Header list of 1tac.pdb file
Complete list - v 3 2 Bytes
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
Complete list - v 3 2 Bytes