HEADER METAL BINDING PROTEIN 18-AUG-24 9D86 TITLE CRYSTAL STRUCTURE OF EPOXYQUEUOSINE REDUCTASE QUEH C9S MUTANT FROM TITLE 2 THERMOTOGA MARITIMA COMPND MOL_ID: 1; COMPND 2 MOLECULE: EPOXYQUEUOSINE REDUCTASE QUEH; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: QUEUOSINE BIOSYNTHESIS PROTEIN QUEH; COMPND 5 EC: 1.17.99.6; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA MSB8; SOURCE 3 ORGANISM_TAXID: 243274; SOURCE 4 GENE: QUEH, TM_0731; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS QUEUOSINE BIOSYNTHESIS, EPOXYQUEUOSINE REDUCTASE, METALLOENZYME, KEYWDS 2 METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.HU,S.D.BRUNER REVDAT 1 18-DEC-24 9D86 0 JRNL AUTH Y.HU,M.JAROCH,G.SUN,P.C.DEDON,V.DE CRECY-LAGARD,S.D.BRUNER JRNL TITL MECHANISM OF CATALYSIS AND SUBSTRATE BINDING OF JRNL TITL 2 EPOXYQUEUOSINE REDUCTASE IN THE BIOSYNTHETIC PATHWAY TO JRNL TITL 3 QUEUOSINE-MODIFIED TRNA. JRNL REF BIOCHEMISTRY 2024 JRNL REFN ISSN 0006-2960 JRNL PMID 39644232 JRNL DOI 10.1021/ACS.BIOCHEM.4C00524 REMARK 2 REMARK 2 RESOLUTION. 1.88 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) : 1.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 16851 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 822 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 30.1500 - 3.4200 1.00 2815 139 0.1782 0.2226 REMARK 3 2 3.4200 - 2.7200 1.00 2702 125 0.2190 0.2721 REMARK 3 3 2.7200 - 2.3700 1.00 2637 157 0.2263 0.2722 REMARK 3 4 2.3700 - 2.1600 1.00 2648 140 0.2314 0.2531 REMARK 3 5 2.1600 - 2.0000 1.00 2653 132 0.2412 0.2932 REMARK 3 6 2.0000 - 1.8800 0.98 2574 129 0.3249 0.4044 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.288 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.880 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.62 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 1516 REMARK 3 ANGLE : 1.026 2043 REMARK 3 CHIRALITY : 0.057 214 REMARK 3 PLANARITY : 0.012 261 REMARK 3 DIHEDRAL : 5.441 203 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 9D86 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-AUG-24. REMARK 100 THE DEPOSITION ID IS D_1000287397. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-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 : 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) : 1.03321 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16852 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.880 REMARK 200 RESOLUTION RANGE LOW (A) : 30.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.5100 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) : 1.95 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS-HCL PH5.5, 0.2 M REMARK 280 LITHIUM SULFATE MONOHYDRATE, 25% (W/V) POLYETHYLENE GLYCEROL REMARK 280 (PEG) 3350, 10 MM CACL2, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.83900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.83900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 26.37100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.48500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 26.37100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.48500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 36.83900 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 26.37100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 52.48500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 36.83900 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 26.37100 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 52.48500 REMARK 290 SMTRY3 8 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 GLY A 2 REMARK 465 LYS A 181 REMARK 465 HIS A 182 REMARK 465 ALA A 183 REMARK 465 GLU A 184 REMARK 465 ILE A 185 REMARK 465 SER A 186 REMARK 465 ARG A 187 REMARK 465 LYS A 188 REMARK 465 ARG A 189 REMARK 465 GLY A 190 REMARK 465 HIS A 191 REMARK 465 MET A 192 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 OE2 GLU A 96 OH TYR A 136 2.14 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 ASN A 30 63.04 -153.90 REMARK 500 SER A 111 -167.57 -161.15 REMARK 500 REMARK 500 REMARK: NULL 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 SF4 A 201 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 87 SG REMARK 620 2 SF4 A 201 S1 122.3 REMARK 620 3 SF4 A 201 S3 113.0 103.3 REMARK 620 4 SF4 A 201 S4 105.9 105.4 105.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 201 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 90 SG REMARK 620 2 SF4 A 201 S1 109.0 REMARK 620 3 SF4 A 201 S2 117.1 105.2 REMARK 620 4 SF4 A 201 S4 112.6 106.4 105.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 201 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 169 SG REMARK 620 2 SF4 A 201 S2 116.8 REMARK 620 3 SF4 A 201 S3 107.6 104.5 REMARK 620 4 SF4 A 201 S4 116.0 105.8 104.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 201 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 171 SG REMARK 620 2 SF4 A 201 S1 120.9 REMARK 620 3 SF4 A 201 S2 107.2 105.6 REMARK 620 4 SF4 A 201 S3 112.6 103.9 105.5 REMARK 620 N 1 2 3 DBREF 9D86 A 1 192 UNP Q9WZJ0 QUEH_THEMA 1 192 SEQADV 9D86 SER A 9 UNP Q9WZJ0 CYS 9 ENGINEERED MUTATION SEQRES 1 A 192 MET GLY THR VAL LEU ILE HIS VAL SER CYS ALA PRO ASP SEQRES 2 A 192 LEU LEU THR THR ILE PHE HIS VAL ARG ASP ALA GLU PHE SEQRES 3 A 192 PHE PHE TYR ASN PRO ASN ILE GLN PRO LEU SER GLU TYR SEQRES 4 A 192 GLU LYS ARG ARG GLU ALA VAL ASP LYS VAL ALA ASN HIS SEQRES 5 A 192 PHE SER LEU ASN VAL ARG TYR GLY GLU TYR SER THR GLU SEQRES 6 A 192 GLU ILE ARG LYS TRP TYR THR ALA VAL LYS ASP TYR LYS SEQRES 7 A 192 ASP LEU GLY GLU GLY SER LYS ARG CYS GLU ARG CYS ILE SEQRES 8 A 192 SER PHE LEU LEU GLU ARG THR ALA GLN GLU ALA ARG LYS SEQRES 9 A 192 ARG GLY HIS GLU SER PHE SER THR THR LEU LEU ALA SER SEQRES 10 A 192 PRO ARG LYS ASN LEU PRO MET ILE GLU ASN ILE GLY LYS SEQRES 11 A 192 THR ILE GLU GLU LYS TYR GLY VAL LYS PHE PHE PHE LYS SEQRES 12 A 192 ASN PHE ARG LYS GLY GLY ALA TYR GLN GLU GLY VAL ARG SEQRES 13 A 192 LEU SER LYS GLU LEU GLY ILE TYR ARG GLN ASN TYR CYS SEQRES 14 A 192 GLY CYS VAL PHE SER LEU LEU GLU ARG ARG GLU LYS HIS SEQRES 15 A 192 ALA GLU ILE SER ARG LYS ARG GLY HIS MET HET SF4 A 201 8 HETNAM SF4 IRON/SULFUR CLUSTER FORMUL 2 SF4 FE4 S4 FORMUL 3 HOH *35(H2 O) HELIX 1 AA1 CYS A 10 PHE A 19 1 10 HELIX 2 AA2 PRO A 35 SER A 54 1 20 HELIX 3 AA3 SER A 63 LYS A 75 1 13 HELIX 4 AA4 ASP A 76 LYS A 78 5 3 HELIX 5 AA5 SER A 84 GLY A 106 1 23 HELIX 6 AA6 LEU A 114 SER A 117 5 4 HELIX 7 AA7 ASN A 121 GLY A 137 1 17 HELIX 8 AA8 GLY A 149 GLY A 162 1 14 HELIX 9 AA9 CYS A 171 GLU A 180 1 10 SHEET 1 AA1 5 VAL A 57 TYR A 59 0 SHEET 2 AA1 5 ALA A 24 PHE A 28 1 N PHE A 26 O ARG A 58 SHEET 3 AA1 5 VAL A 4 VAL A 8 1 N ILE A 6 O GLU A 25 SHEET 4 AA1 5 SER A 109 THR A 112 1 O SER A 111 N HIS A 7 SHEET 5 AA1 5 LYS A 139 PHE A 140 1 O LYS A 139 N PHE A 110 LINK SG CYS A 87 FE2 SF4 A 201 1555 1555 2.35 LINK SG CYS A 90 FE3 SF4 A 201 1555 1555 2.28 LINK SG CYS A 169 FE1 SF4 A 201 1555 1555 2.27 LINK SG CYS A 171 FE4 SF4 A 201 1555 1555 2.26 CISPEP 1 GLN A 34 PRO A 35 0 0.11 CRYST1 52.742 104.970 73.678 90.00 90.00 90.00 C 2 2 21 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 0.018960 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009527 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013573 0.00000