HEADER TRANSCRIPTION 18-MAR-19 6JNY TITLE CRYSTAL STRUCTURE OF BACTERIOPHAGE 21 Q PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTITERMINATOR Q PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE SFI; SOURCE 3 ORGANISM_TAXID: 1225789; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RNA POLYMERASE, ANTITERMINATION, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR Y.FENG,J.SHI REVDAT 3 22-NOV-23 6JNY 1 REMARK REVDAT 2 17-JUL-19 6JNY 1 JRNL REVDAT 1 12-JUN-19 6JNY 0 JRNL AUTH J.SHI,X.GAO,T.TIAN,Z.YU,B.GAO,A.WEN,L.YOU,S.CHANG,X.ZHANG, JRNL AUTH 2 Y.ZHANG,Y.FENG JRNL TITL STRUCTURAL BASIS OF Q-DEPENDENT TRANSCRIPTION JRNL TITL 2 ANTITERMINATION. JRNL REF NAT COMMUN V. 10 2925 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 31266960 JRNL DOI 10.1038/S41467-019-10958-8 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 56680 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.480 REMARK 3 FREE R VALUE TEST SET COUNT : 1971 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 31.2210 - 3.4958 0.92 3927 141 0.1972 0.1963 REMARK 3 2 3.4958 - 2.7753 0.99 4146 148 0.2130 0.2375 REMARK 3 3 2.7753 - 2.4246 0.93 3904 141 0.2110 0.2240 REMARK 3 4 2.4246 - 2.2030 0.98 4072 146 0.2123 0.2484 REMARK 3 5 2.2030 - 2.0451 0.98 4063 146 0.2076 0.2182 REMARK 3 6 2.0451 - 1.9246 0.98 4063 145 0.2208 0.2365 REMARK 3 7 1.9246 - 1.8282 0.98 4047 147 0.2218 0.2570 REMARK 3 8 1.8282 - 1.7486 0.91 3822 138 0.2172 0.2208 REMARK 3 9 1.7486 - 1.6813 0.94 3939 140 0.2139 0.2715 REMARK 3 10 1.6813 - 1.6233 0.96 3927 143 0.2217 0.2205 REMARK 3 11 1.6233 - 1.5726 0.94 3925 144 0.2207 0.2314 REMARK 3 12 1.5726 - 1.5276 0.91 3816 135 0.2234 0.2492 REMARK 3 13 1.5276 - 1.4874 0.90 3710 137 0.2318 0.2675 REMARK 3 14 1.4874 - 1.4511 0.80 3348 120 0.2462 0.2670 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) : 23.810 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.84 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 : 0.005 2324 REMARK 3 ANGLE : 0.735 3119 REMARK 3 CHIRALITY : 0.057 326 REMARK 3 PLANARITY : 0.004 390 REMARK 3 DIHEDRAL : 10.821 875 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 6JNY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1300011293. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-OCT-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57774 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.45500 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: MOLREP REMARK 200 STARTING MODEL: 1OR7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M KF AND 14% PEG3350, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 38.91350 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 GLY A 2 REMARK 465 ILE A 3 REMARK 465 ARG A 4 REMARK 465 GLU A 5 REMARK 465 LEU A 6 REMARK 465 VAL A 47 REMARK 465 GLU A 48 REMARK 465 PRO A 49 REMARK 465 GLY A 50 REMARK 465 ARG A 51 REMARK 465 VAL A 52 REMARK 465 MET A 53 REMARK 465 THR A 54 REMARK 465 LYS A 157 REMARK 465 ILE A 158 REMARK 465 LYS A 159 REMARK 465 HIS A 160 REMARK 465 VAL A 161 REMARK 465 ALA A 162 REMARK 465 MET B 1 REMARK 465 GLY B 2 REMARK 465 ILE B 3 REMARK 465 ARG B 4 REMARK 465 GLU B 5 REMARK 465 LEU B 6 REMARK 465 VAL B 47 REMARK 465 GLU B 48 REMARK 465 PRO B 49 REMARK 465 GLY B 50 REMARK 465 ARG B 51 REMARK 465 VAL B 52 REMARK 465 MET B 53 REMARK 465 THR B 54 REMARK 465 LEU B 111 REMARK 465 CYS B 112 REMARK 465 ARG B 113 REMARK 465 GLY B 114 REMARK 465 LYS B 157 REMARK 465 ILE B 158 REMARK 465 LYS B 159 REMARK 465 HIS B 160 REMARK 465 VAL B 161 REMARK 465 ALA B 162 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 SER A 37 110.00 -173.64 REMARK 500 SER B 37 114.18 -165.19 REMARK 500 REMARK 500 REMARK: NULL DBREF 6JNY A 1 162 UNP M1FPN0 M1FPN0_9CAUD 1 162 DBREF 6JNY B 1 162 UNP M1FPN0 M1FPN0_9CAUD 1 162 SEQRES 1 A 162 MET GLY ILE ARG GLU LEU ASN LEU THR LYS GLU GLN HIS SEQRES 2 A 162 GLU TRP LEU ASN GLY TRP LEU GLU LEU TRP GLY ALA TRP SEQRES 3 A 162 VAL TYR SER GLY ARG LEU GLU LYS ARG MET SER SER VAL SEQRES 4 A 162 ILE ALA LYS PHE MET GLU SER VAL GLU PRO GLY ARG VAL SEQRES 5 A 162 MET THR ARG PRO MET CYS ASN ASP ASP ASP GLY MET LEU SEQRES 6 A 162 ILE SER GLN VAL VAL ASP SER VAL MET TYR ILE ASP LYS SEQRES 7 A 162 LYS ALA PHE GLY ILE LEU LEU SER TYR TYR ALA HIS GLY SEQRES 8 A 162 SER SER LYS HIS ALA ILE ALA SER TYR TYR HIS ARG VAL SEQRES 9 A 162 ALA ARG PRO ARG LYS MET LEU CYS ARG GLY GLY GLY ARG SEQRES 10 A 162 ILE GLN LYS PRO SER LEU ALA THR CYS ARG ARG GLU VAL SEQRES 11 A 162 ASP GLU ILE LEU ASN ALA SER LEU PHE MET ILE TYR PRO SEQRES 12 A 162 VAL LEU ASP SER ALA PHE LYS ASN ARG LYS ARG VAL GLU SEQRES 13 A 162 LYS ILE LYS HIS VAL ALA SEQRES 1 B 162 MET GLY ILE ARG GLU LEU ASN LEU THR LYS GLU GLN HIS SEQRES 2 B 162 GLU TRP LEU ASN GLY TRP LEU GLU LEU TRP GLY ALA TRP SEQRES 3 B 162 VAL TYR SER GLY ARG LEU GLU LYS ARG MET SER SER VAL SEQRES 4 B 162 ILE ALA LYS PHE MET GLU SER VAL GLU PRO GLY ARG VAL SEQRES 5 B 162 MET THR ARG PRO MET CYS ASN ASP ASP ASP GLY MET LEU SEQRES 6 B 162 ILE SER GLN VAL VAL ASP SER VAL MET TYR ILE ASP LYS SEQRES 7 B 162 LYS ALA PHE GLY ILE LEU LEU SER TYR TYR ALA HIS GLY SEQRES 8 B 162 SER SER LYS HIS ALA ILE ALA SER TYR TYR HIS ARG VAL SEQRES 9 B 162 ALA ARG PRO ARG LYS MET LEU CYS ARG GLY GLY GLY ARG SEQRES 10 B 162 ILE GLN LYS PRO SER LEU ALA THR CYS ARG ARG GLU VAL SEQRES 11 B 162 ASP GLU ILE LEU ASN ALA SER LEU PHE MET ILE TYR PRO SEQRES 12 B 162 VAL LEU ASP SER ALA PHE LYS ASN ARG LYS ARG VAL GLU SEQRES 13 B 162 LYS ILE LYS HIS VAL ALA FORMUL 3 HOH *183(H2 O) HELIX 1 AA1 THR A 9 SER A 29 1 21 HELIX 2 AA2 GLU A 33 MET A 36 5 4 HELIX 3 AA3 SER A 37 SER A 46 1 10 HELIX 4 AA4 ASN A 59 TYR A 75 1 17 HELIX 5 AA5 ASP A 77 ALA A 89 1 13 HELIX 6 AA6 SER A 93 VAL A 104 1 12 HELIX 7 AA7 SER A 122 GLU A 156 1 35 HELIX 8 AA8 THR B 9 SER B 29 1 21 HELIX 9 AA9 GLU B 33 MET B 36 5 4 HELIX 10 AB1 SER B 37 SER B 46 1 10 HELIX 11 AB2 ASN B 59 TYR B 75 1 17 HELIX 12 AB3 ASP B 77 ALA B 89 1 13 HELIX 13 AB4 SER B 93 ALA B 105 1 13 HELIX 14 AB5 SER B 122 GLU B 156 1 35 SHEET 1 AA1 2 ARG A 108 CYS A 112 0 SHEET 2 AA1 2 GLY A 115 GLN A 119 -1 O ARG A 117 N MET A 110 SHEET 1 AA2 2 ARG B 108 MET B 110 0 SHEET 2 AA2 2 ARG B 117 GLN B 119 -1 O ARG B 117 N MET B 110 CRYST1 32.902 77.827 68.692 90.00 98.59 90.00 P 1 21 1 4 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 0.030393 0.000000 0.004593 0.00000 SCALE2 0.000000 0.012849 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014723 0.00000