HEADER TRANSCRIPTION 28-SEP-17 6ELB TITLE TRYPTOPHAN REPRESSOR TRPR FROM E.COLI VARIANT M42F T44L T81M N87G S88Y TITLE 2 WITH INDOLE-3-ACETIC ACID AS LIGAND COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRP OPERON REPRESSOR; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: TRPR; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PET21 KEYWDS LIGAND BINDING, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR A.C.STIEL,S.SHANMUGARATNAM,O.HERUD-SIKIMIC,G.JUERGENS,B.HOCKER REVDAT 3 17-JAN-24 6ELB 1 REMARK REVDAT 2 07-APR-21 6ELB 1 JRNL REVDAT 1 06-FEB-19 6ELB 0 JRNL AUTH O.HERUD-SIKIMIC,A.C.STIEL,M.KOLB,S.SHANMUGARATNAM, JRNL AUTH 2 K.W.BERENDZEN,C.FELDHAUS,B.HOCKER,G.JUERGENS JRNL TITL A BIOSENSOR FOR THE DIRECT VISUALIZATION OF AUXIN JRNL REF NATURE 2021 JRNL REFN ESSN 1476-4687 JRNL DOI 10.1038/S41586-021-03425-2 REMARK 2 REMARK 2 RESOLUTION. 1.44 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) : 1.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 41354 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2068 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 45.3922 - 3.5445 0.99 2826 149 0.1686 0.1984 REMARK 3 2 3.5445 - 2.8135 1.00 2719 143 0.1583 0.2084 REMARK 3 3 2.8135 - 2.4579 0.99 2665 141 0.1510 0.1712 REMARK 3 4 2.4579 - 2.2331 1.00 2672 140 0.1310 0.1597 REMARK 3 5 2.2331 - 2.0731 0.99 2650 140 0.1279 0.1435 REMARK 3 6 2.0731 - 1.9509 0.99 2620 138 0.1391 0.1991 REMARK 3 7 1.9509 - 1.8532 0.99 2614 137 0.1400 0.1921 REMARK 3 8 1.8532 - 1.7725 0.99 2624 138 0.1410 0.2020 REMARK 3 9 1.7725 - 1.7042 0.98 2594 137 0.1451 0.2111 REMARK 3 10 1.7042 - 1.6454 0.98 2588 136 0.1491 0.2392 REMARK 3 11 1.6454 - 1.5940 0.98 2593 136 0.1528 0.2060 REMARK 3 12 1.5940 - 1.5484 0.98 2574 136 0.1468 0.1912 REMARK 3 13 1.5484 - 1.5076 0.98 2582 136 0.1666 0.2050 REMARK 3 14 1.5076 - 1.4709 0.98 2556 134 0.1929 0.2713 REMARK 3 15 1.4709 - 1.4374 0.92 2409 127 0.2475 0.3212 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.68 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 : 0.006 1839 REMARK 3 ANGLE : 0.821 2499 REMARK 3 CHIRALITY : 0.058 271 REMARK 3 PLANARITY : 0.006 329 REMARK 3 DIHEDRAL : 15.463 731 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 6ELB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1200006783. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAY-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 : SI111-DCM WITH SAGITAL BENDER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41356 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.437 REMARK 200 RESOLUTION RANGE LOW (A) : 45.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 7.179 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.9100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.65 REMARK 200 R MERGE FOR SHELL (I) : 1.18500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.6.0 REMARK 200 STARTING MODEL: 1TRO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350 0.17M KCL 3% D-(+) REMARK 280 TREHALOSE DIHYDRATE, PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 27.54500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.52500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.65500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.52500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.54500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.65500 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: 5600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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 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 SER A 107 REMARK 465 ASP A 108 REMARK 465 LEU A 109 REMARK 465 GLU A 110 REMARK 465 HIS A 111 REMARK 465 HIS A 112 REMARK 465 HIS A 113 REMARK 465 HIS A 114 REMARK 465 HIS A 115 REMARK 465 HIS A 116 REMARK 465 MET B 1 REMARK 465 SER B 107 REMARK 465 ASP B 108 REMARK 465 LEU B 109 REMARK 465 GLU B 110 REMARK 465 HIS B 111 REMARK 465 HIS B 112 REMARK 465 HIS B 113 REMARK 465 HIS B 114 REMARK 465 HIS B 115 REMARK 465 HIS B 116 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IAC A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IAC B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6EJW RELATED DB: PDB REMARK 900 RELATED ID: 6EKP RELATED DB: PDB REMARK 900 RELATED ID: 6ENN RELATED DB: PDB REMARK 900 RELATED ID: 6ELF RELATED DB: PDB REMARK 900 RELATED ID: 6ELG RELATED DB: PDB REMARK 900 RELATED ID: 6EJZ RELATED DB: PDB REMARK 900 RELATED ID: 6ENI RELATED DB: PDB DBREF 6ELB A 1 108 UNP P0A881 TRPR_ECOLI 1 108 DBREF 6ELB B 1 108 UNP P0A881 TRPR_ECOLI 1 108 SEQADV 6ELB PHE A 42 UNP P0A881 MET 42 ENGINEERED MUTATION SEQADV 6ELB LEU A 44 UNP P0A881 THR 44 ENGINEERED MUTATION SEQADV 6ELB MET A 81 UNP P0A881 THR 81 ENGINEERED MUTATION SEQADV 6ELB GLY A 87 UNP P0A881 ASN 87 ENGINEERED MUTATION SEQADV 6ELB TYR A 88 UNP P0A881 SER 88 ENGINEERED MUTATION SEQADV 6ELB LEU A 109 UNP P0A881 EXPRESSION TAG SEQADV 6ELB GLU A 110 UNP P0A881 EXPRESSION TAG SEQADV 6ELB HIS A 111 UNP P0A881 EXPRESSION TAG SEQADV 6ELB HIS A 112 UNP P0A881 EXPRESSION TAG SEQADV 6ELB HIS A 113 UNP P0A881 EXPRESSION TAG SEQADV 6ELB HIS A 114 UNP P0A881 EXPRESSION TAG SEQADV 6ELB HIS A 115 UNP P0A881 EXPRESSION TAG SEQADV 6ELB HIS A 116 UNP P0A881 EXPRESSION TAG SEQADV 6ELB PHE B 42 UNP P0A881 MET 42 ENGINEERED MUTATION SEQADV 6ELB LEU B 44 UNP P0A881 THR 44 ENGINEERED MUTATION SEQADV 6ELB MET B 81 UNP P0A881 THR 81 ENGINEERED MUTATION SEQADV 6ELB GLY B 87 UNP P0A881 ASN 87 ENGINEERED MUTATION SEQADV 6ELB TYR B 88 UNP P0A881 SER 88 ENGINEERED MUTATION SEQADV 6ELB LEU B 109 UNP P0A881 EXPRESSION TAG SEQADV 6ELB GLU B 110 UNP P0A881 EXPRESSION TAG SEQADV 6ELB HIS B 111 UNP P0A881 EXPRESSION TAG SEQADV 6ELB HIS B 112 UNP P0A881 EXPRESSION TAG SEQADV 6ELB HIS B 113 UNP P0A881 EXPRESSION TAG SEQADV 6ELB HIS B 114 UNP P0A881 EXPRESSION TAG SEQADV 6ELB HIS B 115 UNP P0A881 EXPRESSION TAG SEQADV 6ELB HIS B 116 UNP P0A881 EXPRESSION TAG SEQRES 1 A 116 MET ALA GLN GLN SER PRO TYR SER ALA ALA MET ALA GLU SEQRES 2 A 116 GLN ARG HIS GLN GLU TRP LEU ARG PHE VAL ASP LEU LEU SEQRES 3 A 116 LYS ASN ALA TYR GLN ASN ASP LEU HIS LEU PRO LEU LEU SEQRES 4 A 116 ASN LEU PHE LEU LEU PRO ASP GLU ARG GLU ALA LEU GLY SEQRES 5 A 116 THR ARG VAL ARG ILE VAL GLU GLU LEU LEU ARG GLY GLU SEQRES 6 A 116 MET SER GLN ARG GLU LEU LYS ASN GLU LEU GLY ALA GLY SEQRES 7 A 116 ILE ALA MET ILE THR ARG GLY SER GLY TYR LEU LYS ALA SEQRES 8 A 116 ALA PRO VAL GLU LEU ARG GLN TRP LEU GLU GLU VAL LEU SEQRES 9 A 116 LEU LYS SER ASP LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 116 MET ALA GLN GLN SER PRO TYR SER ALA ALA MET ALA GLU SEQRES 2 B 116 GLN ARG HIS GLN GLU TRP LEU ARG PHE VAL ASP LEU LEU SEQRES 3 B 116 LYS ASN ALA TYR GLN ASN ASP LEU HIS LEU PRO LEU LEU SEQRES 4 B 116 ASN LEU PHE LEU LEU PRO ASP GLU ARG GLU ALA LEU GLY SEQRES 5 B 116 THR ARG VAL ARG ILE VAL GLU GLU LEU LEU ARG GLY GLU SEQRES 6 B 116 MET SER GLN ARG GLU LEU LYS ASN GLU LEU GLY ALA GLY SEQRES 7 B 116 ILE ALA MET ILE THR ARG GLY SER GLY TYR LEU LYS ALA SEQRES 8 B 116 ALA PRO VAL GLU LEU ARG GLN TRP LEU GLU GLU VAL LEU SEQRES 9 B 116 LEU LYS SER ASP LEU GLU HIS HIS HIS HIS HIS HIS HET IAC A 201 21 HET IAC B 201 21 HETNAM IAC 1H-INDOL-3-YLACETIC ACID HETSYN IAC INDOLE ACETIC ACID FORMUL 3 IAC 2(C10 H9 N O2) FORMUL 5 HOH *294(H2 O) HELIX 1 AA1 SER A 5 ASN A 32 1 28 HELIX 2 AA2 LEU A 34 LEU A 43 1 10 HELIX 3 AA3 LEU A 44 GLY A 64 1 21 HELIX 4 AA4 SER A 67 GLY A 76 1 10 HELIX 5 AA5 GLY A 78 ALA A 92 1 15 HELIX 6 AA6 PRO A 93 LEU A 105 1 13 HELIX 7 AA7 SER B 5 ASN B 32 1 28 HELIX 8 AA8 LEU B 34 LEU B 43 1 10 HELIX 9 AA9 LEU B 44 GLY B 64 1 21 HELIX 10 AB1 SER B 67 GLY B 76 1 10 HELIX 11 AB2 GLY B 78 ALA B 92 1 15 HELIX 12 AB3 PRO B 93 LEU B 105 1 13 SITE 1 AC1 6 ARG A 54 ARG A 84 TYR A 88 HOH A 318 SITE 2 AC1 6 HOH A 392 LEU B 41 SITE 1 AC2 7 LEU A 41 PHE A 42 ARG B 54 ARG B 84 SITE 2 AC2 7 TYR B 88 HOH B 305 HOH B 358 CRYST1 55.090 63.310 65.050 90.00 90.00 90.00 P 21 21 21 8 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 0.018152 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015795 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015373 0.00000