PDB Short entry for 1J9I HEADER VIRAL PROTEIN 25-MAY-01 1J9I TITLE STRUCTURE OF THE DNA BINDING DOMAIN OF THE GPNU1 SUBUNIT OF LAMBDA TITLE 2 TERMINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TERMINASE SMALL SUBUNIT; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: DNA BINDING DOMAIN, RESIDUES 1-68; COMPND 5 SYNONYM: DNA PACKAGING PROTEIN NU1; GPNU1 DBD; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE LAMBDA; SOURCE 3 ORGANISM_TAXID: 10710; SOURCE 4 GENE: NU1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS DNA BINDING DOMAIN, HOMODIMER, VIRAL ASSEMBLY, LAMBDA, WINGED HELIX- KEYWDS 2 TURN-HELIX, TERMINASE, VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.DE BEER,J.MEYER,M.ORTEGA,Q.YANG,L.MAES,C.DUFFY,N.BERTON,J.SIPPY, AUTHOR 2 M.OVERDUIN,M.FEISS,C.CATALANO REVDAT 4 23-FEB-22 1J9I 1 REMARK REVDAT 3 24-FEB-09 1J9I 1 VERSN REVDAT 2 01-APR-03 1J9I 1 JRNL REVDAT 1 14-AUG-02 1J9I 0 JRNL AUTH T.DE BEER,J.FANG,M.ORTEGA,Q.YANG,L.MAES,C.DUFFY,N.BERTON, JRNL AUTH 2 J.SIPPY,M.OVERDUIN,M.FEISS,C.E.CATALANO JRNL TITL INSIGHTS INTO SPECIFIC DNA RECOGNITION DURING THE ASSEMBLY JRNL TITL 2 OF A VIRAL GENOME PACKAGING MACHINE. JRNL REF MOL.CELL V. 9 981 2002 JRNL REFN ISSN 1097-2765 JRNL PMID 12049735 JRNL DOI 10.1016/S1097-2765(02)00537-3 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 1, X-PLOR 3.851 REMARK 3 AUTHORS : DELAGLIO ET AL. (NMRPIPE), BRUNGER ET AL. (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE R-6 SUMMATION METHOD WAS USED REMARK 3 WITHIN A SIMULATED ANNEALING PROTOCOL. REMARK 4 REMARK 4 1J9I COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-01. REMARK 100 THE DEPOSITION ID IS D_1000013528. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.00 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 20 MM DEUTERATED TRIS REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM HOMONUCLEAR GPNU1 DBD; 1 MM REMARK 210 HOMONUCLEAR GPNU1 DBD; 1 MM {15N} REMARK 210 GPNU1 DBD; 1 MM {13C,15N} GPNU1 REMARK 210 DBD; 1 MM {13C,15N} GPNU1 DBD; 1 REMARK 210 MM 50%/50% {13C,15N} GPNU1 DBD/{ REMARK 210 12C,14N}GPNU1 DBD REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; HNHA; 3D_13C- REMARK 210 SEPARATED_NOESY; 4D_13C- REMARK 210 SEPARATED_NOESY; 2D_HALF- REMARK 210 FILTERED_13C/15N_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW 5.0, PIPP 1, X-PLOR REMARK 210 3.851 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: MIXING TIMES WERE 50 OR 100 MS 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 O ILE A 47 H ALA A 51 1.43 REMARK 500 O ILE B 47 H ALA B 51 1.45 REMARK 500 O ILE A 57 H GLU A 60 1.46 REMARK 500 O GLY A 13 HZ3 LYS A 61 1.46 REMARK 500 O ASP B 42 H VAL B 46 1.48 REMARK 500 O ASN A 4 H LEU A 8 1.48 REMARK 500 O GLN A 7 H ILE A 11 1.49 REMARK 500 O ASP A 42 H VAL A 46 1.50 REMARK 500 O GLU B 56 H ASN B 59 1.50 REMARK 500 O TRP A 22 H GLN A 25 1.51 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 7 ARG B 53 N - CA - CB ANGL. DEV. = -11.1 DEGREES REMARK 500 7 ALA B 55 N - CA - CB ANGL. DEV. = -9.6 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 LEU A 30 -71.82 -53.41 REMARK 500 1 VAL A 39 126.51 58.24 REMARK 500 1 ASP A 42 84.50 -64.38 REMARK 500 1 SER A 43 -33.01 -33.08 REMARK 500 1 ARG A 53 -30.40 -176.08 REMARK 500 1 ARG A 64 -103.53 -76.10 REMARK 500 1 GLU A 67 -53.89 -174.10 REMARK 500 1 LEU B 30 -73.79 -42.56 REMARK 500 1 LYS B 35 72.92 44.15 REMARK 500 1 ASN B 37 -76.53 -89.82 REMARK 500 1 GLU B 38 42.04 174.60 REMARK 500 1 VAL B 39 116.06 -37.64 REMARK 500 1 ASP B 42 87.62 -61.90 REMARK 500 1 SER B 43 -33.35 -37.49 REMARK 500 1 ARG B 53 -28.05 -159.01 REMARK 500 2 LYS A 6 -71.47 -81.83 REMARK 500 2 LEU A 30 -71.61 -69.67 REMARK 500 2 LYS A 35 -177.17 54.18 REMARK 500 2 ASN A 37 -86.64 -96.05 REMARK 500 2 GLU A 38 -28.17 176.73 REMARK 500 2 VAL A 39 106.44 47.72 REMARK 500 2 SER A 43 -32.12 -33.83 REMARK 500 2 ARG A 53 -27.73 -179.76 REMARK 500 2 VAL A 66 -89.04 -51.10 REMARK 500 2 GLU A 67 -55.49 70.22 REMARK 500 2 LYS B 35 40.96 -173.11 REMARK 500 2 GLU B 38 11.92 -149.81 REMARK 500 2 VAL B 39 107.62 -45.69 REMARK 500 2 SER B 43 -28.82 -36.53 REMARK 500 2 ARG B 53 -28.62 -176.66 REMARK 500 2 LEU B 62 29.27 -150.59 REMARK 500 2 ARG B 64 -44.15 -168.64 REMARK 500 2 GLU B 65 50.05 -103.70 REMARK 500 2 GLU B 67 -54.37 72.87 REMARK 500 3 LEU A 30 -71.65 -53.11 REMARK 500 3 LYS A 35 -153.42 -130.67 REMARK 500 3 ASN A 37 -71.74 -99.92 REMARK 500 3 GLU A 38 40.76 -178.61 REMARK 500 3 ASP A 42 86.36 -62.96 REMARK 500 3 SER A 43 -30.68 -36.46 REMARK 500 3 ARG A 53 -28.34 -179.68 REMARK 500 3 ILE A 57 -70.25 -38.37 REMARK 500 3 LEU A 62 28.50 -142.61 REMARK 500 3 ARG A 63 -73.65 -110.66 REMARK 500 3 VAL A 66 -92.33 -75.67 REMARK 500 3 GLU A 67 119.51 75.74 REMARK 500 3 GLU B 38 35.41 -157.63 REMARK 500 3 ASP B 42 85.61 -60.75 REMARK 500 3 SER B 43 -36.95 -33.79 REMARK 500 3 ARG B 53 -32.01 -161.11 REMARK 500 REMARK 500 THIS ENTRY HAS 400 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 17 0.31 SIDE CHAIN REMARK 500 1 ARG A 31 0.12 SIDE CHAIN REMARK 500 1 ARG A 53 0.29 SIDE CHAIN REMARK 500 1 ARG A 63 0.19 SIDE CHAIN REMARK 500 1 ARG A 64 0.31 SIDE CHAIN REMARK 500 1 ARG B 17 0.14 SIDE CHAIN REMARK 500 1 ARG B 31 0.32 SIDE CHAIN REMARK 500 1 ARG B 53 0.30 SIDE CHAIN REMARK 500 1 ARG B 63 0.29 SIDE CHAIN REMARK 500 1 ARG B 64 0.15 SIDE CHAIN REMARK 500 2 ARG A 17 0.32 SIDE CHAIN REMARK 500 2 ARG A 31 0.28 SIDE CHAIN REMARK 500 2 ARG A 53 0.19 SIDE CHAIN REMARK 500 2 ARG A 63 0.26 SIDE CHAIN REMARK 500 2 ARG A 64 0.28 SIDE CHAIN REMARK 500 2 ARG B 17 0.26 SIDE CHAIN REMARK 500 2 ARG B 31 0.32 SIDE CHAIN REMARK 500 2 ARG B 53 0.17 SIDE CHAIN REMARK 500 2 ARG B 63 0.16 SIDE CHAIN REMARK 500 2 ARG B 64 0.31 SIDE CHAIN REMARK 500 3 ARG A 17 0.23 SIDE CHAIN REMARK 500 3 ARG A 31 0.32 SIDE CHAIN REMARK 500 3 ARG A 63 0.31 SIDE CHAIN REMARK 500 3 ARG A 64 0.24 SIDE CHAIN REMARK 500 3 ARG B 17 0.32 SIDE CHAIN REMARK 500 3 ARG B 31 0.21 SIDE CHAIN REMARK 500 3 ARG B 53 0.09 SIDE CHAIN REMARK 500 3 ARG B 63 0.24 SIDE CHAIN REMARK 500 3 ARG B 64 0.21 SIDE CHAIN REMARK 500 4 ARG A 17 0.30 SIDE CHAIN REMARK 500 4 ARG A 31 0.32 SIDE CHAIN REMARK 500 4 ARG A 53 0.30 SIDE CHAIN REMARK 500 4 ARG A 63 0.19 SIDE CHAIN REMARK 500 4 ARG A 64 0.32 SIDE CHAIN REMARK 500 4 ARG B 17 0.22 SIDE CHAIN REMARK 500 4 ARG B 31 0.30 SIDE CHAIN REMARK 500 4 ARG B 53 0.17 SIDE CHAIN REMARK 500 4 ARG B 63 0.31 SIDE CHAIN REMARK 500 4 ARG B 64 0.19 SIDE CHAIN REMARK 500 5 ARG A 31 0.32 SIDE CHAIN REMARK 500 5 ARG A 53 0.27 SIDE CHAIN REMARK 500 5 ARG A 63 0.22 SIDE CHAIN REMARK 500 5 ARG A 64 0.27 SIDE CHAIN REMARK 500 5 ARG B 17 0.15 SIDE CHAIN REMARK 500 5 ARG B 31 0.26 SIDE CHAIN REMARK 500 5 ARG B 63 0.23 SIDE CHAIN REMARK 500 5 ARG B 64 0.16 SIDE CHAIN REMARK 500 6 ARG A 17 0.25 SIDE CHAIN REMARK 500 6 ARG A 31 0.29 SIDE CHAIN REMARK 500 6 ARG A 53 0.27 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 188 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4752 RELATED DB: BMRB REMARK 900 CHEMICAL SHIFT ASSIGNMENT DBREF 1J9I A 1 68 UNP P03707 TERS_LAMBD 1 68 DBREF 1J9I B 1 68 UNP P03707 TERS_LAMBD 1 68 SEQRES 1 A 68 MET GLU VAL ASN LYS LYS GLN LEU ALA ASP ILE PHE GLY SEQRES 2 A 68 ALA SER ILE ARG THR ILE GLN ASN TRP GLN GLU GLN GLY SEQRES 3 A 68 MET PRO VAL LEU ARG GLY GLY GLY LYS GLY ASN GLU VAL SEQRES 4 A 68 LEU TYR ASP SER ALA ALA VAL ILE LYS TRP TYR ALA GLU SEQRES 5 A 68 ARG ASP ALA GLU ILE GLU ASN GLU LYS LEU ARG ARG GLU SEQRES 6 A 68 VAL GLU GLU SEQRES 1 B 68 MET GLU VAL ASN LYS LYS GLN LEU ALA ASP ILE PHE GLY SEQRES 2 B 68 ALA SER ILE ARG THR ILE GLN ASN TRP GLN GLU GLN GLY SEQRES 3 B 68 MET PRO VAL LEU ARG GLY GLY GLY LYS GLY ASN GLU VAL SEQRES 4 B 68 LEU TYR ASP SER ALA ALA VAL ILE LYS TRP TYR ALA GLU SEQRES 5 B 68 ARG ASP ALA GLU ILE GLU ASN GLU LYS LEU ARG ARG GLU SEQRES 6 B 68 VAL GLU GLU HELIX 1 1 LYS A 5 PHE A 12 1 8 HELIX 2 2 SER A 15 GLN A 23 1 9 HELIX 3 3 SER A 43 ALA A 51 1 9 HELIX 4 4 ARG A 53 ARG A 64 5 12 HELIX 5 5 ASN B 4 PHE B 12 1 9 HELIX 6 6 SER B 15 GLN B 23 1 9 HELIX 7 7 GLY B 32 GLY B 36 5 5 HELIX 8 8 ALA B 44 ALA B 51 1 8 HELIX 9 9 GLU B 56 GLU B 58 5 3 HELIX 10 10 ASN B 59 GLU B 65 1 7 SHEET 1 A 2 GLU A 2 ASN A 4 0 SHEET 2 A 2 LEU A 40 ASP A 42 -1 O TYR A 41 N VAL A 3 SHEET 1 B 2 GLU B 2 VAL B 3 0 SHEET 2 B 2 TYR B 41 ASP B 42 -1 N TYR B 41 O VAL B 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