HEADER TRANSCRIPTION REGULATOR 23-FEB-12 4DVD TITLE CRYSTAL STRUCTURE OF THE DISULPHIDE LINKED KNOTTED HOMODIMER OF PSU COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLARITY SUPPRESSION PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AMBER MUTATION-SUPPRESSING PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE P4; SOURCE 3 ORGANISM_TAXID: 10680; SOURCE 4 GENE: PSU; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A+ KEYWDS ALL ALPHA PROTEIN, TRANSCRIPTION TERMINATION INHIBITOR, RHO BINDING, KEYWDS 2 CAPSID DECORATION PROTEIN OF BACTERIOPHAGE P4, TRANSCRIPTION KEYWDS 3 TERMINATOR RHO HELICASE, TRANSCRIPTION REGULATOR EXPDTA X-RAY DIFFRACTION AUTHOR R.BANERJEE,S.NATH,U.SEN REVDAT 3 08-NOV-23 4DVD 1 SEQADV REVDAT 2 19-JUN-13 4DVD 1 JRNL REVDAT 1 21-NOV-12 4DVD 0 JRNL AUTH R.BANERJEE,S.NATH,A.RANJAN,S.KHAMRUI,B.PANI,R.SEN,U.SEN JRNL TITL THE FIRST STRUCTURE OF POLARITY SUPPRESSION PROTEIN, PSU JRNL TITL 2 FROM ENTEROBACTERIA PHAGE P4, REVEALS A NOVEL FOLD AND A JRNL TITL 3 KNOTTED DIMER JRNL REF J.BIOL.CHEM. V. 287 44667 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 23150672 JRNL DOI 10.1074/JBC.M112.423202 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.1_743) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.3 REMARK 3 NUMBER OF REFLECTIONS : 6838 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.680 REMARK 3 FREE R VALUE TEST SET COUNT : 320 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 47.3167 - 3.7799 0.92 3304 167 0.2129 0.2458 REMARK 3 2 3.7799 - 3.0003 0.93 3214 153 0.2628 0.3241 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.33 REMARK 3 B_SOL : 21.70 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.610 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.360 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 51.09 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 7.99830 REMARK 3 B22 (A**2) : 7.99830 REMARK 3 B33 (A**2) : -15.99650 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.011 1501 REMARK 3 ANGLE : 1.252 2027 REMARK 3 CHIRALITY : 0.068 225 REMARK 3 PLANARITY : 0.005 270 REMARK 3 DIHEDRAL : 16.118 567 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 4DVD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070829. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : ENRAF-NONIUS FR591 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : OSMIC MAXFLUX REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6846 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 47.311 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.11500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3RX6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 7.5%(W/V) PEG 6000, 5%(V/V) GLYCEROL, REMARK 280 0.1M HEPES, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 74.80500 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 74.80500 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 31.35000 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 74.80500 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 74.80500 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 31.35000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 74.80500 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 74.80500 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 31.35000 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 74.80500 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 74.80500 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 31.35000 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 74.80500 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 74.80500 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 31.35000 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 74.80500 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 74.80500 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 31.35000 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 74.80500 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 74.80500 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 31.35000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 74.80500 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 74.80500 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 31.35000 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 KCAL/MOL 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 350 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 SER A 3 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OG SER A 189 OG SER A 189 16445 1.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3RX6 RELATED DB: PDB DBREF 4DVD A 1 190 UNP P05460 VPSU_BPP4 1 190 SEQADV 4DVD SER A 13 UNP P05460 CYS 13 ENGINEERED MUTATION SEQADV 4DVD SER A 117 UNP P05460 CYS 117 ENGINEERED MUTATION SEQADV 4DVD CYS A 123 UNP P05460 THR 123 ENGINEERED MUTATION SEQRES 1 A 190 MET GLU SER THR ALA LEU GLN GLN ALA PHE ASP THR SER SEQRES 2 A 190 GLN ASN ASN LYS ALA ALA TRP LEU GLN ARG LYS ASN GLU SEQRES 3 A 190 LEU ALA ALA ALA GLU GLN GLU TYR LEU ARG LEU LEU SER SEQRES 4 A 190 GLY GLU GLY ARG ASN VAL SER ARG LEU ASP GLU LEU ARG SEQRES 5 A 190 ASN ILE ILE GLU VAL ARG LYS TRP GLN VAL ASN GLN ALA SEQRES 6 A 190 ALA GLY ARG TYR ILE ARG SER HIS GLU ALA VAL GLN HIS SEQRES 7 A 190 ILE SER ILE ARG ASP ARG LEU ASN ASP PHE MET GLN GLN SEQRES 8 A 190 HIS GLY THR ALA LEU ALA ALA ALA LEU ALA PRO GLU LEU SEQRES 9 A 190 MET GLY TYR SER GLU LEU THR ALA ILE ALA ARG ASN SER SEQRES 10 A 190 ALA ILE GLN ARG ALA CYS ASP ALA LEU ARG GLU ALA LEU SEQRES 11 A 190 LEU SER TRP LEU ALA LYS GLY GLU LYS ILE ASN TYR SER SEQRES 12 A 190 ALA GLN ASP SER ASP ILE LEU THR THR ILE GLY PHE ARG SEQRES 13 A 190 PRO ASP VAL ALA SER VAL ASP ASP SER ARG GLU LYS PHE SEQRES 14 A 190 THR PRO ALA GLN ASN MET ILE PHE SER ARG LYS SER ALA SEQRES 15 A 190 GLN LEU ALA SER ARG GLN SER VAL HELIX 1 1 THR A 4 GLY A 40 1 37 HELIX 2 2 ASN A 44 LEU A 100 1 57 HELIX 3 3 LEU A 100 MET A 105 1 6 HELIX 4 4 THR A 111 ALA A 135 1 25 HELIX 5 5 SER A 143 GLN A 145 5 3 HELIX 6 6 ASP A 146 GLY A 154 1 9 HELIX 7 7 ASP A 158 SER A 165 1 8 HELIX 8 8 THR A 170 ARG A 187 1 18 SSBOND 1 CYS A 123 CYS A 123 1555 8555 2.12 CRYST1 149.610 149.610 62.700 90.00 90.00 90.00 I 4 2 2 16 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 0.006684 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006684 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015949 0.00000