HEADER GENE REGULATION 21-FEB-24 8YE5 TITLE STRUCTURAL AND FUNCTIONAL RESEARCH OF REDUCTIVE DEHALOGENASES TMRC TITLE 2 USING A CELL-FREE EXPRESSION SYSTEM FOR HETEROLOGOUS EXPRESSION COMPND MOL_ID: 1; COMPND 2 MOLECULE: TMRC; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: CELL-FREE SYNTHESIS SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DEHALOBACTER SP.; SOURCE 3 ORGANISM_TAXID: 1962289; SOURCE 4 EXPRESSION_SYSTEM: CELL-FREE GATEWAY CLONING VECTOR N-TERM 8XHIS SOURCE 5 MCHERRY PCELLFREE_G05; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 1508208 KEYWDS DEHALOBACTER RESPIRATORY REDUCTIVE DEHALOGENASES, CELL-FREE GENE KEYWDS 2 EXPRESSION, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR X.Y.ZHANG,Y.Q.LIU REVDAT 1 06-MAR-24 8YE5 0 JRNL AUTH X.Y.ZHANG,Y.Q.LIU JRNL TITL STRUCTURAL AND FUNCTIONAL RESEARCH OF REDUCTIVE JRNL TITL 2 DEHALOGENASES TMRC USING A CELL-FREE EXPRESSION SYSTEM FOR JRNL TITL 3 HETEROLOGOUS EXPRESSION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 37403 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1794 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 29.4000 - 3.5000 0.96 2805 126 0.1770 0.2088 REMARK 3 2 3.5000 - 2.7800 0.98 2790 133 0.1784 0.2117 REMARK 3 3 2.7800 - 2.4300 0.99 2752 126 0.1858 0.2119 REMARK 3 4 2.4300 - 2.2100 0.99 2758 161 0.1799 0.1941 REMARK 3 5 2.2100 - 2.0500 0.99 2765 110 0.1727 0.2155 REMARK 3 6 2.0500 - 1.9300 1.00 2728 162 0.1938 0.2077 REMARK 3 7 1.9300 - 1.8300 1.00 2716 159 0.1885 0.1973 REMARK 3 8 1.8300 - 1.7500 1.00 2736 141 0.1916 0.2561 REMARK 3 9 1.7500 - 1.6800 1.00 2763 134 0.2004 0.2091 REMARK 3 10 1.6800 - 1.6300 1.00 2756 138 0.1982 0.2336 REMARK 3 11 1.6300 - 1.5700 1.00 2722 140 0.2014 0.2223 REMARK 3 12 1.5700 - 1.5300 0.98 2687 141 0.2051 0.2601 REMARK 3 13 1.5300 - 1.4900 0.96 2631 123 0.2275 0.2458 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) : 0.137 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.329 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.02 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.16 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 1987 REMARK 3 ANGLE : 0.874 2666 REMARK 3 CHIRALITY : 0.059 269 REMARK 3 PLANARITY : 0.014 353 REMARK 3 DIHEDRAL : 15.122 270 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 8YE5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1300045477. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-SEP-22 REMARK 200 TEMPERATURE (KELVIN) : 293 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 : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979183 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37410 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.490 REMARK 200 RESOLUTION RANGE LOW (A) : 55.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.30600 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200MM POTASSIUM PHOSPHATE, 10% PEG REMARK 280 3500, EVAPORATION, TEMPERATURE 293K 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 15.79500 REMARK 290 SMTRY3 2 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 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 GLY A -1 REMARK 465 PRO A 0 REMARK 465 ALA A 126 REMARK 465 PRO A 127 REMARK 465 GLY B -1 REMARK 465 PRO B 0 REMARK 465 SER B 1 REMARK 465 PRO B 2 REMARK 465 ASN B 3 REMARK 465 LEU B 4 REMARK 465 ASP B 5 REMARK 465 ARG B 125 REMARK 465 ALA B 126 REMARK 465 PRO B 127 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 ARG A 125 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 296 O HOH A 317 2.09 REMARK 500 OE2 GLU B 11 O HOH B 201 2.10 REMARK 500 OE2 GLU A 110 O HOH A 201 2.13 REMARK 500 O HOH B 254 O HOH B 272 2.15 REMARK 500 OE2 GLU B 15 O HOH B 202 2.18 REMARK 500 O HOH B 210 O HOH B 286 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 234 O HOH B 293 2555 2.15 REMARK 500 O HOH A 278 O HOH A 294 1545 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 89 75.03 -104.01 REMARK 500 ASP B 89 75.33 -102.63 REMARK 500 MET B 123 -160.55 -121.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 79 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8YE5 A -1 127 PDB 8YE5 8YE5 -1 127 DBREF 8YE5 B -1 127 PDB 8YE5 8YE5 -1 127 SEQRES 1 A 129 GLY PRO SER PRO ASN LEU ASP GLY THR ARG LEU ARG GLU SEQRES 2 A 129 GLU GLY ASN GLU ALA PHE LYS ALA GLY ARG TYR HIS GLU SEQRES 3 A 129 ALA ILE ARG TYR TYR THR GLN ALA ILE GLU VAL ASP PRO SEQRES 4 A 129 ASP SER GLU PHE LEU TYR THR ASN ARG SER PHE ALA TYR SEQRES 5 A 129 PHE ASN ILE LYS GLU PHE GLU LYS SER ALA ALA ASP ALA SEQRES 6 A 129 ALA LYS ALA VAL GLU ILE ASN ALA ASN PHE PHE LYS GLY SEQRES 7 A 129 HIS TYR ARG LEU GLY LEU ALA GLN MET SER LEU ASN ASP SEQRES 8 A 129 PHE GLY HIS ALA MET GLU SER LEU ARG LYS ALA TRP ALA SEQRES 9 A 129 LEU ALA PRO SER GLU ASN LYS GLU ALA ILE ARG VAL ALA SEQRES 10 A 129 MET ALA LYS CYS GLU SER LYS MET ALA ARG ALA PRO SEQRES 1 B 129 GLY PRO SER PRO ASN LEU ASP GLY THR ARG LEU ARG GLU SEQRES 2 B 129 GLU GLY ASN GLU ALA PHE LYS ALA GLY ARG TYR HIS GLU SEQRES 3 B 129 ALA ILE ARG TYR TYR THR GLN ALA ILE GLU VAL ASP PRO SEQRES 4 B 129 ASP SER GLU PHE LEU TYR THR ASN ARG SER PHE ALA TYR SEQRES 5 B 129 PHE ASN ILE LYS GLU PHE GLU LYS SER ALA ALA ASP ALA SEQRES 6 B 129 ALA LYS ALA VAL GLU ILE ASN ALA ASN PHE PHE LYS GLY SEQRES 7 B 129 HIS TYR ARG LEU GLY LEU ALA GLN MET SER LEU ASN ASP SEQRES 8 B 129 PHE GLY HIS ALA MET GLU SER LEU ARG LYS ALA TRP ALA SEQRES 9 B 129 LEU ALA PRO SER GLU ASN LYS GLU ALA ILE ARG VAL ALA SEQRES 10 B 129 MET ALA LYS CYS GLU SER LYS MET ALA ARG ALA PRO FORMUL 3 HOH *243(H2 O) HELIX 1 AA1 ASP A 5 ALA A 19 1 15 HELIX 2 AA2 ARG A 21 ASP A 36 1 16 HELIX 3 AA3 SER A 39 ILE A 53 1 15 HELIX 4 AA4 GLU A 55 ASN A 70 1 16 HELIX 5 AA5 PHE A 73 LEU A 87 1 15 HELIX 6 AA6 ASP A 89 ALA A 104 1 16 HELIX 7 AA7 ASN A 108 LYS A 122 1 15 HELIX 8 AA8 THR B 7 ALA B 19 1 13 HELIX 9 AA9 ARG B 21 ASP B 36 1 16 HELIX 10 AB1 SER B 39 ILE B 53 1 15 HELIX 11 AB2 GLU B 55 ASN B 70 1 16 HELIX 12 AB3 PHE B 73 LEU B 87 1 15 HELIX 13 AB4 ASP B 89 ALA B 104 1 16 HELIX 14 AB5 PRO B 105 GLU B 107 5 3 HELIX 15 AB6 ASN B 108 LYS B 122 1 15 CRYST1 59.202 31.590 65.651 90.00 109.88 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 0.016891 0.000000 0.006108 0.00000 SCALE2 0.000000 0.031656 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016197 0.00000