HEADER DNA BINDING PROTEIN 24-NOV-20 7KUA TITLE CRYSTAL STRUCTURE OF THE MARR FAMILY TRANSCRIPTIONAL REGULATOR FROM TITLE 2 PSEUDOMONAS PUTIDA BOUND TO INDOLE 3 ACETIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR, MARR FAMILY; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IACR PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PUTIDA; SOURCE 3 ORGANISM_TAXID: 303; SOURCE 4 GENE: IACR, E6B08_12615; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSCRIPTIONAL REGULATOR, LIGAND BINDING, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR W.G.WALTON,A.D.LIETZAN,M.R.REDINBO,J.L.DANGL REVDAT 3 25-OCT-23 7KUA 1 REMARK REVDAT 2 23-NOV-22 7KUA 1 JRNL REVDAT 1 01-DEC-21 7KUA 0 JRNL AUTH J.M.CONWAY,W.G.WALTON,I.SALAS-GONZALEZ,T.F.LAW,C.A.LINDBERG, JRNL AUTH 2 L.E.CROOK,S.M.KOSINA,C.R.FITZPATRICK,A.D.LIETZAN, JRNL AUTH 3 T.R.NORTHEN,C.D.JONES,O.M.FINKEL,M.R.REDINBO,J.L.DANGL JRNL TITL DIVERSE MARR BACTERIAL REGULATORS OF AUXIN CATABOLISM IN THE JRNL TITL 2 PLANT MICROBIOME. JRNL REF NAT MICROBIOL V. 7 1817 2022 JRNL REFN ESSN 2058-5276 JRNL PMID 36266335 JRNL DOI 10.1038/S41564-022-01244-3 REMARK 2 REMARK 2 RESOLUTION. 1.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 14518 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1460 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 25.9900 - 4.0600 1.00 1412 160 0.1614 0.2020 REMARK 3 2 4.0600 - 3.2200 1.00 1335 152 0.1626 0.1689 REMARK 3 3 3.2200 - 2.8200 1.00 1320 147 0.1839 0.2338 REMARK 3 4 2.8200 - 2.5600 1.00 1316 146 0.1884 0.2510 REMARK 3 5 2.5600 - 2.3800 1.00 1296 145 0.1837 0.2139 REMARK 3 6 2.3800 - 2.2400 1.00 1307 147 0.1904 0.2237 REMARK 3 7 2.2400 - 2.1200 1.00 1273 144 0.1860 0.2623 REMARK 3 8 2.1200 - 2.0300 1.00 1306 140 0.2027 0.2570 REMARK 3 9 2.0300 - 1.9500 1.00 1282 145 0.2235 0.2675 REMARK 3 10 1.9500 - 1.8900 0.93 1211 134 0.2829 0.3369 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.201 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.033 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.48 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.08 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 : 0.010 1312 REMARK 3 ANGLE : 0.918 1778 REMARK 3 CHIRALITY : 0.368 193 REMARK 3 PLANARITY : 0.005 233 REMARK 3 DIHEDRAL : 23.136 504 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 7KUA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1000253168. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-20 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 : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03322 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14591 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.880 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.88 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: PHENIX REMARK 200 STARTING MODEL: 3CJN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ANATRACE MCSG2 SCREEN 35 % (V/V) REMARK 280 MICROLYTIC MIX(1), PH 7.0, WHICH CONSISTS OF: 1.8305 M MALONIC REMARK 280 ACID, 0.25 M AMMONIUM CITRATE TRIBASIC, 0.12 M SUCCINIC ACID, REMARK 280 0.3 M DL-MALIC ACID, 0.4 M SODIUM ACETATE TRIHYDRATE, 0.5 M REMARK 280 SODIUM FORMATE, 0.16 M AMMONIUM TARTRATE DIBASIC, THE MIXTURE REMARK 280 TITRATED TO PH 7.0 USING SODIUM HYDROXIDE, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.46133 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 60.92267 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 60.92267 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 30.46133 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: 7360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 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 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 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 -23 REMARK 465 HIS A -22 REMARK 465 HIS A -21 REMARK 465 HIS A -20 REMARK 465 HIS A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 SER A -16 REMARK 465 SER A -15 REMARK 465 GLY A -14 REMARK 465 VAL A -13 REMARK 465 ASP A -12 REMARK 465 LEU A -11 REMARK 465 GLY A -10 REMARK 465 THR A -9 REMARK 465 GLU A -8 REMARK 465 ASN A -7 REMARK 465 LEU A -6 REMARK 465 TYR A -5 REMARK 465 PHE A -4 REMARK 465 GLN A -3 REMARK 465 SER A -2 REMARK 465 ASN A -1 REMARK 465 ALA A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 ASN A 3 REMARK 465 ALA A 4 REMARK 465 LYS A 5 REMARK 465 ASN A 6 REMARK 465 THR A 7 REMARK 465 SER A 8 REMARK 465 ALA A 9 REMARK 465 ALA A 10 REMARK 465 SER A 11 REMARK 465 PRO A 12 REMARK 465 ALA A 13 REMARK 465 ARG A 14 REMARK 465 LYS A 15 REMARK 465 GLY A 16 REMARK 465 HIS A 17 REMARK 465 SER A 18 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 DBREF 7KUA A 1 167 UNP B0FXI7 B0FXI7_PSEPU 1 167 SEQADV 7KUA MET A -23 UNP B0FXI7 INITIATING METHIONINE SEQADV 7KUA HIS A -22 UNP B0FXI7 EXPRESSION TAG SEQADV 7KUA HIS A -21 UNP B0FXI7 EXPRESSION TAG SEQADV 7KUA HIS A -20 UNP B0FXI7 EXPRESSION TAG SEQADV 7KUA HIS A -19 UNP B0FXI7 EXPRESSION TAG SEQADV 7KUA HIS A -18 UNP B0FXI7 EXPRESSION TAG SEQADV 7KUA HIS A -17 UNP B0FXI7 EXPRESSION TAG SEQADV 7KUA SER A -16 UNP B0FXI7 EXPRESSION TAG SEQADV 7KUA SER A -15 UNP B0FXI7 EXPRESSION TAG SEQADV 7KUA GLY A -14 UNP B0FXI7 EXPRESSION TAG SEQADV 7KUA VAL A -13 UNP B0FXI7 EXPRESSION TAG SEQADV 7KUA ASP A -12 UNP B0FXI7 EXPRESSION TAG SEQADV 7KUA LEU A -11 UNP B0FXI7 EXPRESSION TAG SEQADV 7KUA GLY A -10 UNP B0FXI7 EXPRESSION TAG SEQADV 7KUA THR A -9 UNP B0FXI7 EXPRESSION TAG SEQADV 7KUA GLU A -8 UNP B0FXI7 EXPRESSION TAG SEQADV 7KUA ASN A -7 UNP B0FXI7 EXPRESSION TAG SEQADV 7KUA LEU A -6 UNP B0FXI7 EXPRESSION TAG SEQADV 7KUA TYR A -5 UNP B0FXI7 EXPRESSION TAG SEQADV 7KUA PHE A -4 UNP B0FXI7 EXPRESSION TAG SEQADV 7KUA GLN A -3 UNP B0FXI7 EXPRESSION TAG SEQADV 7KUA SER A -2 UNP B0FXI7 EXPRESSION TAG SEQADV 7KUA ASN A -1 UNP B0FXI7 EXPRESSION TAG SEQADV 7KUA ALA A 0 UNP B0FXI7 EXPRESSION TAG SEQRES 1 A 191 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 A 191 GLY THR GLU ASN LEU TYR PHE GLN SER ASN ALA MET SER SEQRES 3 A 191 ASN ALA LYS ASN THR SER ALA ALA SER PRO ALA ARG LYS SEQRES 4 A 191 GLY HIS SER HIS HIS ASP PRO ALA SER ASP GLU PHE ARG SEQRES 5 A 191 LYS GLU ASP PHE PRO PHE TYR TRP LEU ALA ARG VAL HIS SEQRES 6 A 191 GLY ARG TYR THR GLN ASN MET GLU ARG LEU LEU LYS LYS SEQRES 7 A 191 ILE ASP LEU ASP VAL PRO ARG TRP ARG VAL LEU TRP ILE SEQRES 8 A 191 LEU ASN GLU ASN GLY GLU SER SER ILE SER GLU ILE SER SEQRES 9 A 191 THR HIS ALA ILE ALA LYS LEU SER THR ILE THR LYS ILE SEQRES 10 A 191 VAL TYR ARG MET LYS GLU ASP GLY LEU VAL ASP THR ALA SEQRES 11 A 191 PRO SER PRO GLU ASP GLY ARG VAL THR GLN VAL ARG ILE SEQRES 12 A 191 THR GLU VAL GLY LEU GLN ASN ILE GLU ARG MET GLN GLU SEQRES 13 A 191 VAL THR ARG GLU LEU PHE GLN ARG SER PHE LYS GLY LEU SEQRES 14 A 191 THR GLU ALA GLN VAL GLN ARG LEU ASN ARG MET LEU GLU SEQRES 15 A 191 VAL VAL PHE HIS ASN LEU GLU THR LEU HET IAC A 201 21 HETNAM IAC 1H-INDOL-3-YLACETIC ACID HETSYN IAC INDOLE ACETIC ACID FORMUL 2 IAC C10 H9 N O2 FORMUL 3 HOH *58(H2 O) HELIX 1 AA1 ARG A 28 ASP A 31 5 4 HELIX 2 AA2 PHE A 32 LYS A 54 1 23 HELIX 3 AA3 ASP A 58 GLY A 72 1 15 HELIX 4 AA4 ILE A 76 ILE A 84 1 9 HELIX 5 AA5 LYS A 86 ASP A 100 1 15 HELIX 6 AA6 THR A 120 THR A 134 1 15 HELIX 7 AA7 THR A 134 PHE A 142 1 9 HELIX 8 AA8 THR A 146 GLU A 165 1 20 SHEET 1 AA1 3 SER A 74 SER A 75 0 SHEET 2 AA1 3 THR A 115 ILE A 119 -1 O VAL A 117 N SER A 74 SHEET 3 AA1 3 VAL A 103 PRO A 107 -1 N ALA A 106 O GLN A 116 SITE 1 AC1 9 PHE A 32 PHE A 34 TYR A 35 TYR A 44 SITE 2 AC1 9 TRP A 62 ARG A 63 TRP A 66 HIS A 82 SITE 3 AC1 9 ILE A 84 CRYST1 57.557 57.557 91.384 90.00 90.00 120.00 P 31 2 1 6 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 0.017374 0.010031 0.000000 0.00000 SCALE2 0.000000 0.020062 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010943 0.00000