HEADER METAL BINDING PROTEIN 15-JUL-22 8AF3 TITLE STEROL CARRIER PROTEIN ARTIFICAL METALLOENZYME INCORPORATING Q111C TITLE 2 MUTATION COUPLED TO 2,2'-BIPYRIDINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENOYL-COA HYDRATASE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 3-ALPHA,7-ALPHA,12-ALPHA-TRIHYDROXY-5-BETA-CHOLEST-24-ENOYL- COMPND 5 COA HYDRATASE; COMPND 6 EC: 4.2.1.107,4.2.1.119; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: 2,2-BIPYRIDINE WAS COUPLED TO A CYSTEINE AT POSITION COMPND 9 111 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HSD17B4, EDH17B4, SDR8C1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DE NOVO PROTEIN, ARTIFICIAL METALLOENZYME, BIPYRIDINE ADDUCT, METAL KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.M.RICHARDSON,E.KLEMENCIC,A.G.JARVIS REVDAT 4 03-APR-24 8AF3 1 JRNL REVDAT 3 28-FEB-24 8AF3 1 JRNL REVDAT 2 15-NOV-23 8AF3 1 LINK REVDAT 1 16-AUG-23 8AF3 0 JRNL AUTH E.KLEMENCIC,R.C.BREWSTER,H.S.ALI,J.M.RICHARDSON,A.G.JARVIS JRNL TITL USING BPYALA TO GENERATE COPPER ARTIFICIAL METALLOENZYMES: A JRNL TITL 2 CATALYTIC AND STRUCTURAL STUDY. JRNL REF CATALYSIS SCIENCE AND V. 14 1622 2024 JRNL REF 2 TECHNOLOGY JRNL REFN ISSN 2044-4753 JRNL PMID 38505507 JRNL DOI 10.1039/D3CY01648J REMARK 2 REMARK 2 RESOLUTION. 1.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 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) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.920 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 32696 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.770 REMARK 3 FREE R VALUE TEST SET COUNT : 1559 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 39.6800 - 3.3800 0.99 2904 127 0.1978 0.2116 REMARK 3 2 3.3800 - 2.6800 1.00 2901 144 0.2216 0.2482 REMARK 3 3 2.6800 - 2.3400 1.00 2929 142 0.2413 0.2249 REMARK 3 4 2.3400 - 2.1300 1.00 2931 146 0.2419 0.2676 REMARK 3 5 2.1300 - 1.9800 1.00 2911 156 0.2485 0.1870 REMARK 3 6 1.9800 - 1.8600 1.00 2925 143 0.2792 0.3511 REMARK 3 7 1.8600 - 1.7700 1.00 2890 142 0.2900 0.2999 REMARK 3 8 1.7700 - 1.6900 1.00 2945 150 0.2893 0.3093 REMARK 3 9 1.6900 - 1.6300 1.00 2907 151 0.3056 0.2952 REMARK 3 10 1.6300 - 1.5700 0.91 2696 125 0.3427 0.4507 REMARK 3 11 1.5700 - 1.5200 0.77 2198 133 0.4018 0.4185 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.77 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.82 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 : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 28.1941 31.4984 10.9324 REMARK 3 T TENSOR REMARK 3 T11: 0.3051 T22: 0.2048 REMARK 3 T33: 0.1935 T12: 0.0014 REMARK 3 T13: 0.0169 T23: 0.0164 REMARK 3 L TENSOR REMARK 3 L11: 7.3092 L22: 4.6237 REMARK 3 L33: 3.6303 L12: 0.0013 REMARK 3 L13: 1.7090 L23: -1.5778 REMARK 3 S TENSOR REMARK 3 S11: 0.1599 S12: -0.3986 S13: -0.3993 REMARK 3 S21: 0.1594 S22: 0.0601 S23: 0.1563 REMARK 3 S31: 0.0388 S32: -0.1367 S33: -0.1643 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 8AF3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1292124345. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-19 REMARK 200 TEMPERATURE (KELVIN) : 81 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.378 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32696 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.520 REMARK 200 RESOLUTION RANGE LOW (A) : 39.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 11.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.52 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) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.400 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: 1IKT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: WELL SOLUTION 2.3M AMMONIUM SULPHATE, REMARK 280 100 MM CITRIC ACID PH 5.6 AND 200 MM NACL, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 278K 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 17.58000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.53000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.52500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.53000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.58000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.52500 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: 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 1 REMARK 465 GLU A 2 REMARK 465 GLY A 3 REMARK 465 GLY A 4 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 LYS A 5 CG CD CE NZ REMARK 470 LEU A 114 CG CD1 CD2 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 204 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 Q8X A 111 N2 REMARK 620 2 Q8X A 111 N3 85.8 REMARK 620 3 HOH A 328 O 178.5 93.7 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8AF2 RELATED DB: PDB REMARK 900 STRUCTURE OF THE SCP PROTEIN WITH THE UNNATURAL AMINO ACID REMARK 900 BIPYRIDINE ALANINE INCORPORATED AT THE SAME POSITION (111) DBREF 8AF3 A 2 120 UNP P51659 DHB4_HUMAN 618 736 SEQADV 8AF3 MET A 1 UNP P51659 INITIATING METHIONINE SEQADV 8AF3 Q8X A 111 UNP P51659 GLN 727 CONFLICT SEQRES 1 A 120 MET GLU GLY GLY LYS LEU GLN SER THR PHE VAL PHE GLU SEQRES 2 A 120 GLU ILE GLY ARG ARG LEU LYS ASP ILE GLY PRO GLU VAL SEQRES 3 A 120 VAL LYS LYS VAL ASN ALA VAL PHE GLU TRP HIS ILE THR SEQRES 4 A 120 LYS GLY GLY ASN ILE GLY ALA LYS TRP THR ILE ASP LEU SEQRES 5 A 120 LYS SER GLY SER GLY LYS VAL TYR GLN GLY PRO ALA LYS SEQRES 6 A 120 GLY ALA ALA ASP THR THR ILE ILE LEU SER ASP GLU ASP SEQRES 7 A 120 PHE MET GLU VAL VAL LEU GLY LYS LEU ASP PRO GLN LYS SEQRES 8 A 120 ALA PHE PHE SER GLY ARG LEU LYS ALA ARG GLY ASN ILE SEQRES 9 A 120 MET LEU SER GLN LYS LEU Q8X MET ILE LEU LYS ASP TYR SEQRES 10 A 120 ALA LYS LEU HET Q8X A 111 32 HET TRT A 201 61 HET SO4 A 202 5 HET SO4 A 203 5 HET CU A 204 1 HETNAM Q8X (2~{R})-2-AZANYL-3-[(6-PYRIDIN-2-YLPYRIDIN-3-YL) HETNAM 2 Q8X METHYLSULFANYL]PROPANAL HETNAM TRT FRAGMENT OF TRITON X-100 HETNAM SO4 SULFATE ION HETNAM CU COPPER (II) ION HETSYN TRT 1-{2-[2-(2-METHOXYETHOXY)ETHOXY]ETHOXY}-4-(1,1,3,3- HETSYN 2 TRT TETRAMETHYLBUTYL)BENZENE FORMUL 1 Q8X C14 H15 N3 O S FORMUL 2 TRT C21 H36 O4 FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 CU CU 2+ FORMUL 6 HOH *44(H2 O) HELIX 1 AA1 GLN A 7 ASN A 31 1 25 HELIX 2 AA2 ASP A 76 LEU A 84 1 9 HELIX 3 AA3 ASP A 88 SER A 95 1 8 HELIX 4 AA4 LEU A 106 TYR A 117 1 12 HELIX 5 AA5 ALA A 118 LEU A 120 5 3 SHEET 1 AA1 5 LYS A 58 GLN A 61 0 SHEET 2 AA1 5 ILE A 44 LEU A 52 -1 N THR A 49 O TYR A 60 SHEET 3 AA1 5 ALA A 32 THR A 39 -1 N TRP A 36 O TRP A 48 SHEET 4 AA1 5 THR A 70 SER A 75 1 O ILE A 72 N HIS A 37 SHEET 5 AA1 5 LYS A 99 GLY A 102 -1 O ARG A 101 N THR A 71 LINK C LEU A 110 N Q8X A 111 1555 1555 1.32 LINK C Q8X A 111 N MET A 112 1555 1555 1.32 LINK N2 Q8X A 111 CU CU A 204 1555 1555 2.02 LINK N3 Q8X A 111 CU CU A 204 1555 1555 2.06 LINK CU CU A 204 O HOH A 328 1555 1555 2.08 CRYST1 35.160 51.050 63.060 90.00 90.00 90.00 P 21 21 21 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 0.028441 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019589 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015858 0.00000