HEADER VIRAL PROTEIN 12-DEC-08 2KBZ TITLE NMR STRUCTURE OF PROTEIN GP15 OF BACTERIOPHAGE SPP1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 15 PROTEIN (BACTERIOPHAGE SPP1 COMPLETE NUCLEOTIDE COMPND 3 SEQUENCE); COMPND 4 CHAIN: A; COMPND 5 SYNONYM: GP15; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS PHAGE SPP1; SOURCE 3 ORGANISM_COMMON: BACTERIOPHAGE SPP1; SOURCE 4 ORGANISM_TAXID: 10724; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PLYSS KEYWDS THREE ALPHA-HELIX BUNDLE, VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.GALLOPIN,B.GILQUIN,S.ZINN-JUSTIN REVDAT 2 16-MAR-22 2KBZ 1 REMARK REVDAT 1 09-JUN-09 2KBZ 0 JRNL AUTH S.LHUILLIER,M.GALLOPIN,B.GILQUIN,S.BRASILES,N.LANCELOT, JRNL AUTH 2 G.LETELLIER,M.GILLES,G.DETHAN,E.V.ORLOVA,J.COUPRIE, JRNL AUTH 3 P.TAVARES,S.ZINN-JUSTIN JRNL TITL STRUCTURE OF BACTERIOPHAGE SPP1 HEAD-TO-TAIL CONNECTION JRNL TITL 2 REVEALS MECHANISM FOR VIRAL DNA GATING JRNL REF PROC.NATL.ACAD.SCI.USA V. 106 8507 2009 JRNL REFN ISSN 0027-8424 JRNL PMID 19433794 JRNL DOI 10.1073/PNAS.0812407106 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SPARKY 3.113, INCA 1.0 REMARK 3 AUTHORS : GODDARD (SPARKY), SAVARIN (INCA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KBZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-DEC-08. REMARK 100 THE DEPOSITION ID IS D_1000100931. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 0.3 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-100% 15N] GP15-1, 0.5 REMARK 210 MM [U-100% 13C; U-100% 15N] GP15- REMARK 210 2, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D H-D EXCHANGE; REMARK 210 3D HNHA; 3D 1H-15N NOESY; 2D 1H- REMARK 210 15N NOE TRANSFER; 3D HNCO; 3D REMARK 210 HNCA; 3D 1H-13C NOESY; 3D HNCACO; REMARK 210 3D HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 HBHA(CO)NH; 3D HCCH-COSY; 3D REMARK 210 HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE 2 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3.113 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 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: 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 O GLN A 97 HG1 THR A 101 1.54 REMARK 500 O ASP A 53 HG1 THR A 57 1.55 REMARK 500 O ASP A 111 HG1 THR A 112 1.57 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 60 CA - C - N ANGL. DEV. = 17.4 DEGREES REMARK 500 1 GLU A 70 C - N - CA ANGL. DEV. = 15.4 DEGREES REMARK 500 1 PHE A 98 CB - CG - CD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 PHE A 98 CB - CG - CD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 1 GLY A 107 C - N - CA ANGL. DEV. = 12.8 DEGREES REMARK 500 1 TYR A 115 N - CA - C ANGL. DEV. = 16.2 DEGREES REMARK 500 1 LEU A 129 CA - CB - CG ANGL. DEV. = 15.2 DEGREES REMARK 500 1 LEU A 129 CB - CG - CD2 ANGL. DEV. = 13.2 DEGREES REMARK 500 2 VAL A 60 CA - C - N ANGL. DEV. = 22.6 DEGREES REMARK 500 2 GLU A 65 CB - CA - C ANGL. DEV. = 12.9 DEGREES REMARK 500 2 PHE A 91 CB - CG - CD2 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 PHE A 91 CB - CG - CD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 2 PHE A 98 CB - CG - CD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 3 PHE A 75 CB - CG - CD1 ANGL. DEV. = 4.8 DEGREES REMARK 500 3 PHE A 98 CB - CG - CD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 3 PHE A 98 CB - CG - CD1 ANGL. DEV. = 6.9 DEGREES REMARK 500 3 TYR A 115 CB - CG - CD2 ANGL. DEV. = -5.2 DEGREES REMARK 500 3 TYR A 115 CB - CG - CD1 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 TYR A 132 CB - CG - CD1 ANGL. DEV. = 4.0 DEGREES REMARK 500 4 VAL A 60 CA - C - N ANGL. DEV. = 17.3 DEGREES REMARK 500 4 PRO A 131 C - N - CA ANGL. DEV. = 9.8 DEGREES REMARK 500 5 TYR A 55 CB - CG - CD1 ANGL. DEV. = 4.1 DEGREES REMARK 500 5 LEU A 56 CB - CG - CD2 ANGL. DEV. = 10.6 DEGREES REMARK 500 5 VAL A 60 CA - C - N ANGL. DEV. = 19.9 DEGREES REMARK 500 5 ALA A 96 CB - CA - C ANGL. DEV. = 9.3 DEGREES REMARK 500 5 LYS A 134 C - N - CA ANGL. DEV. = 18.2 DEGREES REMARK 500 5 MET A 135 C - N - CA ANGL. DEV. = 16.3 DEGREES REMARK 500 6 VAL A 60 CA - C - N ANGL. DEV. = 21.2 DEGREES REMARK 500 6 ILE A 121 CB - CA - C ANGL. DEV. = 12.5 DEGREES REMARK 500 6 ILE A 121 CA - C - N ANGL. DEV. = 17.9 DEGREES REMARK 500 6 ILE A 125 CA - CB - CG1 ANGL. DEV. = 12.8 DEGREES REMARK 500 7 TYR A 99 CB - CG - CD2 ANGL. DEV. = 4.2 DEGREES REMARK 500 7 TYR A 99 CB - CG - CD1 ANGL. DEV. = -4.7 DEGREES REMARK 500 7 SER A 114 N - CA - CB ANGL. DEV. = 9.7 DEGREES REMARK 500 7 TYR A 115 CB - CG - CD1 ANGL. DEV. = 4.7 DEGREES REMARK 500 8 ASN A 73 N - CA - CB ANGL. DEV. = -12.5 DEGREES REMARK 500 8 ALA A 96 CB - CA - C ANGL. DEV. = 10.0 DEGREES REMARK 500 8 TYR A 115 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 8 TYR A 115 CB - CG - CD1 ANGL. DEV. = 4.1 DEGREES REMARK 500 8 PHE A 117 CB - CG - CD2 ANGL. DEV. = -4.8 DEGREES REMARK 500 9 VAL A 60 CA - C - N ANGL. DEV. = 22.1 DEGREES REMARK 500 9 PHE A 66 CB - CG - CD1 ANGL. DEV. = 4.3 DEGREES REMARK 500 9 TYR A 132 CB - CG - CD1 ANGL. DEV. = 4.5 DEGREES REMARK 500 10 VAL A 60 CA - C - N ANGL. DEV. = 21.4 DEGREES REMARK 500 10 PHE A 98 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 10 TYR A 132 CB - CG - CD2 ANGL. DEV. = -4.5 DEGREES REMARK 500 10 TYR A 132 CB - CG - CD1 ANGL. DEV. = 5.0 DEGREES REMARK 500 11 VAL A 60 CA - C - N ANGL. DEV. = 22.3 DEGREES REMARK 500 11 ALA A 96 CB - CA - C ANGL. DEV. = 10.0 DEGREES REMARK 500 11 PHE A 98 CB - CG - CD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 99 ANGLE DEVIATIONS. 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 ARG A 40 -19.67 87.57 REMARK 500 1 ILE A 47 -119.79 -105.91 REMARK 500 1 ASN A 49 -80.40 -156.55 REMARK 500 1 ASN A 102 -63.34 -95.10 REMARK 500 1 ARG A 108 -10.87 87.15 REMARK 500 1 MET A 110 145.99 80.52 REMARK 500 1 THR A 112 115.74 165.69 REMARK 500 1 TYR A 115 137.07 -22.53 REMARK 500 1 ILE A 121 122.46 82.92 REMARK 500 1 LYS A 134 -55.66 68.36 REMARK 500 1 MET A 135 -30.50 68.73 REMARK 500 2 ARG A 40 107.84 83.80 REMARK 500 2 ILE A 47 -54.06 -124.52 REMARK 500 2 THR A 48 76.52 -101.99 REMARK 500 2 ASN A 49 -68.64 164.62 REMARK 500 2 LYS A 51 -16.63 -41.11 REMARK 500 2 HIS A 72 -40.16 93.98 REMARK 500 2 PHE A 75 60.50 39.69 REMARK 500 2 LYS A 78 -14.39 -45.46 REMARK 500 2 THR A 106 38.71 -92.28 REMARK 500 2 MET A 110 -77.12 104.87 REMARK 500 2 ASP A 111 71.98 98.03 REMARK 500 2 THR A 112 -48.93 75.05 REMARK 500 2 VAL A 113 -39.17 106.63 REMARK 500 2 TYR A 115 -98.82 54.78 REMARK 500 2 ASN A 116 22.36 -179.38 REMARK 500 2 GLU A 120 -150.73 -114.04 REMARK 500 2 ILE A 121 123.10 73.28 REMARK 500 2 TYR A 132 -87.05 -98.13 REMARK 500 2 ARG A 133 -69.12 74.87 REMARK 500 2 LYS A 134 35.18 -171.72 REMARK 500 3 ILE A 47 -53.44 -123.41 REMARK 500 3 ASN A 49 -62.14 156.38 REMARK 500 3 PRO A 74 54.39 -95.24 REMARK 500 3 ASN A 102 60.50 162.77 REMARK 500 3 ARG A 108 -39.62 -168.23 REMARK 500 3 MET A 110 -129.41 -106.97 REMARK 500 3 ASP A 111 79.99 -116.38 REMARK 500 3 THR A 112 55.96 77.61 REMARK 500 3 VAL A 113 66.26 -116.23 REMARK 500 3 SER A 114 -48.02 62.41 REMARK 500 3 TYR A 115 -92.06 74.95 REMARK 500 3 ASN A 116 14.05 -173.31 REMARK 500 3 GLU A 120 -145.40 -116.48 REMARK 500 3 ILE A 121 128.04 76.71 REMARK 500 3 SER A 123 -50.03 -23.84 REMARK 500 3 TYR A 132 -142.85 -56.16 REMARK 500 3 LYS A 134 32.92 75.97 REMARK 500 4 ILE A 47 -76.41 -127.02 REMARK 500 4 ASN A 49 -57.39 158.64 REMARK 500 REMARK 500 THIS ENTRY HAS 319 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 PHE A 75 0.11 SIDE CHAIN REMARK 500 2 TYR A 132 0.07 SIDE CHAIN REMARK 500 3 PHE A 75 0.12 SIDE CHAIN REMARK 500 4 PHE A 75 0.16 SIDE CHAIN REMARK 500 4 TYR A 99 0.08 SIDE CHAIN REMARK 500 4 TYR A 132 0.07 SIDE CHAIN REMARK 500 5 PHE A 75 0.11 SIDE CHAIN REMARK 500 5 PHE A 117 0.08 SIDE CHAIN REMARK 500 5 TYR A 132 0.13 SIDE CHAIN REMARK 500 6 PHE A 75 0.14 SIDE CHAIN REMARK 500 6 TYR A 115 0.17 SIDE CHAIN REMARK 500 6 TYR A 132 0.08 SIDE CHAIN REMARK 500 7 TYR A 115 0.14 SIDE CHAIN REMARK 500 8 PHE A 75 0.12 SIDE CHAIN REMARK 500 8 TYR A 132 0.07 SIDE CHAIN REMARK 500 9 PHE A 75 0.14 SIDE CHAIN REMARK 500 9 TYR A 99 0.12 SIDE CHAIN REMARK 500 9 TYR A 115 0.10 SIDE CHAIN REMARK 500 9 TYR A 132 0.09 SIDE CHAIN REMARK 500 10 PHE A 75 0.07 SIDE CHAIN REMARK 500 10 TYR A 115 0.10 SIDE CHAIN REMARK 500 10 TYR A 132 0.14 SIDE CHAIN REMARK 500 11 PHE A 75 0.17 SIDE CHAIN REMARK 500 11 TYR A 99 0.07 SIDE CHAIN REMARK 500 11 TYR A 132 0.16 SIDE CHAIN REMARK 500 12 PHE A 75 0.13 SIDE CHAIN REMARK 500 12 TYR A 99 0.08 SIDE CHAIN REMARK 500 12 TYR A 115 0.08 SIDE CHAIN REMARK 500 12 TYR A 132 0.17 SIDE CHAIN REMARK 500 13 PHE A 75 0.09 SIDE CHAIN REMARK 500 14 TYR A 55 0.08 SIDE CHAIN REMARK 500 14 PHE A 75 0.14 SIDE CHAIN REMARK 500 14 TYR A 132 0.15 SIDE CHAIN REMARK 500 15 TYR A 55 0.09 SIDE CHAIN REMARK 500 15 TYR A 99 0.19 SIDE CHAIN REMARK 500 16 PHE A 75 0.11 SIDE CHAIN REMARK 500 16 TYR A 99 0.09 SIDE CHAIN REMARK 500 16 TYR A 132 0.10 SIDE CHAIN REMARK 500 17 PHE A 75 0.20 SIDE CHAIN REMARK 500 17 TYR A 99 0.07 SIDE CHAIN REMARK 500 17 TYR A 132 0.17 SIDE CHAIN REMARK 500 18 PHE A 75 0.16 SIDE CHAIN REMARK 500 18 TYR A 132 0.11 SIDE CHAIN REMARK 500 19 PHE A 75 0.15 SIDE CHAIN REMARK 500 19 PHE A 117 0.09 SIDE CHAIN REMARK 500 19 TYR A 132 0.09 SIDE CHAIN REMARK 500 20 PHE A 75 0.15 SIDE CHAIN REMARK 500 20 TYR A 99 0.07 SIDE CHAIN REMARK 500 20 TYR A 132 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2KBZ A 39 137 UNP Q38584 Q38584_BPSPP 4 102 SEQRES 1 A 99 GLN ARG VAL LYS ARG LEU LEU SER ILE THR ASN ASP LYS SEQRES 2 A 99 HIS ASP GLU TYR LEU THR GLU MET VAL PRO LEU LEU VAL SEQRES 3 A 99 GLU PHE ALA LYS ASP GLU CYS HIS ASN PRO PHE ILE ASP SEQRES 4 A 99 LYS ASP GLY ASN GLU SER ILE PRO SER GLY VAL LEU ILE SEQRES 5 A 99 PHE VAL ALA LYS ALA ALA GLN PHE TYR MET THR ASN ALA SEQRES 6 A 99 GLY LEU THR GLY ARG SER MET ASP THR VAL SER TYR ASN SEQRES 7 A 99 PHE ALA THR GLU ILE PRO SER THR ILE LEU LYS LYS LEU SEQRES 8 A 99 ASN PRO TYR ARG LYS MET ALA ARG HELIX 1 1 VAL A 41 SER A 46 1 6 HELIX 2 2 HIS A 52 ASP A 69 1 18 HELIX 3 3 PRO A 85 GLY A 104 1 20 HELIX 4 4 THR A 124 LYS A 128 5 5 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