 3 SYSTEM WAS COOLED FROM 1000 K TO 100 K WITHIN 90 PS, APPLYING REMARK 3 THE HIGH FORCE CONSTANTS OBTAINED AT THE END OF THE PREVIOUS REMARK 3 COOLING STAGE. DURING ALL STAGES OF THE CALCULATION A TIMESTEP REMARK 3 OF 3 FS WAS USED. THEN, 500 STEPS OF POWELL ENERGY MINIMIZATION REMARK 3 WERE PERFORMED, USING AN ATTRACTIVE LENARD-JONES POTENTIAL, BUT REMARK 3 NO EXPLICIT ELECTROSTATICS AND RAMACHANDRAN DATABASIS POTENTIAL. REMARK 3 OF THE 240 RESULTING STRUCTURES, THOSE 10 STRUCTURES THAT SHOWED REMARK 3 THE LOWEST ENERGY AND THE LEAST VIOLATION OF THE EXPERIMENTAL REMARK 3 DATA WERE SELECTED FOR FURTHER CHARACTERIZATION. GEOMETRY OF THE REMARK 3 STRUCTURES AND ELEMENTS OF SECONDARY STRUCTURE WERE ANALYZED REMARK 3 USING PROCHECK AND DSSP. REMARK 4 REMARK 4 1TAC COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000176576. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.0 REMARK 210 IONIC STRENGTH : 0.85 M REMARK 210 PRESSURE : 10E+5 PA ATM REMARK 210 SAMPLE CONTENTS : H2O/D2O (9:1) REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; TOCSY; COSY; 1H-15N-HSQC; REMARK 210 15N-NOESY-HMQC; 15N-TOCSY-HMQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NDEE, X-PLOR REMARK 210 METHOD USED : SIMULATED ANNEALING, RESTRAINED REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 240 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : ENERGY, AGREEMENT WITH REMARK 210 EXPERIMENTAL DATA REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 1 VAL A 36 CA - CB - CG2 ANGL. DEV. = 13.4 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 1 PRO A 3 -86.98 -86.12 REMARK 500 1 ASP A 5 -70.64 -154.40 REMARK 500 1 PRO A 10 37.69 -85.81 REMARK 500 1 TRP A 11 52.23 -101.90 REMARK 500 1 GLN A 17 -62.40 -135.78 REMARK 500 1 ALA A 21 4.14 59.45 REMARK 500 1 ARG A 24 -68.95 -148.87 REMARK 500 1 HIS A 26 -62.64 -165.26 REMARK 500 1 SER A 30 35.18 28.98 REMARK 500 1 TYR A 32 37.82 -149.29 REMARK 500 1 HIS A 33 18.73 54.60 REMARK 500 1 SER A 34 -125.58 57.10 REMARK 500 1 GLN A 35 -17.57 78.82 REMARK 500 1 VAL A 36 -162.84 49.50 REMARK 500 1 PHE A 38 -141.29 -96.25 REMARK 500 1 SER A 46 34.71 -179.06 REMARK 500 1 LYS A 51 -49.42 71.06 REMARK 500 1 ARG A 56 41.19 -160.44 REMARK 500 1 GLN A 60 -84.33 -133.63 REMARK 500 1 THR A 64 62.41 66.90 REMARK 500 1 GLN A 66 -56.55 -134.67 REMARK 500 1 SER A 75 -34.38 168.21 REMARK 500 1 ARG A 78 35.36 -141.03 REMARK 500 2 PRO A 3 -88.44 -84.98 REMARK 500 2 ASP A 5 -72.91 -157.92 REMARK 500 2 PRO A 10 36.07 -93.05 REMARK 500 2 TRP A 11 45.28 -104.48 REMARK 500 2 SER A 16 3.92 -151.06 REMARK 500 2 GLN A 17 -62.76 -138.03 REMARK 500 2 THR A 20 -38.17 -153.26 REMARK 500 2 ASN A 23 -152.25 -77.77 REMARK 500 2 ARG A 24 -72.94 -41.30 REMARK 500 2 HIS A 26 -54.95 -165.01 REMARK 500 2 SER A 30 47.29 -73.51 REMARK 500 2 ALA A 31 72.40 37.17 REMARK 500 2 TYR A 32 42.26 -155.91 REMARK 500 2 SER A 34 76.60 52.42 REMARK 500 2 ALA A 37 95.63 56.65 REMARK 500 2 PHE A 38 -142.61 -137.13 REMARK 500 2 SER A 46 27.74 -176.70 REMARK 500 2 LYS A 51 -49.63 71.74 REMARK 500 2 ARG A 56 40.16 -163.08 REMARK 500 2 GLN A 60 26.54 -146.33 REMARK 500 2 GLN A 72 -172.80 -172.29 REMARK 500 2 SER A 74 134.17 59.50 REMARK 500 2 GLN A 76 -58.93 -135.84 REMARK 500 3 ASP A 2 75.94 61.50 REMARK 500 3 PRO A 3 -86.40 -89.57 REMARK 500 3 ASP A 5 -65.13 -160.24 REMARK 500 3 PRO A 10 40.31 -91.54 REMARK 500 REMARK 500 THIS ENTRY HAS 232 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 24 0.32 SIDE CHAIN REMARK 500 1 ARG A 49 0.28 SIDE CHAIN REMARK 500 1 ARG A 52 0.31 SIDE CHAIN REMARK 500 1 ARG A 53 0.32 SIDE CHAIN REMARK 500 1 ARG A 55 0.30 SIDE CHAIN REMARK 500 1 ARG A 56 0.29 SIDE CHAIN REMARK 500 1 ARG A 57 0.29 SIDE CHAIN REMARK 500 1 ARG A 78 0.31 SIDE CHAIN REMARK 500 2 ARG A 24 0.20 SIDE CHAIN REMARK 500 2 ARG A 49 0.26 SIDE CHAIN REMARK 500 2 ARG A 52 0.30 SIDE CHAIN REMARK 500 2 ARG A 53 0.17 SIDE CHAIN REMARK 500 2 ARG A 55 0.31 SIDE CHAIN REMARK 500 2 ARG A 56 0.32 SIDE CHAIN REMARK 500 2 ARG A 57 0.31 SIDE CHAIN REMARK 500 2 ARG A 78 0.31 SIDE CHAIN REMARK 500 3 ARG A 24 0.32 SIDE CHAIN REMARK 500 3 ARG A 49 0.24 SIDE CHAIN REMARK 500 3 ARG A 52 0.32 SIDE CHAIN REMARK 500 3 ARG A 53 0.32 SIDE CHAIN REMARK 500 3 ARG A 55 0.32 SIDE CHAIN REMARK 500 3 ARG A 56 0.32 SIDE CHAIN REMARK 500 3 ARG A 57 0.29 SIDE CHAIN REMARK 500 3 ARG A 78 0.28 SIDE CHAIN REMARK 500 4 ARG A 24 0.29 SIDE CHAIN REMARK 500 4 ARG A 49 0.26 SIDE CHAIN REMARK 500 4 ARG A 52 0.27 SIDE CHAIN REMARK 500 4 ARG A 53 0.32 SIDE CHAIN REMARK 500 4 ARG A 55 0.31 SIDE CHAIN REMARK 500 4 ARG A 56 0.25 SIDE CHAIN REMARK 500 4 ARG A 57 0.27 SIDE CHAIN REMARK 500 4 ARG A 78 0.30 SIDE CHAIN REMARK 500 5 ARG A 24 0.32 SIDE CHAIN REMARK 500 5 ARG A 49 0.24 SIDE CHAIN REMARK 500 5 ARG A 52 0.27 SIDE CHAIN REMARK 500 5 ARG A 53 0.16 SIDE CHAIN REMARK 500 5 ARG A 55 0.32 SIDE CHAIN REMARK 500 5 ARG A 56 0.30 SIDE CHAIN REMARK 500 5 ARG A 57 0.26 SIDE CHAIN REMARK 500 5 ARG A 78 0.30 SIDE CHAIN REMARK 500 6 ARG A 24 0.31 SIDE CHAIN REMARK 500 6 ARG A 49 0.24 SIDE CHAIN REMARK 500 6 ARG A 52 0.29 SIDE CHAIN REMARK 500 6 ARG A 53 0.29 SIDE CHAIN REMARK 500 6 ARG A 55 0.26 SIDE CHAIN REMARK 500 6 ARG A 56 0.24 SIDE CHAIN REMARK 500 6 ARG A 57 0.31 SIDE CHAIN REMARK 500 6 ARG A 78 0.32 SIDE CHAIN REMARK 500 7 ARG A 24 0.28 SIDE CHAIN REMARK 500 7 ARG A 49 0.20 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 80 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1TAC A 2 86 UNP P12506 TAT_HV1Z2 2 86 SEQADV 1TAC SER A 22 UNP P12506 CYS 22 ENGINEERED MUTATION SEQADV 1TAC ALA A 25 UNP P12506 CYS 25 ENGINEERED MUTATION SEQADV 1TAC ALA A 27 UNP P12506 CYS 27 ENGINEERED MUTATION SEQADV 1TAC SER A 30 UNP P12506 CYS 30 ENGINEERED MUTATION SEQADV 1TAC ALA A 31 UNP P12506 CYS 31 ENGINEERED MUTATION SEQADV 1TAC SER A 34 UNP P12506 CYS 34 ENGINEERED MUTATION SEQADV 1TAC ALA A 37 UNP P12506 CYS 37 ENGINEERED MUTATION SEQRES 1 A 86 LEU ASP PRO VAL ASP PRO ASN ILE GLU PRO TRP ASN HIS SEQRES 2 A 86 PRO GLY SER GLN PRO LYS THR ALA SER ASN ARG ALA HIS SEQRES 3 A 86 ALA LYS LYS SER ALA TYR HIS SER GLN VAL ALA PHE ILE SEQRES 4 A 86 THR LYS GLY LEU GLY ILE SER TYR GLY ARG LYS LYS ARG SEQRES 5 A 86 ARG GLN ARG ARG ARG PRO SER GLN GLY GLY GLN THR HIS SEQRES 6 A 86 GLN ASP PRO ILE PRO LYS GLN PRO SER SER GLN PRO ARG SEQRES 7 A 86 GLY ASP PRO THR GLY PRO LYS GLU HELIX 1 1 ARG A 52 GLN A 54 5 3 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1