HEADER FLAVOPROTEIN 21-APR-23 8J4V TITLE STRUCTURE OF MYCOBACTERIUM THERMORESISTIBILE NRDI(OXIDISED) DETERMINED TITLE 2 AT 1.1 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN NRDI; COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: RIBONUCLEOTIDE REDUCTASE METAL COFACTOR SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOLICIBACTERIUM THERMORESISTIBILE ATCC 19527; SOURCE 3 ORGANISM_TAXID: 1797; SOURCE 4 STRAIN: ATCC 19527; SOURCE 5 GENE: NRDI; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ORIGAMI 2 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET32A+ KEYWDS RIBONUCLEOTIDE REDUCTASE ACCESSORY PROTEIN. METAL COFACTOR ASSEMBLY, KEYWDS 2 FLAVOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.R.YADAV,S.C.MANDE REVDAT 1 09-OCT-24 8J4V 0 JRNL AUTH L.R.YADAV,V.SHARMA,M.SHANMUGAM,S.C.MANDE JRNL TITL STRUCTURAL INSIGHTS INTO THE INITIATION OF FREE RADICAL JRNL TITL 2 FORMATION IN THE CLASS IB RIBONUCLEOTIDE REDUCTASES IN JRNL TITL 3 MYCOBACTERIA JRNL REF CURR RES STRUCT BIOL V. 8 00157 2024 JRNL REFN ESSN 2665-928X JRNL DOI 10.1016/J.CRSTBI.2024.100157 REMARK 2 REMARK 2 RESOLUTION. 1.11 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) : 1.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 47065 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.139 REMARK 3 R VALUE (WORKING SET) : 0.138 REMARK 3 FREE R VALUE : 0.158 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 2317 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 44.9800 - 2.8500 1.00 2697 159 0.1537 0.1644 REMARK 3 2 2.8500 - 2.2700 1.00 2644 156 0.1527 0.1683 REMARK 3 3 2.2700 - 1.9800 1.00 2669 125 0.1333 0.1367 REMARK 3 4 1.9800 - 1.8000 1.00 2636 122 0.1245 0.1608 REMARK 3 5 1.8000 - 1.6700 1.00 2658 134 0.1272 0.1407 REMARK 3 6 1.6700 - 1.5700 0.99 2625 135 0.1196 0.1471 REMARK 3 7 1.5700 - 1.4900 1.00 2653 127 0.1151 0.1409 REMARK 3 8 1.4900 - 1.4300 1.00 2605 143 0.1200 0.1524 REMARK 3 9 1.4300 - 1.3700 1.00 2611 154 0.1230 0.1516 REMARK 3 10 1.3700 - 1.3200 0.99 2578 146 0.1336 0.1453 REMARK 3 11 1.3200 - 1.2800 1.00 2635 118 0.1244 0.1560 REMARK 3 12 1.2800 - 1.2500 1.00 2649 112 0.1327 0.1409 REMARK 3 13 1.2500 - 1.2100 1.00 2633 147 0.1274 0.1541 REMARK 3 14 1.2100 - 1.1800 0.99 2619 134 0.1375 0.1482 REMARK 3 15 1.1800 - 1.1600 1.00 2613 109 0.1404 0.1956 REMARK 3 16 1.1600 - 1.1300 1.00 2614 155 0.1534 0.1873 REMARK 3 17 1.1300 - 1.1100 1.00 2609 141 0.1833 0.2140 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) : 0.088 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.121 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.49 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 : 0.005 1303 REMARK 3 ANGLE : 0.900 1803 REMARK 3 CHIRALITY : 0.082 196 REMARK 3 PLANARITY : 0.006 234 REMARK 3 DIHEDRAL : 5.516 201 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 8J4V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-APR-23. REMARK 100 THE DEPOSITION ID IS D_1300037115. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 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 : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47159 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.110 REMARK 200 RESOLUTION RANGE LOW (A) : 44.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 35.8200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 11.20 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: RECTANGULAR YELLOW COLOR SMALL SIZED CRYSTALS OF 50-80 REMARK 200 MICRON REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.15M POTASSIUM PHOSPHATE MONOBASIC REMARK 280 AND 18% PEG 3350, PH 7.8, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293.15K 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 18.60000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 VAL C 1 REMARK 465 GLN C 147 REMARK 465 SER C 148 REMARK 465 ARG C 149 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 C 53 CG CD NE CZ NH1 NH2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 THR C 55 CB OG1 CG2 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 TYR C 49 -165.96 -116.82 REMARK 500 LEU C 117 -127.81 53.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH C 427 DISTANCE = 6.64 ANGSTROMS DBREF 8J4V C 4 149 UNP G7CEK1 G7CEK1_MYCT3 2 147 SEQADV 8J4V VAL C 1 UNP G7CEK1 EXPRESSION TAG SEQADV 8J4V THR C 2 UNP G7CEK1 EXPRESSION TAG SEQADV 8J4V VAL C 3 UNP G7CEK1 EXPRESSION TAG SEQRES 1 C 149 VAL THR VAL GLY GLY LEU VAL TYR PHE SER SER VAL SER SEQRES 2 C 149 GLU TYR THR HIS ARG PHE VAL GLU LYS LEU GLY LEU PRO SEQRES 3 C 149 ALA THR ARG ILE PRO LEU HIS GLY ARG ILE GLU VAL ASP SEQRES 4 C 149 GLU PRO TYR VAL LEU ILE LEU PRO THR TYR GLY GLY GLY SEQRES 5 C 149 ARG ALA THR PRO ASP ILE ASN HIS GLY GLY TYR VAL PRO SEQRES 6 C 149 LYS GLN VAL ILE ALA PHE LEU ASN ASN GLU HIS ASN ARG SEQRES 7 C 149 SER LEU LEU ARG GLY VAL ILE ALA ALA GLY ASN THR ASN SEQRES 8 C 149 PHE GLY ALA GLU PHE ALA TYR ALA GLY ASN VAL VAL SER SEQRES 9 C 149 ARG LYS CYS GLY VAL PRO TYR LEU TYR ARG PHE GLU LEU SEQRES 10 C 149 MET GLY THR PRO ASP ASP VAL GLU ALA VAL ARG ALA GLY SEQRES 11 C 149 LEU ALA ASP PHE TRP LYS GLU GLN THR CYS HIS LEU PRO SEQRES 12 C 149 SER GLN LEU GLN SER ARG HET FMN C 201 31 HET PO4 C 202 5 HET GOL C 203 6 HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM PO4 PHOSPHATE ION HETNAM GOL GLYCEROL HETSYN FMN RIBOFLAVIN MONOPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 FMN C17 H21 N4 O9 P FORMUL 3 PO4 O4 P 3- FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *127(H2 O) HELIX 1 AA1 GLU C 14 GLY C 24 1 11 HELIX 2 AA2 PRO C 65 ASN C 74 1 10 HELIX 3 AA3 ASN C 74 LEU C 80 1 7 HELIX 4 AA4 ASN C 89 PHE C 96 5 8 HELIX 5 AA5 ALA C 97 GLY C 108 1 12 HELIX 6 AA6 THR C 120 THR C 139 1 20 SHEET 1 AA1 5 THR C 28 ARG C 29 0 SHEET 2 AA1 5 LEU C 6 TYR C 8 1 N LEU C 6 O THR C 28 SHEET 3 AA1 5 TYR C 42 PRO C 47 1 O ILE C 45 N VAL C 7 SHEET 4 AA1 5 LEU C 81 GLY C 88 1 O ILE C 85 N LEU C 44 SHEET 5 AA1 5 TYR C 111 GLU C 116 1 O LEU C 112 N VAL C 84 CRYST1 36.010 37.200 48.380 90.00 111.61 90.00 P 1 21 1 2 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 0.027770 0.000000 0.011001 0.00000 SCALE2 0.000000 0.026882 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022232 0.00000