HEADER PHOTOSYNTHESIS 07-MAY-24 8ZF1 TITLE CRYSTAL STRUCTURE OF A CHEMO TRIPLET PHOTOENZYME (CTPE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR, PADR-LIKE FAMILY; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOCOCCUS LACTIS SUBSP. CREMORIS (STRAIN SOURCE 3 MG1363); SOURCE 4 ORGANISM_TAXID: 416870; SOURCE 5 GENE: LLMG_0323; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ARITIFICIAL ENZYME, PROTEIN MODIFICATION, BIOCATALYSIS, ENERGY KEYWDS 2 TRANSFER, PHOTOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR X.CHEN,J.Y.QIAN,J.GUO,Y.Z.WU,F.R.ZHONG REVDAT 3 13-NOV-24 8ZF1 1 REMARK REVDAT 2 24-JUL-24 8ZF1 1 JRNL REVDAT 1 17-JUL-24 8ZF1 0 JRNL AUTH J.GUO,J.QIAN,D.CAI,J.HUANG,X.YANG,N.SUN,J.ZHANG,T.PANG, JRNL AUTH 2 W.ZHAO,G.WU,X.CHEN,F.ZHONG,Y.WU JRNL TITL CHEMOGENETIC EVOLUTION OF DIVERSIFIED PHOTOENZYMES FOR JRNL TITL 2 ENANTIOSELECTIVE [2 + 2] CYCLOADDITIONS IN WHOLE CELLS. JRNL REF J.AM.CHEM.SOC. V. 146 19030 2024 JRNL REFN ESSN 1520-5126 JRNL PMID 38976645 JRNL DOI 10.1021/JACS.4C03087 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.16_3549: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 5523 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.273 REMARK 3 R VALUE (WORKING SET) : 0.271 REMARK 3 FREE R VALUE : 0.302 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 277 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 35.4620 - 3.2754 1.00 2654 150 0.2436 0.2800 REMARK 3 2 3.2754 - 2.6001 0.99 2592 127 0.3751 0.3974 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) : 0.430 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.600 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.037 884 REMARK 3 ANGLE : 1.633 1186 REMARK 3 CHIRALITY : 0.461 127 REMARK 3 PLANARITY : 0.005 152 REMARK 3 DIHEDRAL : 23.404 334 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 11.7278 22.5701 -8.9693 REMARK 3 T TENSOR REMARK 3 T11: 0.4548 T22: 0.8161 REMARK 3 T33: 0.5092 T12: -0.2265 REMARK 3 T13: 0.0189 T23: -0.1431 REMARK 3 L TENSOR REMARK 3 L11: 5.0021 L22: 3.5521 REMARK 3 L33: 1.4707 L12: -3.3203 REMARK 3 L13: -0.0474 L23: -1.1791 REMARK 3 S TENSOR REMARK 3 S11: 0.1502 S12: 0.0175 S13: 0.4281 REMARK 3 S21: -0.3024 S22: -0.1612 S23: 0.1111 REMARK 3 S31: 0.0255 S32: 0.1752 S33: 0.1095 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 8ZF1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 15-MAY-24. REMARK 100 THE DEPOSITION ID IS D_1300047598. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-SEP-22 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 : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPX REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5561 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 43.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.90 REMARK 200 R MERGE (I) : 0.12600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 10.80 REMARK 200 R MERGE FOR SHELL (I) : 2.47000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 M NAH2PO4/K2HPO4, PH=8.2, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 1 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -Y,-X,-Z+1/3 REMARK 290 5555 -X+Y,Y,-Z+2/3 REMARK 290 6555 X,X-Y,-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 -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 40.82133 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 20.41067 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 20.41067 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 40.82133 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 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: MONOMERIC 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 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 GLY A 1 REMARK 465 ALA A 2 REMARK 465 GLU A 3 REMARK 465 ILE A 4 REMARK 465 SER A 71 REMARK 465 GLN A 72 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 GLY A 119 REMARK 465 GLY A 120 REMARK 465 SER A 121 REMARK 465 GLY A 122 REMARK 465 GLY A 123 REMARK 465 TRP A 124 REMARK 465 SER A 125 REMARK 465 HIS A 126 REMARK 465 PRO A 127 REMARK 465 GLN A 128 REMARK 465 PHE A 129 REMARK 465 GLU A 130 REMARK 465 LYS A 131 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 GLU A 42 -26.77 -149.93 REMARK 500 ASP A 60 4.04 -69.67 REMARK 500 ARG A 76 116.93 -160.78 REMARK 500 LYS A 110 -58.94 -145.19 REMARK 500 REMARK 500 REMARK: NULL DBREF 8ZF1 A 2 116 UNP A2RI36 A2RI36_LACLM 2 116 SEQADV 8ZF1 MET A 0 UNP A2RI36 INITIATING METHIONINE SEQADV 8ZF1 GLY A 1 UNP A2RI36 EXPRESSION TAG SEQADV 8ZF1 LEU A 8 UNP A2RI36 MET 8 ENGINEERED MUTATION SEQADV 8ZF1 ASP A 55 UNP A2RI36 LYS 55 ENGINEERED MUTATION SEQADV 8ZF1 GLN A 59 UNP A2RI36 LYS 59 ENGINEERED MUTATION SEQADV 8ZF1 HIS A 88 UNP A2RI36 ASN 88 ENGINEERED MUTATION SEQADV 8ZF1 CYS A 93 UNP A2RI36 PHE 93 ENGINEERED MUTATION SEQADV 8ZF1 LEU A 96 UNP A2RI36 TRP 96 ENGINEERED MUTATION SEQADV 8ZF1 SER A 117 UNP A2RI36 EXPRESSION TAG SEQADV 8ZF1 ARG A 118 UNP A2RI36 EXPRESSION TAG SEQADV 8ZF1 GLY A 119 UNP A2RI36 EXPRESSION TAG SEQADV 8ZF1 GLY A 120 UNP A2RI36 EXPRESSION TAG SEQADV 8ZF1 SER A 121 UNP A2RI36 EXPRESSION TAG SEQADV 8ZF1 GLY A 122 UNP A2RI36 EXPRESSION TAG SEQADV 8ZF1 GLY A 123 UNP A2RI36 EXPRESSION TAG SEQADV 8ZF1 TRP A 124 UNP A2RI36 EXPRESSION TAG SEQADV 8ZF1 SER A 125 UNP A2RI36 EXPRESSION TAG SEQADV 8ZF1 HIS A 126 UNP A2RI36 EXPRESSION TAG SEQADV 8ZF1 PRO A 127 UNP A2RI36 EXPRESSION TAG SEQADV 8ZF1 GLN A 128 UNP A2RI36 EXPRESSION TAG SEQADV 8ZF1 PHE A 129 UNP A2RI36 EXPRESSION TAG SEQADV 8ZF1 GLU A 130 UNP A2RI36 EXPRESSION TAG SEQADV 8ZF1 LYS A 131 UNP A2RI36 EXPRESSION TAG SEQRES 1 A 132 MET GLY ALA GLU ILE PRO LYS GLU LEU LEU ARG ALA GLN SEQRES 2 A 132 THR ASN VAL ILE LEU LEU ASN VAL LEU LYS GLN GLY ASP SEQRES 3 A 132 ASN TYR VAL TYR GLY ILE ILE LYS GLN VAL LYS GLU ALA SEQRES 4 A 132 SER ASN GLY GLU MET GLU LEU ASN GLU ALA THR LEU TYR SEQRES 5 A 132 THR ILE PHE ASP ARG LEU GLU GLN ASP GLY ILE ILE SER SEQRES 6 A 132 SER TYR TRP GLY ASP GLU SER GLN GLY GLY ARG ARG LYS SEQRES 7 A 132 TYR TYR ARG LEU THR GLU ILE GLY HIS GLU HIS MET ARG SEQRES 8 A 132 LEU ALA CYS GLU SER LEU SER ARG VAL ASP LYS ILE ILE SEQRES 9 A 132 GLU ASN LEU GLU ALA ASN LYS LYS SER GLU ALA ILE LYS SEQRES 10 A 132 SER ARG GLY GLY SER GLY GLY TRP SER HIS PRO GLN PHE SEQRES 11 A 132 GLU LYS HET U1O A 201 19 HETNAM U1O N-(9-OXIDANYLIDENETHIOXANTHEN-2-YL)ETHANAMIDE FORMUL 2 U1O C15 H11 N O2 S HELIX 1 AA1 PRO A 5 LEU A 21 1 17 HELIX 2 AA2 TYR A 27 SER A 39 1 13 HELIX 3 AA3 ASN A 46 ASP A 60 1 15 HELIX 4 AA4 THR A 82 ASN A 109 1 28 SHEET 1 AA1 2 ILE A 63 TRP A 67 0 SHEET 2 AA1 2 LYS A 77 LEU A 81 -1 O TYR A 78 N TYR A 66 LINK SG CYS A 93 C18 U1O A 201 1555 1555 1.85 CRYST1 70.923 70.923 61.232 90.00 90.00 120.00 P 32 1 2 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 0.014100 0.008140 0.000000 0.00000 SCALE2 0.000000 0.016281 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016331 0.00000