HEADER DNA BINDING PROTEIN 14-MAR-19 6R1L TITLE CRYSTAL STRUCTURE OF LMRR WITH BOUND COPPER PHENANTHROLINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR, PADR-LIKE FAMILY; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: LMRR CARRYING A C-TERMINAL STREP-TAG SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOCOCCUS LACTIS SUBSP. CREMORIS MG1363; SOURCE 3 ORGANISM_TAXID: 416870; SOURCE 4 GENE: LLMG_0323; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PADR FAMILY, TRANSCRIPTIONAL REGULATOR, ARTIFICIAL METALLOENZYME, KEYWDS 2 PHENANTHROLINE, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.REDDEM,A.M.W.H.THUNNISSEN REVDAT 3 24-JAN-24 6R1L 1 REMARK REVDAT 2 13-OCT-21 6R1L 1 SOURCE JRNL LINK REVDAT 1 01-APR-20 6R1L 0 JRNL AUTH L.VILLARINO,S.CHORDIA,L.ALONSO-COTCHICO,E.REDDEM,Z.ZHOU, JRNL AUTH 2 A.M.W.H.THUNNISSEN,J.D.MARECHAL,G.ROELFES JRNL TITL COFACTOR BINDING DYNAMICS INFLUENCE THE CATALYTIC ACTIVITY JRNL TITL 2 AND SELECTIVITY OF AN ARTIFICIAL METALLOENZYME. JRNL REF ACS CATALYSIS V. 10 11783 2020 JRNL REFN ESSN 2155-5435 JRNL PMID 33101759 JRNL DOI 10.1021/ACSCATAL.0C01619 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14RC1_3161 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) : 34.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.650 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 12273 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1232 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 34.2024 - 4.3555 1.00 1221 132 0.1858 0.2306 REMARK 3 2 4.3555 - 3.4581 1.00 1228 141 0.1730 0.2068 REMARK 3 3 3.4581 - 3.0213 1.00 1248 133 0.2017 0.2415 REMARK 3 4 3.0213 - 2.7452 1.00 1209 138 0.2077 0.2928 REMARK 3 5 2.7452 - 2.5485 1.00 1252 141 0.2193 0.2468 REMARK 3 6 2.5485 - 2.3983 1.00 1218 146 0.2339 0.3207 REMARK 3 7 2.3983 - 2.2782 1.00 1218 134 0.2398 0.2936 REMARK 3 8 2.2782 - 2.1791 1.00 1212 130 0.2356 0.2955 REMARK 3 9 2.1791 - 2.0952 0.98 1235 137 0.2702 0.3068 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.17 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6R1L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1292101280. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9660 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 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7167 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.090 REMARK 200 RESOLUTION RANGE LOW (A) : 34.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 9.200 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 9.40 REMARK 200 R MERGE FOR SHELL (I) : 0.93200 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: PDB ENTRY 3F8C REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM CACODYLATE, 300 MM SODIUM REMARK 280 ACETATE, 25% PEG 200 MME, 5 MM CU-PHENANTHROLINE, PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 88.73450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 17.42550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 17.42550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 133.10175 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 17.42550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 17.42550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 44.36725 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 17.42550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 17.42550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 133.10175 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 17.42550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 17.42550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 44.36725 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 88.73450 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: 3920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 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 ALA A 2 REMARK 465 GLU A 3 REMARK 465 ILE A 4 REMARK 465 GLU A 70 REMARK 465 SER A 71 REMARK 465 GLN A 72 REMARK 465 GLY A 73 REMARK 465 ASN A 109 REMARK 465 LYS A 110 REMARK 465 LYS A 111 REMARK 465 SER A 112 REMARK 465 GLU A 113 REMARK 465 ALA A 114 REMARK 465 ILE A 115 REMARK 465 LYS A 116 REMARK 465 SER A 117 REMARK 465 ARG A 118 REMARK 465 TRP A 119 REMARK 465 SER A 120 REMARK 465 HIS A 121 REMARK 465 PRO A 122 REMARK 465 GLN A 123 REMARK 465 PHE A 124 REMARK 465 GLU A 125 REMARK 465 LYS A 126 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 202 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHN A 201 N1 REMARK 620 2 PHN A 201 N10 86.8 REMARK 620 3 PHN A 201 N1 0.0 86.8 REMARK 620 4 PHN A 201 N10 86.8 0.0 86.8 REMARK 620 5 HOH A 306 O 133.2 112.3 133.2 112.3 REMARK 620 6 HOH A 306 O 104.3 122.5 104.3 122.5 100.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PHN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU A 202 DBREF 6R1L A 1 116 UNP A2RI36 A2RI36_LACLM 1 116 SEQADV 6R1L SER A 117 UNP A2RI36 EXPRESSION TAG SEQADV 6R1L ARG A 118 UNP A2RI36 EXPRESSION TAG SEQADV 6R1L TRP A 119 UNP A2RI36 EXPRESSION TAG SEQADV 6R1L SER A 120 UNP A2RI36 EXPRESSION TAG SEQADV 6R1L HIS A 121 UNP A2RI36 EXPRESSION TAG SEQADV 6R1L PRO A 122 UNP A2RI36 EXPRESSION TAG SEQADV 6R1L GLN A 123 UNP A2RI36 EXPRESSION TAG SEQADV 6R1L PHE A 124 UNP A2RI36 EXPRESSION TAG SEQADV 6R1L GLU A 125 UNP A2RI36 EXPRESSION TAG SEQADV 6R1L LYS A 126 UNP A2RI36 EXPRESSION TAG SEQRES 1 A 126 MET ALA GLU ILE PRO LYS GLU MET LEU ARG ALA GLN THR SEQRES 2 A 126 ASN VAL ILE LEU LEU ASN VAL LEU LYS GLN GLY ASP ASN SEQRES 3 A 126 TYR VAL TYR GLY ILE ILE LYS GLN VAL LYS GLU ALA SER SEQRES 4 A 126 ASN GLY GLU MET GLU LEU ASN GLU ALA THR LEU TYR THR SEQRES 5 A 126 ILE PHE LYS ARG LEU GLU LYS ASP GLY ILE ILE SER SER SEQRES 6 A 126 TYR TRP GLY ASP GLU SER GLN GLY GLY ARG ARG LYS TYR SEQRES 7 A 126 TYR ARG LEU THR GLU ILE GLY HIS GLU ASN MET ARG LEU SEQRES 8 A 126 ALA PHE GLU SER TRP SER ARG VAL ASP LYS ILE ILE GLU SEQRES 9 A 126 ASN LEU GLU ALA ASN LYS LYS SER GLU ALA ILE LYS SER SEQRES 10 A 126 ARG TRP SER HIS PRO GLN PHE GLU LYS HET PHN A 201 14 HET CU A 202 1 HETNAM PHN 1,10-PHENANTHROLINE HETNAM CU COPPER (II) ION FORMUL 2 PHN C12 H8 N2 FORMUL 3 CU CU 2+ FORMUL 4 HOH *22(H2 O) HELIX 1 AA1 PRO A 5 GLN A 23 1 19 HELIX 2 AA2 VAL A 28 SER A 39 1 12 HELIX 3 AA3 ASN A 46 ASP A 60 1 15 HELIX 4 AA4 THR A 82 ALA A 108 1 27 SHEET 1 AA1 3 ASN A 26 TYR A 27 0 SHEET 2 AA1 3 ARG A 76 LEU A 81 -1 O TYR A 79 N ASN A 26 SHEET 3 AA1 3 ILE A 63 GLY A 68 -1 N TYR A 66 O TYR A 78 LINK N1 PHN A 201 CU CU A 202 1555 1555 2.04 LINK N10 PHN A 201 CU CU A 202 1555 1555 2.03 LINK N1 PHN A 201 CU CU A 202 1555 7555 2.01 LINK N10 PHN A 201 CU CU A 202 1555 7555 2.12 LINK CU CU A 202 O HOH A 306 1555 1555 2.04 LINK CU CU A 202 O HOH A 306 1555 7555 2.39 SITE 1 AC1 3 VAL A 15 TRP A 96 CU A 202 SITE 1 AC2 2 PHN A 201 HOH A 306 CRYST1 34.851 34.851 177.469 90.00 90.00 90.00 P 43 21 2 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 0.028694 0.000000 0.000000 0.00000 SCALE2 0.000000 0.028694 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005635 0.00000