HEADER VIRAL PROTEIN 08-MAR-18 6FXA TITLE DIMERIZATION DOMAIN OF TP901-1 CI REPRESSOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: CI; COMPND 3 CHAIN: A, B, C, D, E, F; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: LACTOCOCCUS PHAGE TP901-1; SOURCE 4 ORGANISM_TAXID: 35345 KEYWDS CI REPRESSOR, DIMERIZATION DOMAIN, HELICAL HOOK, TRANSCRIPTION, VIRAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.K.VARMING,K.K.RASMUSSEN,L.LO LEGGIO REVDAT 3 08-MAY-24 6FXA 1 REMARK REVDAT 2 13-JUN-18 6FXA 1 JRNL REVDAT 1 30-MAY-18 6FXA 0 JRNL AUTH K.K.RASMUSSEN,A.K.VARMING,S.N.SCHMIDT,K.E.H.FRANDSEN, JRNL AUTH 2 P.W.THULSTRUP,M.R.JENSEN,L.LO LEGGIO JRNL TITL STRUCTURAL BASIS OF THE BACTERIOPHAGE TP901-1 CI REPRESSOR JRNL TITL 2 DIMERIZATION AND INTERACTION WITH DNA. JRNL REF FEBS LETT. V. 592 1738 2018 JRNL REFN ISSN 1873-3468 JRNL PMID 29683476 JRNL DOI 10.1002/1873-3468.13060 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.23 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 31119 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.148 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1494 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 40.2395 - 3.3333 1.00 2862 155 0.1530 0.1812 REMARK 3 2 3.3333 - 2.6459 1.00 2739 140 0.1454 0.1684 REMARK 3 3 2.6459 - 2.3114 1.00 2715 137 0.1312 0.2017 REMARK 3 4 2.3114 - 2.1001 1.00 2679 164 0.1212 0.1901 REMARK 3 5 2.1001 - 1.9496 1.00 2705 105 0.1439 0.2099 REMARK 3 6 1.9496 - 1.8347 1.00 2670 131 0.1426 0.2219 REMARK 3 7 1.8347 - 1.7428 1.00 2663 126 0.1505 0.2315 REMARK 3 8 1.7428 - 1.6669 1.00 2650 156 0.1694 0.2256 REMARK 3 9 1.6669 - 1.6027 1.00 2648 145 0.1673 0.2578 REMARK 3 10 1.6027 - 1.5474 1.00 2645 133 0.1543 0.2364 REMARK 3 11 1.5474 - 1.4990 0.99 2649 102 0.1606 0.2064 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.860 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6FXA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1200008914. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-SEP-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, DESY REMARK 200 BEAMLINE : P11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : SI-111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31189 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 40.225 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 11.95 REMARK 200 R MERGE (I) : 0.17500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.2200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 11.29 REMARK 200 R MERGE FOR SHELL (I) : 0.79100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.740 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.7.16 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE, 0.1 M SODIUM REMARK 280 ACETATE, PH 4.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 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 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 21.92000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.58000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.28000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.58000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.92000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.28000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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 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 GLN D 35 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 OE1 GLU C 1 O HOH C 201 1.69 REMARK 500 O HOH E 123 O HOH E 128 1.94 REMARK 500 O3 SO4 A 102 O HOH A 201 1.95 REMARK 500 O HOH D 123 O HOH F 121 2.09 REMARK 500 O HOH D 123 O HOH F 114 2.09 REMARK 500 O HOH B 123 O HOH B 133 2.10 REMARK 500 O HOH E 101 O HOH E 127 2.17 REMARK 500 OE2 GLU C 14 O HOH C 202 2.18 REMARK 500 O HOH F 114 O HOH F 121 2.19 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 ASN E 2 -18.67 -143.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 C 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5A7L RELATED DB: PDB REMARK 900 TP901-1 CI NTD (RES 1-80) REMARK 900 RELATED ID: 3ZHI RELATED DB: PDB REMARK 900 TP901-1 CI NTD (RES 2-74) DBREF 6FXA A 1 35 UNP O48503 O48503_9CAUD 90 124 DBREF 6FXA B 1 35 UNP O48503 O48503_9CAUD 90 124 DBREF 6FXA C 1 35 UNP O48503 O48503_9CAUD 90 124 DBREF 6FXA D 1 35 UNP O48503 O48503_9CAUD 90 124 DBREF 6FXA E 1 35 UNP O48503 O48503_9CAUD 90 124 DBREF 6FXA F 1 35 UNP O48503 O48503_9CAUD 90 124 SEQRES 1 A 35 GLU ASN ILE GLU GLU THR ILE THR VAL MET LYS LYS LEU SEQRES 2 A 35 GLU GLU PRO ARG GLN LYS VAL VAL LEU ASP THR ALA LYS SEQRES 3 A 35 ILE GLN LEU LYS GLU GLN ASP GLU GLN SEQRES 1 B 35 GLU ASN ILE GLU GLU THR ILE THR VAL MET LYS LYS LEU SEQRES 2 B 35 GLU GLU PRO ARG GLN LYS VAL VAL LEU ASP THR ALA LYS SEQRES 3 B 35 ILE GLN LEU LYS GLU GLN ASP GLU GLN SEQRES 1 C 35 GLU ASN ILE GLU GLU THR ILE THR VAL MET LYS LYS LEU SEQRES 2 C 35 GLU GLU PRO ARG GLN LYS VAL VAL LEU ASP THR ALA LYS SEQRES 3 C 35 ILE GLN LEU LYS GLU GLN ASP GLU GLN SEQRES 1 D 35 GLU ASN ILE GLU GLU THR ILE THR VAL MET LYS LYS LEU SEQRES 2 D 35 GLU GLU PRO ARG GLN LYS VAL VAL LEU ASP THR ALA LYS SEQRES 3 D 35 ILE GLN LEU LYS GLU GLN ASP GLU GLN SEQRES 1 E 35 GLU ASN ILE GLU GLU THR ILE THR VAL MET LYS LYS LEU SEQRES 2 E 35 GLU GLU PRO ARG GLN LYS VAL VAL LEU ASP THR ALA LYS SEQRES 3 E 35 ILE GLN LEU LYS GLU GLN ASP GLU GLN SEQRES 1 F 35 GLU ASN ILE GLU GLU THR ILE THR VAL MET LYS LYS LEU SEQRES 2 F 35 GLU GLU PRO ARG GLN LYS VAL VAL LEU ASP THR ALA LYS SEQRES 3 F 35 ILE GLN LEU LYS GLU GLN ASP GLU GLN HET SO4 A 101 5 HET SO4 A 102 5 HET SO4 C 101 5 HETNAM SO4 SULFATE ION FORMUL 7 SO4 3(O4 S 2-) FORMUL 10 HOH *216(H2 O) HELIX 1 AA1 GLU A 1 LYS A 11 1 11 HELIX 2 AA2 GLU A 14 GLU A 34 1 21 HELIX 3 AA3 ASN B 2 LYS B 11 1 10 HELIX 4 AA4 GLU B 14 GLN B 35 1 22 HELIX 5 AA5 ASN C 2 LEU C 13 1 12 HELIX 6 AA6 GLU C 14 GLN C 35 1 22 HELIX 7 AA7 ASN D 2 LYS D 11 1 10 HELIX 8 AA8 GLU D 14 GLU D 34 1 21 HELIX 9 AA9 ASN E 2 LEU E 13 1 12 HELIX 10 AB1 GLU E 14 GLN E 35 1 22 HELIX 11 AB2 ASN F 2 LYS F 11 1 10 HELIX 12 AB3 GLU F 14 GLN F 35 1 22 SITE 1 AC1 7 GLU A 15 LYS A 19 HOH A 205 LYS C 30 SITE 2 AC1 7 GLU D 14 GLU D 15 LYS F 30 SITE 1 AC2 5 LYS A 30 HOH A 201 HOH A 204 HOH A 210 SITE 2 AC2 5 LYS C 19 SITE 1 AC3 9 LYS A 30 GLU B 14 GLU B 15 GLU C 15 SITE 2 AC3 9 PRO C 16 LYS C 19 HOH C 204 HOH C 212 SITE 3 AC3 9 HOH C 215 CRYST1 43.840 42.560 101.160 90.00 90.00 90.00 P 21 21 21 24 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 0.022810 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023496 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009885 0.00000