HEADER TRANSCRIPTION 24-JUL-17 5OJX TITLE CRYSTAL STRUCTURE OF REGULATOR PROTEIN 2 (PAMR2) FROM THE PAMAMYCIN TITLE 2 BIOSYNTHETIC GENE CLUSTER OF STREPTOMYCES ALBONIGER COMPND MOL_ID: 1; COMPND 2 MOLECULE: TETR FAMILY TRANSCRIPTION REGULATOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PAMAMYCIN REGULATOR PROTEIN 2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES ALBONIGER; SOURCE 3 ORGANISM_TAXID: 132473; SOURCE 4 GENE: PAMR2, SALB_00464; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSCRIPTION REGULATOR, TETR FAMILY TRANSCRIPTION REGULATOR, KEYWDS 2 STREPTOMYCES ALBONIGER, REGULATOR PROTEIN 2, PAMAMYCIN BIOSYNTHESIS, KEYWDS 3 TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR S.SCHMELZ,Y.REBETS,A.LUZHETSKYY,A.SCRIMA REVDAT 3 17-JAN-24 5OJX 1 REMARK REVDAT 2 25-APR-18 5OJX 1 JRNL REVDAT 1 11-APR-18 5OJX 0 JRNL AUTH Y.REBETS,S.SCHMELZ,O.GROMYKO,S.TISTECHOK,L.PETZKE,A.SCRIMA, JRNL AUTH 2 A.LUZHETSKYY JRNL TITL DESIGN, DEVELOPMENT AND APPLICATION OF WHOLE-CELL BASED JRNL TITL 2 ANTIBIOTIC-SPECIFIC BIOSENSOR. JRNL REF METAB. ENG. V. 47 263 2018 JRNL REFN ISSN 1096-7184 JRNL PMID 29609044 JRNL DOI 10.1016/J.YMBEN.2018.03.019 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.89 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 12402 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 621 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 38.8958 - 3.3331 0.99 2978 157 0.1886 0.2167 REMARK 3 2 3.3331 - 2.6458 0.99 2937 155 0.2837 0.4171 REMARK 3 3 2.6458 - 2.3114 1.00 2928 154 0.2873 0.3340 REMARK 3 4 2.3114 - 2.1001 1.00 2938 155 0.3110 0.3696 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) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.570 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 48.83 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.18 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 : 0.007 1672 REMARK 3 ANGLE : 0.912 2273 REMARK 3 CHIRALITY : 0.046 251 REMARK 3 PLANARITY : 0.006 294 REMARK 3 DIHEDRAL : 19.136 997 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 5OJX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1200005923. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JAN-17 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 : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918400 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20170615 REMARK 200 DATA SCALING SOFTWARE : XSCALE 20170615 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12407 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 38.889 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 4.288 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.0200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.47 REMARK 200 R MERGE FOR SHELL (I) : 0.71700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.860 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: 2Y30 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5MG/ML PAMR2 150 MM NACL 722MM TRI REMARK 280 -LITHIUM CITRATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 X+1/2,Y+1/2,Z 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 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 1.000000 0.000000 0.000000 49.13500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.01500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 49.13500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 28.01500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 4840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 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 -1.000000 0.000000 0.000000 -5.45854 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 38.88878 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 0 REMARK 465 VAL A 1 REMARK 465 ASN A 2 REMARK 465 GLU A 3 REMARK 465 THR A 4 REMARK 465 SER A 5 REMARK 465 GLY A 6 REMARK 465 ARG A 7 REMARK 465 GLU A 8 REMARK 465 ASN A 9 REMARK 465 THR A 10 REMARK 465 PRO A 11 REMARK 465 LYS A 12 REMARK 465 GLY A 13 REMARK 465 VAL A 23 REMARK 465 LYS A 24 REMARK 465 GLN A 25 REMARK 465 ARG A 26 REMARK 465 PRO A 27 REMARK 465 ALA A 28 REMARK 465 ARG A 29 REMARK 465 GLN A 30 REMARK 465 PRO A 31 REMARK 465 GLY A 238 REMARK 465 GLN A 239 REMARK 465 MET A 240 REMARK 465 ARG A 241 REMARK 465 SER A 242 REMARK 465 GLN A 243 REMARK 465 ASP A 244 REMARK 465 SER A 245 REMARK 465 LEU A 246 REMARK 465 GLU A 247 REMARK 465 HIS A 248 REMARK 465 HIS A 249 REMARK 465 HIS A 250 REMARK 465 HIS A 251 REMARK 465 HIS A 252 REMARK 465 HIS A 253 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 14 CG CD OE1 NE2 REMARK 470 ARG A 51 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 57 CG CD OE1 NE2 REMARK 470 ASP A 102 CG OD1 OD2 REMARK 470 ARG A 154 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 189 CG CD OE1 OE2 REMARK 470 GLN A 224 CG CD OE1 NE2 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 ARG A 21 41.77 -96.09 REMARK 500 LEU A 53 85.91 -69.32 REMARK 500 THR A 97 -5.63 -59.53 REMARK 500 HIS A 118 64.53 -118.63 REMARK 500 THR A 222 106.32 -46.00 REMARK 500 CYS A 232 -6.46 -48.62 REMARK 500 REMARK 500 REMARK: NULL DBREF1 5OJX A 2 245 UNP A0A0D3RJT7_STRAD DBREF2 5OJX A A0A0D3RJT7 2 245 SEQADV 5OJX MET A 0 UNP A0A0D3RJT INITIATING METHIONINE SEQADV 5OJX VAL A 1 UNP A0A0D3RJT CLONING ARTIFACT SEQADV 5OJX LEU A 246 UNP A0A0D3RJT EXPRESSION TAG SEQADV 5OJX GLU A 247 UNP A0A0D3RJT EXPRESSION TAG SEQADV 5OJX HIS A 248 UNP A0A0D3RJT EXPRESSION TAG SEQADV 5OJX HIS A 249 UNP A0A0D3RJT EXPRESSION TAG SEQADV 5OJX HIS A 250 UNP A0A0D3RJT EXPRESSION TAG SEQADV 5OJX HIS A 251 UNP A0A0D3RJT EXPRESSION TAG SEQADV 5OJX HIS A 252 UNP A0A0D3RJT EXPRESSION TAG SEQADV 5OJX HIS A 253 UNP A0A0D3RJT EXPRESSION TAG SEQRES 1 A 254 MET VAL ASN GLU THR SER GLY ARG GLU ASN THR PRO LYS SEQRES 2 A 254 GLY GLN PRO GLY SER ILE TRP LEU ARG GLU VAL LYS GLN SEQRES 3 A 254 ARG PRO ALA ARG GLN PRO LEU SER ARG GLU GLN ILE VAL SEQRES 4 A 254 GLN ALA ALA VAL ARG LEU LEU ASP GLU GLY GLY VAL ARG SEQRES 5 A 254 ASN LEU ARG MET ARG GLN LEU ALA ASP SER LEU ASN SER SEQRES 6 A 254 ALA PRO MET SER LEU TYR TRP HIS VAL SER THR LYS ASP SEQRES 7 A 254 ASP LEU LEU GLU LEU ALA ILE ASP ALA VAL PHE PRO ASP SEQRES 8 A 254 PRO PRO SER ARG SER GLY THR GLY ASP TRP ARG ASP ASP SEQRES 9 A 254 ILE LYS ALA GLY ALA THR ASP LEU PHE GLU VAL LEU LEU SEQRES 10 A 254 ARG HIS SER TRP MET ILE GLU LEU MET GLY GLY HIS PRO SEQRES 11 A 254 PRO VAL GLY PRO ARG ALA LEU ALA HIS THR SER ALA ILE SEQRES 12 A 254 ILE GLU ILE LEU GLU GLN ALA HIS PHE SER PRO ARG GLN SEQRES 13 A 254 LEU ASP SER ALA LEU SER ALA ILE TYR TYR TYR THR VAL SEQRES 14 A 254 GLY ALA ALA LEU SER GLU ALA SER TRP GLN ALA MET ALA SEQRES 15 A 254 ARG GLN SER ALA GLU SER GLU GLU GLU TRP VAL SER ARG SEQRES 16 A 254 LEU GLY PRO TYR LEU GLY MET ALA THR GLN SER HIS PRO SEQRES 17 A 254 ALA SER LEU ALA ASP TYR VAL LYS ARG SER ALA SER SER SEQRES 18 A 254 SER THR GLY GLN ARG PHE HIS ASP GLY LEU GLU CYS MET SEQRES 19 A 254 VAL SER GLY MET GLY GLN MET ARG SER GLN ASP SER LEU SEQRES 20 A 254 GLU HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *18(H2 O) HELIX 1 AA1 GLY A 16 GLU A 22 5 7 HELIX 2 AA2 SER A 33 GLY A 48 1 16 HELIX 3 AA3 ARG A 54 LEU A 62 1 9 HELIX 4 AA4 ALA A 65 VAL A 73 1 9 HELIX 5 AA5 THR A 75 VAL A 87 1 13 HELIX 6 AA6 ASP A 99 HIS A 118 1 20 HELIX 7 AA7 TRP A 120 HIS A 128 1 9 HELIX 8 AA8 GLY A 132 GLN A 148 1 17 HELIX 9 AA9 SER A 152 TRP A 177 1 26 HELIX 10 AB1 SER A 187 HIS A 206 1 20 HELIX 11 AB2 PRO A 207 SER A 220 1 14 HELIX 12 AB3 GLY A 223 SER A 235 1 13 CRYST1 98.270 56.030 39.270 90.00 97.99 90.00 C 1 2 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 0.010176 0.000000 0.001428 0.00000 SCALE2 0.000000 0.017848 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025714 0.00000