HEADER BIOSYNTHETIC PROTEIN 16-MAY-23 8P2S TITLE CRYO-EM STRUCTURE OF THE ANAEROBIC RIBONUCLEOTIDE REDUCTASE FROM TITLE 2 PREVOTELLA COPRI IN ITS DIMERIC, ATP/DTTP/GTP-BOUND STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANAEROBIC RIBONUCLEOSIDE-TRIPHOSPHATE REDUCTASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEGATELLA COPRI; SOURCE 3 ORGANISM_TAXID: 165179; SOURCE 4 GENE: BN510_01369; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RIBONUCLEOTIDE REDUCTASE GLYCYL RADICAL ENZYME ALLOSTERIC REGULATION KEYWDS 2 NUCLEOTIDE BIOSYNTHESIS, BIOSYNTHETIC PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR O.BIMAI,I.BANERJEE,B.M.SJOBERG,D.T.LOGAN REVDAT 1 13-SEP-23 8P2S 0 JRNL AUTH O.BIMAI,I.BANERJEE,I.ROZMAN GRINBERG,P.HUANG,D.LUNDIN, JRNL AUTH 2 B.M.SJOBERG,D.T.LOGAN JRNL TITL ACTIVITY MODULATION IN ANAEROBIC RIBONUCLEOTIDE REDUCTASE: JRNL TITL 2 NUCLEOTIDE BINDING TO THE ATP-CONE MEDIATES LONG-RANGE JRNL TITL 3 ORDER-DISORDER TRANSITIONS IN THE ACTIVE SITE JRNL REF ELIFE 2023 JRNL REFN ESSN 2050-084X REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, CRYOSPARC, COOT, REMARK 3 PHENIX, CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : 50.000 REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 2.400 REMARK 3 NUMBER OF PARTICLES : 437866 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8P2S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1292130307. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : ANAEROBIC RIBONUCLEOTIDE REMARK 245 REDUCTASE FROM PREVOTELLA COPRI REMARK 245 IN ITS DIMERIC, ATP/DTTP/GTP- REMARK 245 BOUND STATE REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.50 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : BLOT FORCE 1, 5S BLOT TIME REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 16667 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3400.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4600.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 105000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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 -3 REMARK 465 PRO A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 ILE A 2 REMARK 465 GLN A 3 REMARK 465 THR A 4 REMARK 465 VAL A 5 REMARK 465 VAL A 6 REMARK 465 LYS A 7 REMARK 465 ARG A 8 REMARK 465 ASP A 9 REMARK 465 GLY A 10 REMARK 465 ARG A 11 REMARK 465 ILE A 12 REMARK 465 VAL A 13 REMARK 465 GLY A 14 REMARK 465 PHE A 15 REMARK 465 ASN A 16 REMARK 465 GLU A 17 REMARK 465 GLN A 18 REMARK 465 LYS A 19 REMARK 465 ILE A 20 REMARK 465 MET A 21 REMARK 465 ALA A 22 REMARK 465 ALA A 23 REMARK 465 ILE A 24 REMARK 465 ARG A 25 REMARK 465 LYS A 26 REMARK 465 ALA A 27 REMARK 465 MET A 28 REMARK 465 LEU A 29 REMARK 465 HIS A 30 REMARK 465 THR A 31 REMARK 465 ASP A 32 REMARK 465 LYS A 33 REMARK 465 GLY A 34 REMARK 465 GLU A 35 REMARK 465 ASP A 36 REMARK 465 THR A 37 REMARK 465 THR A 38 REMARK 465 LEU A 39 REMARK 465 ILE A 40 REMARK 465 GLU A 41 REMARK 465 GLN A 42 REMARK 465 ILE A 43 REMARK 465 THR A 44 REMARK 465 ASP A 45 REMARK 465 HIS A 46 REMARK 465 ILE A 47 REMARK 465 SER A 48 REMARK 465 TYR A 49 REMARK 465 ARG A 50 REMARK 465 GLY A 51 REMARK 465 LYS A 52 REMARK 465 SER A 53 REMARK 465 GLN A 54 REMARK 465 MET A 55 REMARK 465 SER A 56 REMARK 465 VAL A 57 REMARK 465 GLU A 58 REMARK 465 ALA A 59 REMARK 465 ILE A 60 REMARK 465 GLN A 61 REMARK 465 ASP A 62 REMARK 465 ALA A 63 REMARK 465 ILE A 64 REMARK 465 GLU A 65 REMARK 465 MET A 66 REMARK 465 GLU A 67 REMARK 465 LEU A 68 REMARK 465 MET A 69 REMARK 465 LYS A 70 REMARK 465 SER A 71 REMARK 465 ALA A 72 REMARK 465 ARG A 73 REMARK 465 LYS A 74 REMARK 465 ASP A 75 REMARK 465 VAL A 76 REMARK 465 ALA A 77 REMARK 465 GLN A 78 REMARK 465 LYS A 79 REMARK 465 TYR A 80 REMARK 465 ILE A 81 REMARK 465 ALA A 82 REMARK 465 TYR A 83 REMARK 465 ARG A 84 REMARK 465 ASN A 85 REMARK 465 GLN A 86 REMARK 465 ARG A 87 REMARK 465 ASN A 88 REMARK 465 ILE A 89 REMARK 465 ALA A 90 REMARK 465 ARG A 91 REMARK 465 LYS A 92 REMARK 465 ALA A 93 REMARK 465 LYS A 94 REMARK 465 THR A 95 REMARK 465 ARG A 96 REMARK 465 ASP A 97 REMARK 465 VAL A 98 REMARK 465 PHE A 99 REMARK 465 MET A 100 REMARK 465 SER A 101 REMARK 465 ILE A 102 REMARK 465 VAL A 103 REMARK 465 ASN A 104 REMARK 465 ALA A 105 REMARK 465 LYS A 106 REMARK 465 ASN A 107 REMARK 465 ASN A 108 REMARK 465 ASP A 109 REMARK 465 ILE A 110 REMARK 465 THR A 111 REMARK 465 ARG A 112 REMARK 465 GLU A 113 REMARK 465 ASN A 114 REMARK 465 ALA A 115 REMARK 465 ASN A 116 REMARK 465 MET A 117 REMARK 465 ASN A 118 REMARK 465 ALA A 119 REMARK 465 ASP A 646 REMARK 465 GLY A 647 REMARK 465 ASP A 648 REMARK 465 ALA A 649 REMARK 465 THR A 650 REMARK 465 HIS A 651 REMARK 465 ASN A 676 REMARK 465 ARG A 677 REMARK 465 ASN A 678 REMARK 465 ARG A 679 REMARK 465 CYS A 680 REMARK 465 LEU A 681 REMARK 465 ASP A 682 REMARK 465 CYS A 683 REMARK 465 GLY A 684 REMARK 465 TYR A 685 REMARK 465 GLU A 686 REMARK 465 ASN A 687 REMARK 465 ALA A 688 REMARK 465 ASP A 689 REMARK 465 ALA A 690 REMARK 465 HIS A 691 REMARK 465 LEU A 692 REMARK 465 GLU A 693 REMARK 465 VAL A 694 REMARK 465 CYS A 695 REMARK 465 PRO A 696 REMARK 465 LYS A 697 REMARK 465 CYS A 698 REMARK 465 GLY A 699 REMARK 465 SER A 700 REMARK 465 HIS A 701 REMARK 465 HIS A 702 REMARK 465 ILE A 703 REMARK 465 ASP A 704 REMARK 465 LYS A 705 REMARK 465 LEU A 706 REMARK 465 GLN A 707 REMARK 465 ARG A 708 REMARK 465 ILE A 709 REMARK 465 THR A 710 REMARK 465 GLY A 711 REMARK 465 TYR A 712 REMARK 465 LEU A 713 REMARK 465 VAL A 714 REMARK 465 GLY A 715 REMARK 465 THR A 716 REMARK 465 THR A 717 REMARK 465 ASP A 718 REMARK 465 ARG A 719 REMARK 465 TRP A 720 REMARK 465 ASN A 721 REMARK 465 SER A 722 REMARK 465 GLY A 723 REMARK 465 LYS A 724 REMARK 465 LEU A 725 REMARK 465 ALA A 726 REMARK 465 GLU A 727 REMARK 465 LEU A 728 REMARK 465 HIS A 729 REMARK 465 ASP A 730 REMARK 465 ARG A 731 REMARK 465 VAL A 732 REMARK 465 THR A 733 REMARK 465 HIS A 734 REMARK 465 ILE A 735 REMARK 465 GLY A 736 REMARK 465 GLY A 737 REMARK 465 GLU A 738 REMARK 465 LYS A 739 REMARK 465 GLY B -3 REMARK 465 PRO B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 ILE B 2 REMARK 465 GLN B 3 REMARK 465 THR B 4 REMARK 465 VAL B 5 REMARK 465 VAL B 6 REMARK 465 LYS B 7 REMARK 465 ARG B 8 REMARK 465 ASP B 9 REMARK 465 GLY B 10 REMARK 465 ARG B 11 REMARK 465 ILE B 12 REMARK 465 VAL B 13 REMARK 465 GLY B 14 REMARK 465 PHE B 15 REMARK 465 ASN B 16 REMARK 465 GLU B 17 REMARK 465 GLN B 18 REMARK 465 LYS B 19 REMARK 465 ILE B 20 REMARK 465 MET B 21 REMARK 465 ALA B 22 REMARK 465 ALA B 23 REMARK 465 ILE B 24 REMARK 465 ARG B 25 REMARK 465 LYS B 26 REMARK 465 ALA B 27 REMARK 465 MET B 28 REMARK 465 LEU B 29 REMARK 465 HIS B 30 REMARK 465 THR B 31 REMARK 465 ASP B 32 REMARK 465 LYS B 33 REMARK 465 GLY B 34 REMARK 465 GLU B 35 REMARK 465 ASP B 36 REMARK 465 THR B 37 REMARK 465 THR B 38 REMARK 465 LEU B 39 REMARK 465 ILE B 40 REMARK 465 GLU B 41 REMARK 465 GLN B 42 REMARK 465 ILE B 43 REMARK 465 THR B 44 REMARK 465 ASP B 45 REMARK 465 HIS B 46 REMARK 465 ILE B 47 REMARK 465 SER B 48 REMARK 465 TYR B 49 REMARK 465 ARG B 50 REMARK 465 GLY B 51 REMARK 465 LYS B 52 REMARK 465 SER B 53 REMARK 465 GLN B 54 REMARK 465 MET B 55 REMARK 465 SER B 56 REMARK 465 VAL B 57 REMARK 465 GLU B 58 REMARK 465 ALA B 59 REMARK 465 ILE B 60 REMARK 465 GLN B 61 REMARK 465 ASP B 62 REMARK 465 ALA B 63 REMARK 465 ILE B 64 REMARK 465 GLU B 65 REMARK 465 MET B 66 REMARK 465 GLU B 67 REMARK 465 LEU B 68 REMARK 465 MET B 69 REMARK 465 LYS B 70 REMARK 465 SER B 71 REMARK 465 ALA B 72 REMARK 465 ARG B 73 REMARK 465 LYS B 74 REMARK 465 ASP B 75 REMARK 465 VAL B 76 REMARK 465 ALA B 77 REMARK 465 GLN B 78 REMARK 465 LYS B 79 REMARK 465 TYR B 80 REMARK 465 ILE B 81 REMARK 465 ALA B 82 REMARK 465 TYR B 83 REMARK 465 ARG B 84 REMARK 465 GLY B 736 REMARK 465 GLY B 737 REMARK 465 GLU B 738 REMARK 465 LYS B 739 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 ASN B 85 CG OD1 ND2 REMARK 470 GLN B 86 CG CD OE1 NE2 REMARK 470 ARG B 87 CG CD NE CZ NH1 NH2 REMARK 470 ILE B 89 CG1 CG2 CD1 REMARK 470 ARG B 91 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 92 CG CD CE NZ REMARK 470 HIS B 701 CG ND1 CD2 CE1 NE2 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 A 141 -8.67 69.58 REMARK 500 TYR A 163 -2.72 81.08 REMARK 500 ALA A 229 -46.36 -172.46 REMARK 500 ASP A 261 -2.36 -144.16 REMARK 500 LEU A 270 40.57 -106.35 REMARK 500 GLN A 309 -7.56 74.80 REMARK 500 ASN A 342 44.64 -141.47 REMARK 500 GLU A 405 37.14 -99.28 REMARK 500 LYS A 408 -5.09 66.57 REMARK 500 ALA A 432 -2.11 67.85 REMARK 500 ASN A 518 49.69 -81.49 REMARK 500 LEU A 583 11.43 -141.06 REMARK 500 VAL A 601 -67.63 -97.70 REMARK 500 THR A 602 62.88 -101.06 REMARK 500 ASP A 603 10.85 -142.38 REMARK 500 LEU B 251 30.24 -95.72 REMARK 500 LEU B 254 31.35 -97.49 REMARK 500 THR B 321 51.66 -91.95 REMARK 500 GLU B 405 -72.30 -64.98 REMARK 500 ARG B 406 -7.22 63.68 REMARK 500 CYS B 416 -73.27 -65.25 REMARK 500 ARG B 417 0.51 -150.85 REMARK 500 PHE B 421 -53.11 -121.53 REMARK 500 CYS B 450 53.57 -92.13 REMARK 500 ASN B 506 52.99 -92.38 REMARK 500 LEU B 533 34.92 -93.77 REMARK 500 VAL B 534 -166.86 -117.26 REMARK 500 HIS B 571 -169.87 -126.84 REMARK 500 LYS B 586 -38.91 -134.71 REMARK 500 TYR B 666 45.86 -95.34 REMARK 500 ASN B 667 47.94 38.80 REMARK 500 THR B 710 -37.71 -134.93 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 MG A 802 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 290 OE1 REMARK 620 2 GLU A 293 OE1 105.1 REMARK 620 3 TTP B 802 O3A 124.8 105.2 REMARK 620 4 TTP B 802 O1G 107.5 124.3 91.5 REMARK 620 5 TTP B 802 O2B 168.2 85.2 55.9 61.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 801 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TTP A 801 O2A REMARK 620 2 TTP A 801 O2B 66.5 REMARK 620 3 TTP A 801 O3G 100.0 80.0 REMARK 620 4 GLN B 290 OE1 127.5 165.4 99.6 REMARK 620 5 GLU B 293 OE1 92.4 82.9 152.8 91.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 804 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 680 SG REMARK 620 2 CYS B 683 SG 111.8 REMARK 620 3 CYS B 695 SG 108.6 113.4 REMARK 620 4 CYS B 698 SG 111.1 103.2 108.6 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8P23 RELATED DB: PDB REMARK 900 RELATED ID: 8P27 RELATED DB: PDB REMARK 900 RELATED ID: 8P28 RELATED DB: PDB REMARK 900 RELATED ID: 8P2C RELATED DB: PDB REMARK 900 RELATED ID: 8P2D RELATED DB: PDB REMARK 900 RELATED ID: 8P39 RELATED DB: PDB REMARK 900 RELATED ID: EMD-17358 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-17359 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-17357 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-17360 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-17361 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-17373 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE ANAEROBIC RIBONUCLEOTIDE REDUCTASE FROM REMARK 900 PREVOTELLA COPRI IN ITS DIMERIC FORM IN ATP/DTTP/GTP-BOUND STATE REMARK 900 RELATED ID: EMD-17385 RELATED DB: EMDB DBREF 8P2S A 1 739 UNP R6BY16 R6BY16_9BACT 1 739 DBREF 8P2S B 1 739 UNP R6BY16 R6BY16_9BACT 1 739 SEQADV 8P2S GLY A -3 UNP R6BY16 EXPRESSION TAG SEQADV 8P2S PRO A -2 UNP R6BY16 EXPRESSION TAG SEQADV 8P2S GLY A -1 UNP R6BY16 EXPRESSION TAG SEQADV 8P2S SER A 0 UNP R6BY16 EXPRESSION TAG SEQADV 8P2S GLY B -3 UNP R6BY16 EXPRESSION TAG SEQADV 8P2S PRO B -2 UNP R6BY16 EXPRESSION TAG SEQADV 8P2S GLY B -1 UNP R6BY16 EXPRESSION TAG SEQADV 8P2S SER B 0 UNP R6BY16 EXPRESSION TAG SEQRES 1 A 743 GLY PRO GLY SER MET ILE GLN THR VAL VAL LYS ARG ASP SEQRES 2 A 743 GLY ARG ILE VAL GLY PHE ASN GLU GLN LYS ILE MET ALA SEQRES 3 A 743 ALA ILE ARG LYS ALA MET LEU HIS THR ASP LYS GLY GLU SEQRES 4 A 743 ASP THR THR LEU ILE GLU GLN ILE THR ASP HIS ILE SER SEQRES 5 A 743 TYR ARG GLY LYS SER GLN MET SER VAL GLU ALA ILE GLN SEQRES 6 A 743 ASP ALA ILE GLU MET GLU LEU MET LYS SER ALA ARG LYS SEQRES 7 A 743 ASP VAL ALA GLN LYS TYR ILE ALA TYR ARG ASN GLN ARG SEQRES 8 A 743 ASN ILE ALA ARG LYS ALA LYS THR ARG ASP VAL PHE MET SEQRES 9 A 743 SER ILE VAL ASN ALA LYS ASN ASN ASP ILE THR ARG GLU SEQRES 10 A 743 ASN ALA ASN MET ASN ALA ASP THR PRO ALA GLY MET MET SEQRES 11 A 743 MET LYS PHE ALA SER GLU THR THR LYS PRO PHE VAL ASP SEQRES 12 A 743 ASP TYR LEU LEU SER GLU ASP VAL ARG ASP ALA VAL MET SEQRES 13 A 743 HIS ASN TYR ILE HIS ILE HIS ASP LYS ASP TYR TYR PRO SEQRES 14 A 743 THR LYS SER LEU THR CYS VAL GLN HIS PRO LEU ASP VAL SEQRES 15 A 743 ILE LEU ASN HIS GLY PHE THR ALA GLY HIS GLY SER SER SEQRES 16 A 743 ARG PRO ALA LYS ARG ILE GLU THR ALA ALA VAL LEU ALA SEQRES 17 A 743 CYS ILE SER LEU GLU THR CYS GLN ASN GLU MET HIS GLY SEQRES 18 A 743 GLY GLN ALA ILE PRO ALA PHE ASP PHE TYR LEU ALA PRO SEQRES 19 A 743 TYR VAL ARG MET SER TYR GLN GLU GLU VAL LYS ASN LEU SEQRES 20 A 743 GLU LYS LEU THR GLY GLU ASP LEU SER ASN LEU TYR ASP SEQRES 21 A 743 ALA PRO ILE ASP ASP TYR ILE GLU LYS PRO LEU ASP GLY SEQRES 22 A 743 LEU GLN GLY ARG GLU ARG LEU GLU GLN HIS ALA ILE ASN SEQRES 23 A 743 LYS THR VAL ASN ARG VAL HIS GLN ALA MET GLU ALA PHE SEQRES 24 A 743 ILE HIS ASN MET ASN THR ILE HIS SER ARG GLY GLY ASN SEQRES 25 A 743 GLN VAL VAL PHE SER SER ILE ASN TYR GLY THR ASP THR SEQRES 26 A 743 SER ALA GLU GLY ARG CYS ILE MET ARG GLU ILE LEU GLN SEQRES 27 A 743 SER THR TYR GLN GLY VAL GLY ASN GLY GLU THR ALA ILE SEQRES 28 A 743 PHE PRO ILE GLN ILE TRP LYS LYS LYS ARG GLY VAL ASN SEQRES 29 A 743 TYR LEU PRO GLU ASP ARG ASN TYR ASP LEU TYR LYS LEU SEQRES 30 A 743 ALA CYS LYS VAL THR ALA ARG ARG PHE PHE PRO ASN PHE SEQRES 31 A 743 LEU ASN LEU ASP ALA THR PHE ASN GLN ASN GLU LYS TRP SEQRES 32 A 743 ARG ALA ASP ASP PRO GLU ARG TYR LYS TRP GLU ILE ALA SEQRES 33 A 743 THR MET GLY CYS ARG THR ARG VAL PHE GLU ASP ARG TRP SEQRES 34 A 743 GLY GLU LYS THR SER ILE ALA ARG GLY ASN LEU SER PHE SEQRES 35 A 743 SER THR ILE ASN ILE VAL LYS LEU ALA ILE GLU CYS MET SEQRES 36 A 743 GLY ILE GLU ASN GLU LYS GLN ARG ILE ASP MET PHE PHE SEQRES 37 A 743 ALA LYS LEU ASP ASN ILE LEU ASP ILE THR ALA LYS GLN SEQRES 38 A 743 LEU ASP GLU ARG PHE GLN PHE GLN LYS THR ALA MET ALA SEQRES 39 A 743 LYS GLN PHE PRO LEU LEU MET LYS TYR LEU TRP VAL GLY SEQRES 40 A 743 ALA GLU ASN LEU LYS PRO GLU GLU THR ILE GLU SER VAL SEQRES 41 A 743 ILE ASN HIS GLY THR LEU GLY ILE GLY PHE ILE GLY LEU SEQRES 42 A 743 ALA GLU CYS LEU VAL ALA LEU ILE GLY LYS HIS HIS GLY SEQRES 43 A 743 GLU SER GLU LYS ALA GLN GLU LEU GLY LEU LYS ILE ILE SEQRES 44 A 743 THR TYR MET ARG ASP ARG ALA ASN GLU PHE SER GLU GLN SEQRES 45 A 743 TYR HIS HIS ASN TYR SER ILE LEU ALA THR PRO ALA GLU SEQRES 46 A 743 GLY LEU SER GLY LYS PHE THR LYS LYS ASP ARG LYS GLN SEQRES 47 A 743 PHE GLY VAL ILE PRO GLY VAL THR ASP ARG ASP TYR TYR SEQRES 48 A 743 THR ASN SER ASN HIS VAL PRO VAL TYR TYR LYS CYS THR SEQRES 49 A 743 ALA LEU LYS LYS ALA GLN ILE GLU ALA PRO TYR HIS ASP SEQRES 50 A 743 LEU THR ARG GLY GLY HIS ILE PHE TYR VAL GLU ILE ASP SEQRES 51 A 743 GLY ASP ALA THR HIS ASN PRO SER VAL ILE GLU SER VAL SEQRES 52 A 743 VAL ASP MET MET ASP LYS TYR ASN MET GLY TYR GLY SER SEQRES 53 A 743 VAL ASN HIS ASN ARG ASN ARG CYS LEU ASP CYS GLY TYR SEQRES 54 A 743 GLU ASN ALA ASP ALA HIS LEU GLU VAL CYS PRO LYS CYS SEQRES 55 A 743 GLY SER HIS HIS ILE ASP LYS LEU GLN ARG ILE THR GLY SEQRES 56 A 743 TYR LEU VAL GLY THR THR ASP ARG TRP ASN SER GLY LYS SEQRES 57 A 743 LEU ALA GLU LEU HIS ASP ARG VAL THR HIS ILE GLY GLY SEQRES 58 A 743 GLU LYS SEQRES 1 B 743 GLY PRO GLY SER MET ILE GLN THR VAL VAL LYS ARG ASP SEQRES 2 B 743 GLY ARG ILE VAL GLY PHE ASN GLU GLN LYS ILE MET ALA SEQRES 3 B 743 ALA ILE ARG LYS ALA MET LEU HIS THR ASP LYS GLY GLU SEQRES 4 B 743 ASP THR THR LEU ILE GLU GLN ILE THR ASP HIS ILE SER SEQRES 5 B 743 TYR ARG GLY LYS SER GLN MET SER VAL GLU ALA ILE GLN SEQRES 6 B 743 ASP ALA ILE GLU MET GLU LEU MET LYS SER ALA ARG LYS SEQRES 7 B 743 ASP VAL ALA GLN LYS TYR ILE ALA TYR ARG ASN GLN ARG SEQRES 8 B 743 ASN ILE ALA ARG LYS ALA LYS THR ARG ASP VAL PHE MET SEQRES 9 B 743 SER ILE VAL ASN ALA LYS ASN ASN ASP ILE THR ARG GLU SEQRES 10 B 743 ASN ALA ASN MET ASN ALA ASP THR PRO ALA GLY MET MET SEQRES 11 B 743 MET LYS PHE ALA SER GLU THR THR LYS PRO PHE VAL ASP SEQRES 12 B 743 ASP TYR LEU LEU SER GLU ASP VAL ARG ASP ALA VAL MET SEQRES 13 B 743 HIS ASN TYR ILE HIS ILE HIS ASP LYS ASP TYR TYR PRO SEQRES 14 B 743 THR LYS SER LEU THR CYS VAL GLN HIS PRO LEU ASP VAL SEQRES 15 B 743 ILE LEU ASN HIS GLY PHE THR ALA GLY HIS GLY SER SER SEQRES 16 B 743 ARG PRO ALA LYS ARG ILE GLU THR ALA ALA VAL LEU ALA SEQRES 17 B 743 CYS ILE SER LEU GLU THR CYS GLN ASN GLU MET HIS GLY SEQRES 18 B 743 GLY GLN ALA ILE PRO ALA PHE ASP PHE TYR LEU ALA PRO SEQRES 19 B 743 TYR VAL ARG MET SER TYR GLN GLU GLU VAL LYS ASN LEU SEQRES 20 B 743 GLU LYS LEU THR GLY GLU ASP LEU SER ASN LEU TYR ASP SEQRES 21 B 743 ALA PRO ILE ASP ASP TYR ILE GLU LYS PRO LEU ASP GLY SEQRES 22 B 743 LEU GLN GLY ARG GLU ARG LEU GLU GLN HIS ALA ILE ASN SEQRES 23 B 743 LYS THR VAL ASN ARG VAL HIS GLN ALA MET GLU ALA PHE SEQRES 24 B 743 ILE HIS ASN MET ASN THR ILE HIS SER ARG GLY GLY ASN SEQRES 25 B 743 GLN VAL VAL PHE SER SER ILE ASN TYR GLY THR ASP THR SEQRES 26 B 743 SER ALA GLU GLY ARG CYS ILE MET ARG GLU ILE LEU GLN SEQRES 27 B 743 SER THR TYR GLN GLY VAL GLY ASN GLY GLU THR ALA ILE SEQRES 28 B 743 PHE PRO ILE GLN ILE TRP LYS LYS LYS ARG GLY VAL ASN SEQRES 29 B 743 TYR LEU PRO GLU ASP ARG ASN TYR ASP LEU TYR LYS LEU SEQRES 30 B 743 ALA CYS LYS VAL THR ALA ARG ARG PHE PHE PRO ASN PHE SEQRES 31 B 743 LEU ASN LEU ASP ALA THR PHE ASN GLN ASN GLU LYS TRP SEQRES 32 B 743 ARG ALA ASP ASP PRO GLU ARG TYR LYS TRP GLU ILE ALA SEQRES 33 B 743 THR MET GLY CYS ARG THR ARG VAL PHE GLU ASP ARG TRP SEQRES 34 B 743 GLY GLU LYS THR SER ILE ALA ARG GLY ASN LEU SER PHE SEQRES 35 B 743 SER THR ILE ASN ILE VAL LYS LEU ALA ILE GLU CYS MET SEQRES 36 B 743 GLY ILE GLU ASN GLU LYS GLN ARG ILE ASP MET PHE PHE SEQRES 37 B 743 ALA LYS LEU ASP ASN ILE LEU ASP ILE THR ALA LYS GLN SEQRES 38 B 743 LEU ASP GLU ARG PHE GLN PHE GLN LYS THR ALA MET ALA SEQRES 39 B 743 LYS GLN PHE PRO LEU LEU MET LYS TYR LEU TRP VAL GLY SEQRES 40 B 743 ALA GLU ASN LEU LYS PRO GLU GLU THR ILE GLU SER VAL SEQRES 41 B 743 ILE ASN HIS GLY THR LEU GLY ILE GLY PHE ILE GLY LEU SEQRES 42 B 743 ALA GLU CYS LEU VAL ALA LEU ILE GLY LYS HIS HIS GLY SEQRES 43 B 743 GLU SER GLU LYS ALA GLN GLU LEU GLY LEU LYS ILE ILE SEQRES 44 B 743 THR TYR MET ARG ASP ARG ALA ASN GLU PHE SER GLU GLN SEQRES 45 B 743 TYR HIS HIS ASN TYR SER ILE LEU ALA THR PRO ALA GLU SEQRES 46 B 743 GLY LEU SER GLY LYS PHE THR LYS LYS ASP ARG LYS GLN SEQRES 47 B 743 PHE GLY VAL ILE PRO GLY VAL THR ASP ARG ASP TYR TYR SEQRES 48 B 743 THR ASN SER ASN HIS VAL PRO VAL TYR TYR LYS CYS THR SEQRES 49 B 743 ALA LEU LYS LYS ALA GLN ILE GLU ALA PRO TYR HIS ASP SEQRES 50 B 743 LEU THR ARG GLY GLY HIS ILE PHE TYR VAL GLU ILE ASP SEQRES 51 B 743 GLY ASP ALA THR HIS ASN PRO SER VAL ILE GLU SER VAL SEQRES 52 B 743 VAL ASP MET MET ASP LYS TYR ASN MET GLY TYR GLY SER SEQRES 53 B 743 VAL ASN HIS ASN ARG ASN ARG CYS LEU ASP CYS GLY TYR SEQRES 54 B 743 GLU ASN ALA ASP ALA HIS LEU GLU VAL CYS PRO LYS CYS SEQRES 55 B 743 GLY SER HIS HIS ILE ASP LYS LEU GLN ARG ILE THR GLY SEQRES 56 B 743 TYR LEU VAL GLY THR THR ASP ARG TRP ASN SER GLY LYS SEQRES 57 B 743 LEU ALA GLU LEU HIS ASP ARG VAL THR HIS ILE GLY GLY SEQRES 58 B 743 GLU LYS HET TTP A 801 29 HET MG A 802 1 HET MG B 801 1 HET TTP B 802 29 HET GTP B 803 32 HET ZN B 804 1 HETNAM TTP THYMIDINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM ZN ZINC ION FORMUL 3 TTP 2(C10 H17 N2 O14 P3) FORMUL 4 MG 2(MG 2+) FORMUL 7 GTP C10 H16 N5 O14 P3 FORMUL 8 ZN ZN 2+ HELIX 1 AA1 THR A 121 ASP A 139 1 19 HELIX 2 AA2 SER A 144 HIS A 153 1 10 HELIX 3 AA3 PRO A 175 GLY A 183 1 9 HELIX 4 AA4 ARG A 196 ASN A 213 1 18 HELIX 5 AA5 ALA A 223 LEU A 228 1 6 HELIX 6 AA6 ALA A 229 GLY A 248 1 20 HELIX 7 AA7 LEU A 251 TYR A 255 5 5 HELIX 8 AA8 GLY A 272 ILE A 302 1 31 HELIX 9 AA9 SER A 322 GLY A 339 1 18 HELIX 10 AB1 ASN A 367 ARG A 381 1 15 HELIX 11 AB2 ALA A 391 GLN A 395 5 5 HELIX 12 AB3 ILE A 443 MET A 451 1 9 HELIX 13 AB4 ASN A 455 LYS A 486 1 32 HELIX 14 AB5 THR A 487 ALA A 488 5 2 HELIX 15 AB6 MET A 489 PHE A 493 5 5 HELIX 16 AB7 GLY A 503 LEU A 507 5 5 HELIX 17 AB8 ILE A 513 ASN A 518 1 6 HELIX 18 AB9 GLY A 528 VAL A 534 1 7 HELIX 19 AC1 SER A 544 HIS A 570 1 27 HELIX 20 AC2 GLY A 585 GLY A 596 1 12 HELIX 21 AC3 THR A 620 THR A 635 1 16 HELIX 22 AC4 PRO A 653 TYR A 666 1 14 HELIX 23 AC5 GLN B 86 ALA B 105 1 20 HELIX 24 AC6 THR B 121 TYR B 141 1 21 HELIX 25 AC7 SER B 144 HIS B 153 1 10 HELIX 26 AC8 ASP B 160 TYR B 164 5 5 HELIX 27 AC9 PRO B 175 GLY B 183 1 9 HELIX 28 AD1 ARG B 196 ASN B 213 1 18 HELIX 29 AD2 ALA B 223 GLY B 248 1 26 HELIX 30 AD3 LEU B 251 TYR B 255 5 5 HELIX 31 AD4 GLY B 272 ILE B 302 1 31 HELIX 32 AD5 SER B 322 GLY B 339 1 18 HELIX 33 AD6 ASN B 367 PHE B 382 1 16 HELIX 34 AD7 ALA B 391 GLN B 395 5 5 HELIX 35 AD8 ILE B 443 CYS B 450 1 8 HELIX 36 AD9 ASN B 455 THR B 487 1 33 HELIX 37 AE1 MET B 489 PHE B 493 5 5 HELIX 38 AE2 LEU B 495 LEU B 500 1 6 HELIX 39 AE3 ILE B 513 ASN B 518 1 6 HELIX 40 AE4 SER B 544 HIS B 570 1 27 HELIX 41 AE5 LYS B 586 PHE B 595 1 10 HELIX 42 AE6 THR B 620 THR B 635 1 16 HELIX 43 AE7 GLY B 647 ASN B 652 1 6 HELIX 44 AE8 PRO B 653 TYR B 666 1 14 HELIX 45 AE9 THR B 716 TRP B 720 5 5 HELIX 46 AF1 ASN B 721 ASP B 730 1 10 SHEET 1 AA1 4 ILE A 156 ILE A 158 0 SHEET 2 AA1 4 ASN A 435 ASN A 442 -1 O THR A 440 N HIS A 157 SHEET 3 AA1 4 THR A 521 ILE A 527 1 O GLY A 525 N SER A 439 SHEET 4 AA1 4 TYR A 573 ALA A 577 1 O SER A 574 N ILE A 524 SHEET 1 AA2 7 VAL A 172 GLN A 173 0 SHEET 2 AA2 7 GLN A 219 ILE A 221 1 O ALA A 220 N VAL A 172 SHEET 3 AA2 7 SER A 313 TYR A 317 1 O ASN A 316 N ILE A 221 SHEET 4 AA2 7 ILE A 350 LYS A 355 1 O ILE A 350 N SER A 313 SHEET 5 AA2 7 ASN A 385 ASN A 388 1 O ASN A 385 N TRP A 353 SHEET 6 AA2 7 TYR A 670 ASN A 674 -1 O GLY A 671 N PHE A 386 SHEET 7 AA2 7 PHE A 641 GLU A 644 1 N VAL A 643 O ASN A 674 SHEET 1 AA3 2 PHE A 184 ALA A 186 0 SHEET 2 AA3 2 GLY A 189 SER A 191 -1 O SER A 191 N PHE A 184 SHEET 1 AA4 4 ILE B 156 ILE B 158 0 SHEET 2 AA4 4 ASN B 435 ASN B 442 -1 O THR B 440 N HIS B 157 SHEET 3 AA4 4 THR B 521 ILE B 527 1 O THR B 521 N LEU B 436 SHEET 4 AA4 4 TYR B 573 LEU B 576 1 O LEU B 576 N ILE B 524 SHEET 1 AA5 7 VAL B 172 GLN B 173 0 SHEET 2 AA5 7 GLN B 219 ILE B 221 1 O ALA B 220 N VAL B 172 SHEET 3 AA5 7 SER B 313 TYR B 317 1 O ASN B 316 N ILE B 221 SHEET 4 AA5 7 ILE B 350 LYS B 355 1 O ILE B 350 N SER B 313 SHEET 5 AA5 7 ASN B 385 ASN B 388 1 O ASN B 385 N TRP B 353 SHEET 6 AA5 7 TYR B 670 ASN B 674 -1 O GLY B 671 N PHE B 386 SHEET 7 AA5 7 PHE B 641 GLU B 644 1 N PHE B 641 O SER B 672 SHEET 1 AA6 2 PHE B 184 ALA B 186 0 SHEET 2 AA6 2 GLY B 189 SER B 191 -1 O GLY B 189 N ALA B 186 SHEET 1 AA7 4 GLU B 686 ASN B 687 0 SHEET 2 AA7 4 ARG B 677 ARG B 679 -1 N ASN B 678 O ASN B 687 SHEET 3 AA7 4 ASP B 704 ARG B 708 -1 O LEU B 706 N ARG B 677 SHEET 4 AA7 4 LEU B 713 VAL B 714 -1 O VAL B 714 N GLN B 707 LINK OE1 GLN A 290 MG MG A 802 1555 1555 2.17 LINK OE1 GLU A 293 MG MG A 802 1555 1555 2.84 LINK O2A TTP A 801 MG MG B 801 1555 1555 2.64 LINK O2B TTP A 801 MG MG B 801 1555 1555 2.32 LINK O3G TTP A 801 MG MG B 801 1555 1555 2.12 LINK MG MG A 802 O3A TTP B 802 1555 1555 2.35 LINK MG MG A 802 O1G TTP B 802 1555 1555 2.95 LINK MG MG A 802 O2B TTP B 802 1555 1555 2.98 LINK OE1 GLN B 290 MG MG B 801 1555 1555 2.93 LINK OE1 GLU B 293 MG MG B 801 1555 1555 2.77 LINK SG CYS B 680 ZN ZN B 804 1555 1555 2.33 LINK SG CYS B 683 ZN ZN B 804 1555 1555 2.33 LINK SG CYS B 695 ZN ZN B 804 1555 1555 2.33 LINK SG CYS B 698 ZN ZN B 804 1555 1555 2.33 CISPEP 1 PHE A 348 PRO A 349 0 -0.37 CISPEP 2 PHE A 383 PRO A 384 0 0.58 CISPEP 3 PHE B 348 PRO B 349 0 0.91 CISPEP 4 PHE B 383 PRO B 384 0 0.23 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000