HEADER TRANSFERASE 03-JAN-19 6QDX TITLE STRUCTURE OF E.COLI RLMJ IN COMPLEX WITH A BISUBSTRATE ANALOGUE (BA4) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE J; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: 23STSA4, RRNA (ADENINE(2030)-N6)-METHYLTRANSFERASE,23S RRNA COMPND 5 M6A2030 METHYLTRANSFERASE; COMPND 6 EC: 2.1.1.266; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: YHIR, RLMJ, PPECC33_03818; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RNA MTASES, METHYLTRANSFERASE, M6A, TRANSITION STATE ANALOGUE, KEYWDS 2 INHIBITOR, RNA BINDING, TRMK, RLMJ, M1A, STRUCTURE., TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.OERUM,M.CATALA,C.ATDJIAN,F.BRACHET,L.PONCHON,P.BARRAUD,L.IANNAZZO, AUTHOR 2 L.DROOGMANS,E.BRAUD,M.ETHEVE-QUELQUEJEU,C.TISNE REVDAT 3 24-JAN-24 6QDX 1 REMARK REVDAT 2 15-MAY-19 6QDX 1 JRNL REVDAT 1 27-MAR-19 6QDX 0 JRNL AUTH S.OERUM,M.CATALA,C.ATDJIAN,F.BRACHET,L.PONCHON,P.BARRAUD, JRNL AUTH 2 L.IANNAZZO,L.DROOGMANS,E.BRAUD,M.ETHEVE-QUELQUEJEU,C.TISNE JRNL TITL BISUBSTRATE ANALOGUES AS STRUCTURAL TOOLS TO INVESTIGATE M6A JRNL TITL 2 METHYLTRANSFERASE ACTIVE SITES. JRNL REF RNA BIOL. V. 16 798 2019 JRNL REFN ESSN 1555-8584 JRNL PMID 30879411 JRNL DOI 10.1080/15476286.2019.1589360 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 75113 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 3751 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 48.3362 - 6.2955 1.00 2680 176 0.2282 0.2467 REMARK 3 2 6.2955 - 4.9986 1.00 2654 180 0.2204 0.2396 REMARK 3 3 4.9986 - 4.3672 1.00 2666 140 0.1834 0.2240 REMARK 3 4 4.3672 - 3.9681 1.00 2666 145 0.1926 0.2324 REMARK 3 5 3.9681 - 3.6838 1.00 2656 142 0.1982 0.2366 REMARK 3 6 3.6838 - 3.4667 0.99 2680 124 0.1987 0.2512 REMARK 3 7 3.4667 - 3.2931 1.00 2680 129 0.2133 0.2941 REMARK 3 8 3.2931 - 3.1498 1.00 2639 152 0.2215 0.2873 REMARK 3 9 3.1498 - 3.0286 1.00 2682 124 0.2098 0.2829 REMARK 3 10 3.0286 - 2.9241 0.99 2630 151 0.2164 0.2613 REMARK 3 11 2.9241 - 2.8327 0.99 2661 146 0.2152 0.3194 REMARK 3 12 2.8327 - 2.7517 0.99 2630 152 0.2281 0.3043 REMARK 3 13 2.7517 - 2.6793 1.00 2666 123 0.2275 0.3288 REMARK 3 14 2.6793 - 2.6139 0.99 2610 146 0.2342 0.3209 REMARK 3 15 2.6139 - 2.5545 0.99 2618 136 0.2363 0.3143 REMARK 3 16 2.5545 - 2.5001 0.99 2668 151 0.2355 0.2977 REMARK 3 17 2.5001 - 2.4501 0.99 2599 141 0.2263 0.3135 REMARK 3 18 2.4501 - 2.4039 0.99 2656 133 0.2230 0.2906 REMARK 3 19 2.4039 - 2.3609 0.98 2622 129 0.2320 0.2635 REMARK 3 20 2.3609 - 2.3209 0.99 2684 118 0.2273 0.3167 REMARK 3 21 2.3209 - 2.2835 0.98 2600 111 0.2373 0.2999 REMARK 3 22 2.2835 - 2.2484 0.99 2632 160 0.2502 0.3144 REMARK 3 23 2.2484 - 2.2153 0.99 2619 107 0.2525 0.3035 REMARK 3 24 2.2153 - 2.1841 0.98 2644 146 0.2562 0.3520 REMARK 3 25 2.1841 - 2.1546 0.99 2629 122 0.2664 0.3083 REMARK 3 26 2.1546 - 2.1266 0.97 2614 123 0.2790 0.3396 REMARK 3 27 2.1266 - 2.1000 0.97 2577 144 0.2886 0.3528 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.770 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 : 0.008 9107 REMARK 3 ANGLE : 1.051 12376 REMARK 3 CHIRALITY : 0.064 1354 REMARK 3 PLANARITY : 0.006 1568 REMARK 3 DIHEDRAL : 11.177 5401 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 6QDX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1200012400. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-APR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98007 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 75173 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 48.323 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.20720 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.6300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.77690 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: 4BLV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MMT PH 6.0, 25% (W/V) PEG1500., REMARK 280 PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 85.36500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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 -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 LEU A 2 REMARK 465 SER A 52 REMARK 465 GLU A 53 REMARK 465 HIS A 54 REMARK 465 ALA A 55 REMARK 465 GLU A 56 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 LEU B 2 REMARK 465 GLU B 53 REMARK 465 HIS B 54 REMARK 465 ALA B 55 REMARK 465 GLU B 56 REMARK 465 ARG B 57 REMARK 465 GLY C -2 REMARK 465 SER C -1 REMARK 465 HIS C 0 REMARK 465 MET C 1 REMARK 465 LEU C 2 REMARK 465 GLU C 53 REMARK 465 HIS C 54 REMARK 465 ALA C 55 REMARK 465 GLU C 56 REMARK 465 ARG C 57 REMARK 465 GLY D -2 REMARK 465 SER D -1 REMARK 465 HIS D 0 REMARK 465 MET D 1 REMARK 465 LEU D 2 REMARK 465 GLU D 53 REMARK 465 HIS D 54 REMARK 465 ALA D 55 REMARK 465 GLU D 56 REMARK 465 ARG D 57 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 32 CE NZ REMARK 470 ARG A 57 CG CD NE CZ NH1 NH2 REMARK 470 MET A 169 CE REMARK 470 ARG A 232 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 34 CG CD CE NZ REMARK 470 THR B 58 OG1 CG2 REMARK 470 GLN B 93 CG CD OE1 NE2 REMARK 470 GLU B 168 CG CD OE1 OE2 REMARK 470 MET B 169 CG SD CE REMARK 470 LYS B 170 CG CD CE NZ REMARK 470 ASP B 231 CG OD1 OD2 REMARK 470 ARG B 232 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 233 CG CD NE CZ NH1 NH2 REMARK 470 MET C 169 SD CE REMARK 470 SER D 52 OG REMARK 470 THR D 58 OG1 CG2 REMARK 470 ARG D 90 CG CD NE CZ NH1 NH2 REMARK 470 ARG D 95 CG CD NE CZ NH1 NH2 REMARK 470 GLU D 168 CG CD OE1 OE2 REMARK 470 MET D 169 CG SD CE REMARK 470 ASP D 231 CG OD1 OD2 REMARK 470 ARG D 232 CG CD NE CZ NH1 NH2 REMARK 470 ARG D 233 CG CD NE CZ NH1 NH2 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 LEU A 94 92.51 -68.04 REMARK 500 PHE A 187 83.28 -150.69 REMARK 500 VAL A 199 -62.00 -104.33 REMARK 500 ASN B 89 44.79 -141.46 REMARK 500 PHE B 187 86.51 -154.84 REMARK 500 LYS B 218 63.00 63.04 REMARK 500 ARG B 232 78.14 -163.55 REMARK 500 ARG B 233 30.56 -146.17 REMARK 500 PHE C 187 77.16 -153.84 REMARK 500 VAL C 199 -77.33 -105.31 REMARK 500 ASP D 164 54.53 -140.71 REMARK 500 TYR D 167 16.83 58.13 REMARK 500 PHE D 187 70.70 -166.29 REMARK 500 ARG D 232 57.35 -163.94 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 A 591 DISTANCE = 6.14 ANGSTROMS REMARK 525 HOH A 592 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH A 593 DISTANCE = 6.70 ANGSTROMS REMARK 525 HOH B 563 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH B 564 DISTANCE = 8.06 ANGSTROMS REMARK 525 HOH C 573 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH C 574 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH C 575 DISTANCE = 6.41 ANGSTROMS REMARK 525 HOH C 576 DISTANCE = 6.80 ANGSTROMS REMARK 525 HOH C 577 DISTANCE = 7.75 ANGSTROMS REMARK 525 HOH C 578 DISTANCE = 8.33 ANGSTROMS REMARK 525 HOH D 572 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH D 573 DISTANCE = 8.05 ANGSTROMS REMARK 525 HOH D 574 DISTANCE = 8.06 ANGSTROMS REMARK 525 HOH D 575 DISTANCE = 10.02 ANGSTROMS REMARK 525 HOH D 576 DISTANCE = 12.02 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 HY8 D 301 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HY8 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HY8 B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HY8 C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HY8 D 301 DBREF1 6QDX A 1 280 UNP A0A0G3KF30_ECOLX DBREF2 6QDX A A0A0G3KF30 1 280 DBREF1 6QDX B 1 280 UNP A0A0G3KF30_ECOLX DBREF2 6QDX B A0A0G3KF30 1 280 DBREF1 6QDX C 1 280 UNP A0A0G3KF30_ECOLX DBREF2 6QDX C A0A0G3KF30 1 280 DBREF1 6QDX D 1 280 UNP A0A0G3KF30_ECOLX DBREF2 6QDX D A0A0G3KF30 1 280 SEQADV 6QDX GLY A -2 UNP A0A0G3KF3 EXPRESSION TAG SEQADV 6QDX SER A -1 UNP A0A0G3KF3 EXPRESSION TAG SEQADV 6QDX HIS A 0 UNP A0A0G3KF3 EXPRESSION TAG SEQADV 6QDX LYS A 60 UNP A0A0G3KF3 GLU 60 ENGINEERED MUTATION SEQADV 6QDX GLY B -2 UNP A0A0G3KF3 EXPRESSION TAG SEQADV 6QDX SER B -1 UNP A0A0G3KF3 EXPRESSION TAG SEQADV 6QDX HIS B 0 UNP A0A0G3KF3 EXPRESSION TAG SEQADV 6QDX LYS B 60 UNP A0A0G3KF3 GLU 60 ENGINEERED MUTATION SEQADV 6QDX GLY C -2 UNP A0A0G3KF3 EXPRESSION TAG SEQADV 6QDX SER C -1 UNP A0A0G3KF3 EXPRESSION TAG SEQADV 6QDX HIS C 0 UNP A0A0G3KF3 EXPRESSION TAG SEQADV 6QDX LYS C 60 UNP A0A0G3KF3 GLU 60 ENGINEERED MUTATION SEQADV 6QDX GLY D -2 UNP A0A0G3KF3 EXPRESSION TAG SEQADV 6QDX SER D -1 UNP A0A0G3KF3 EXPRESSION TAG SEQADV 6QDX HIS D 0 UNP A0A0G3KF3 EXPRESSION TAG SEQADV 6QDX LYS D 60 UNP A0A0G3KF3 GLU 60 ENGINEERED MUTATION SEQRES 1 A 283 GLY SER HIS MET LEU SER TYR ARG HIS SER PHE HIS ALA SEQRES 2 A 283 GLY ASN HIS ALA ASP VAL LEU LYS HIS THR VAL GLN SER SEQRES 3 A 283 LEU ILE ILE GLU SER LEU LYS GLU LYS ASP LYS PRO PHE SEQRES 4 A 283 LEU TYR LEU ASP THR HIS ALA GLY ALA GLY ARG TYR GLN SEQRES 5 A 283 LEU GLY SER GLU HIS ALA GLU ARG THR GLY LYS TYR LEU SEQRES 6 A 283 GLU GLY ILE ALA ARG ILE TRP GLN GLN ASP ASP LEU PRO SEQRES 7 A 283 ALA GLU LEU GLU ALA TYR ILE ASN VAL VAL LYS HIS PHE SEQRES 8 A 283 ASN ARG SER GLY GLN LEU ARG TYR TYR PRO GLY SER PRO SEQRES 9 A 283 LEU ILE ALA ARG GLN LEU LEU ARG GLU GLN ASP SER LEU SEQRES 10 A 283 GLN LEU THR GLU LEU HIS PRO SER ASP TYR PRO LEU LEU SEQRES 11 A 283 ARG SER GLU PHE GLN LYS ASP SER ARG ALA ARG VAL GLU SEQRES 12 A 283 LYS ALA ASP GLY PHE GLN GLN LEU LYS ALA LYS LEU PRO SEQRES 13 A 283 PRO VAL SER ARG ARG GLY LEU ILE LEU ILE ASP PRO PRO SEQRES 14 A 283 TYR GLU MET LYS THR ASP TYR GLN ALA VAL VAL SER GLY SEQRES 15 A 283 ILE ALA GLU GLY TYR LYS ARG PHE ALA THR GLY THR TYR SEQRES 16 A 283 ALA LEU TRP TYR PRO VAL VAL LEU ARG GLN GLN ILE LYS SEQRES 17 A 283 ARG MET ILE HIS ASP LEU GLU ALA THR GLY ILE ARG LYS SEQRES 18 A 283 ILE LEU GLN ILE GLU LEU ALA VAL LEU PRO ASP SER ASP SEQRES 19 A 283 ARG ARG GLY MET THR ALA SER GLY MET ILE VAL ILE ASN SEQRES 20 A 283 PRO PRO TRP LYS LEU GLU GLN GLN MET ASN ASN VAL LEU SEQRES 21 A 283 PRO TRP LEU HIS SER LYS LEU VAL PRO ALA GLY THR GLY SEQRES 22 A 283 HIS ALA THR VAL SER TRP ILE VAL PRO GLU SEQRES 1 B 283 GLY SER HIS MET LEU SER TYR ARG HIS SER PHE HIS ALA SEQRES 2 B 283 GLY ASN HIS ALA ASP VAL LEU LYS HIS THR VAL GLN SER SEQRES 3 B 283 LEU ILE ILE GLU SER LEU LYS GLU LYS ASP LYS PRO PHE SEQRES 4 B 283 LEU TYR LEU ASP THR HIS ALA GLY ALA GLY ARG TYR GLN SEQRES 5 B 283 LEU GLY SER GLU HIS ALA GLU ARG THR GLY LYS TYR LEU SEQRES 6 B 283 GLU GLY ILE ALA ARG ILE TRP GLN GLN ASP ASP LEU PRO SEQRES 7 B 283 ALA GLU LEU GLU ALA TYR ILE ASN VAL VAL LYS HIS PHE SEQRES 8 B 283 ASN ARG SER GLY GLN LEU ARG TYR TYR PRO GLY SER PRO SEQRES 9 B 283 LEU ILE ALA ARG GLN LEU LEU ARG GLU GLN ASP SER LEU SEQRES 10 B 283 GLN LEU THR GLU LEU HIS PRO SER ASP TYR PRO LEU LEU SEQRES 11 B 283 ARG SER GLU PHE GLN LYS ASP SER ARG ALA ARG VAL GLU SEQRES 12 B 283 LYS ALA ASP GLY PHE GLN GLN LEU LYS ALA LYS LEU PRO SEQRES 13 B 283 PRO VAL SER ARG ARG GLY LEU ILE LEU ILE ASP PRO PRO SEQRES 14 B 283 TYR GLU MET LYS THR ASP TYR GLN ALA VAL VAL SER GLY SEQRES 15 B 283 ILE ALA GLU GLY TYR LYS ARG PHE ALA THR GLY THR TYR SEQRES 16 B 283 ALA LEU TRP TYR PRO VAL VAL LEU ARG GLN GLN ILE LYS SEQRES 17 B 283 ARG MET ILE HIS ASP LEU GLU ALA THR GLY ILE ARG LYS SEQRES 18 B 283 ILE LEU GLN ILE GLU LEU ALA VAL LEU PRO ASP SER ASP SEQRES 19 B 283 ARG ARG GLY MET THR ALA SER GLY MET ILE VAL ILE ASN SEQRES 20 B 283 PRO PRO TRP LYS LEU GLU GLN GLN MET ASN ASN VAL LEU SEQRES 21 B 283 PRO TRP LEU HIS SER LYS LEU VAL PRO ALA GLY THR GLY SEQRES 22 B 283 HIS ALA THR VAL SER TRP ILE VAL PRO GLU SEQRES 1 C 283 GLY SER HIS MET LEU SER TYR ARG HIS SER PHE HIS ALA SEQRES 2 C 283 GLY ASN HIS ALA ASP VAL LEU LYS HIS THR VAL GLN SER SEQRES 3 C 283 LEU ILE ILE GLU SER LEU LYS GLU LYS ASP LYS PRO PHE SEQRES 4 C 283 LEU TYR LEU ASP THR HIS ALA GLY ALA GLY ARG TYR GLN SEQRES 5 C 283 LEU GLY SER GLU HIS ALA GLU ARG THR GLY LYS TYR LEU SEQRES 6 C 283 GLU GLY ILE ALA ARG ILE TRP GLN GLN ASP ASP LEU PRO SEQRES 7 C 283 ALA GLU LEU GLU ALA TYR ILE ASN VAL VAL LYS HIS PHE SEQRES 8 C 283 ASN ARG SER GLY GLN LEU ARG TYR TYR PRO GLY SER PRO SEQRES 9 C 283 LEU ILE ALA ARG GLN LEU LEU ARG GLU GLN ASP SER LEU SEQRES 10 C 283 GLN LEU THR GLU LEU HIS PRO SER ASP TYR PRO LEU LEU SEQRES 11 C 283 ARG SER GLU PHE GLN LYS ASP SER ARG ALA ARG VAL GLU SEQRES 12 C 283 LYS ALA ASP GLY PHE GLN GLN LEU LYS ALA LYS LEU PRO SEQRES 13 C 283 PRO VAL SER ARG ARG GLY LEU ILE LEU ILE ASP PRO PRO SEQRES 14 C 283 TYR GLU MET LYS THR ASP TYR GLN ALA VAL VAL SER GLY SEQRES 15 C 283 ILE ALA GLU GLY TYR LYS ARG PHE ALA THR GLY THR TYR SEQRES 16 C 283 ALA LEU TRP TYR PRO VAL VAL LEU ARG GLN GLN ILE LYS SEQRES 17 C 283 ARG MET ILE HIS ASP LEU GLU ALA THR GLY ILE ARG LYS SEQRES 18 C 283 ILE LEU GLN ILE GLU LEU ALA VAL LEU PRO ASP SER ASP SEQRES 19 C 283 ARG ARG GLY MET THR ALA SER GLY MET ILE VAL ILE ASN SEQRES 20 C 283 PRO PRO TRP LYS LEU GLU GLN GLN MET ASN ASN VAL LEU SEQRES 21 C 283 PRO TRP LEU HIS SER LYS LEU VAL PRO ALA GLY THR GLY SEQRES 22 C 283 HIS ALA THR VAL SER TRP ILE VAL PRO GLU SEQRES 1 D 283 GLY SER HIS MET LEU SER TYR ARG HIS SER PHE HIS ALA SEQRES 2 D 283 GLY ASN HIS ALA ASP VAL LEU LYS HIS THR VAL GLN SER SEQRES 3 D 283 LEU ILE ILE GLU SER LEU LYS GLU LYS ASP LYS PRO PHE SEQRES 4 D 283 LEU TYR LEU ASP THR HIS ALA GLY ALA GLY ARG TYR GLN SEQRES 5 D 283 LEU GLY SER GLU HIS ALA GLU ARG THR GLY LYS TYR LEU SEQRES 6 D 283 GLU GLY ILE ALA ARG ILE TRP GLN GLN ASP ASP LEU PRO SEQRES 7 D 283 ALA GLU LEU GLU ALA TYR ILE ASN VAL VAL LYS HIS PHE SEQRES 8 D 283 ASN ARG SER GLY GLN LEU ARG TYR TYR PRO GLY SER PRO SEQRES 9 D 283 LEU ILE ALA ARG GLN LEU LEU ARG GLU GLN ASP SER LEU SEQRES 10 D 283 GLN LEU THR GLU LEU HIS PRO SER ASP TYR PRO LEU LEU SEQRES 11 D 283 ARG SER GLU PHE GLN LYS ASP SER ARG ALA ARG VAL GLU SEQRES 12 D 283 LYS ALA ASP GLY PHE GLN GLN LEU LYS ALA LYS LEU PRO SEQRES 13 D 283 PRO VAL SER ARG ARG GLY LEU ILE LEU ILE ASP PRO PRO SEQRES 14 D 283 TYR GLU MET LYS THR ASP TYR GLN ALA VAL VAL SER GLY SEQRES 15 D 283 ILE ALA GLU GLY TYR LYS ARG PHE ALA THR GLY THR TYR SEQRES 16 D 283 ALA LEU TRP TYR PRO VAL VAL LEU ARG GLN GLN ILE LYS SEQRES 17 D 283 ARG MET ILE HIS ASP LEU GLU ALA THR GLY ILE ARG LYS SEQRES 18 D 283 ILE LEU GLN ILE GLU LEU ALA VAL LEU PRO ASP SER ASP SEQRES 19 D 283 ARG ARG GLY MET THR ALA SER GLY MET ILE VAL ILE ASN SEQRES 20 D 283 PRO PRO TRP LYS LEU GLU GLN GLN MET ASN ASN VAL LEU SEQRES 21 D 283 PRO TRP LEU HIS SER LYS LEU VAL PRO ALA GLY THR GLY SEQRES 22 D 283 HIS ALA THR VAL SER TRP ILE VAL PRO GLU HET HY8 A 301 48 HET HY8 B 301 48 HET HY8 C 301 48 HET HY8 D 301 31 HETNAM HY8 (2~{S})-4-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-AMINOPURIN- HETNAM 2 HY8 9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL-[3-[[9- HETNAM 3 HY8 [(2~{S},3~{R},4~{S},5~{S})-5-(HYDROXYMETHYL)-3,4- HETNAM 4 HY8 BIS(OXIDANYL)OXOLAN-2-YL]PURIN-6- HETNAM 5 HY8 YL]AMINO]PROPYL]AMINO]-2-AZANYL-BUTANOIC ACID FORMUL 5 HY8 4(C27 H38 N12 O9) FORMUL 9 HOH *711(H2 O) HELIX 1 AA1 ASN A 12 LYS A 30 1 19 HELIX 2 AA2 GLY A 59 ILE A 68 5 10 HELIX 3 AA3 PRO A 75 GLU A 77 5 3 HELIX 4 AA4 LEU A 78 PHE A 88 1 11 HELIX 5 AA5 GLY A 99 LEU A 108 1 10 HELIX 6 AA6 ASP A 123 GLU A 130 1 8 HELIX 7 AA7 ASP A 143 LYS A 151 1 9 HELIX 8 AA8 THR A 171 PHE A 187 1 17 HELIX 9 AA9 LEU A 200 THR A 214 1 15 HELIX 10 AB1 LYS A 248 VAL A 265 1 18 HELIX 11 AB2 ASN B 12 LYS B 30 1 19 HELIX 12 AB3 GLY B 59 ILE B 68 5 10 HELIX 13 AB4 PRO B 75 GLU B 77 5 3 HELIX 14 AB5 LEU B 78 PHE B 88 1 11 HELIX 15 AB6 GLY B 99 LEU B 108 1 10 HELIX 16 AB7 ASP B 123 PHE B 131 1 9 HELIX 17 AB8 ASP B 143 LYS B 151 1 9 HELIX 18 AB9 THR B 171 PHE B 187 1 17 HELIX 19 AC1 LEU B 200 THR B 214 1 15 HELIX 20 AC2 LYS B 248 VAL B 265 1 18 HELIX 21 AC3 ASN C 12 LYS C 30 1 19 HELIX 22 AC4 GLY C 59 ILE C 68 5 10 HELIX 23 AC5 PRO C 75 GLU C 77 5 3 HELIX 24 AC6 LEU C 78 PHE C 88 1 11 HELIX 25 AC7 GLY C 99 LEU C 108 1 10 HELIX 26 AC8 ASP C 123 PHE C 131 1 9 HELIX 27 AC9 GLN C 146 LYS C 151 1 6 HELIX 28 AD1 THR C 171 PHE C 187 1 17 HELIX 29 AD2 LEU C 200 THR C 214 1 15 HELIX 30 AD3 LYS C 248 VAL C 265 1 18 HELIX 31 AD4 ASN D 12 LYS D 30 1 19 HELIX 32 AD5 GLY D 59 ILE D 68 5 10 HELIX 33 AD6 PRO D 75 GLU D 77 5 3 HELIX 34 AD7 LEU D 78 PHE D 88 1 11 HELIX 35 AD8 GLY D 99 LEU D 108 1 10 HELIX 36 AD9 SER D 122 PHE D 131 1 10 HELIX 37 AE1 ASP D 143 LYS D 151 1 9 HELIX 38 AE2 THR D 171 PHE D 187 1 17 HELIX 39 AE3 LEU D 200 THR D 214 1 15 HELIX 40 AE4 LYS D 248 VAL D 265 1 18 SHEET 1 AA1 3 ARG A 5 HIS A 6 0 SHEET 2 AA1 3 ARG A 47 GLN A 49 1 O GLN A 49 N ARG A 5 SHEET 3 AA1 3 TYR A 96 PRO A 98 -1 O TYR A 97 N TYR A 48 SHEET 1 AA2 8 ALA A 137 GLU A 140 0 SHEET 2 AA2 8 SER A 113 THR A 117 1 N LEU A 116 O GLU A 140 SHEET 3 AA2 8 LEU A 37 ASP A 40 1 N TYR A 38 O GLN A 115 SHEET 4 AA2 8 GLY A 159 ILE A 163 1 O LEU A 162 N LEU A 39 SHEET 5 AA2 8 THR A 191 VAL A 198 1 O ALA A 193 N ILE A 161 SHEET 6 AA2 8 ALA A 237 ILE A 243 -1 O ALA A 237 N VAL A 198 SHEET 7 AA2 8 ILE A 219 ALA A 225 -1 N ILE A 222 O MET A 240 SHEET 8 AA2 8 HIS A 271 VAL A 278 -1 O HIS A 271 N ALA A 225 SHEET 1 AA3 8 ALA B 137 GLU B 140 0 SHEET 2 AA3 8 SER B 113 THR B 117 1 N LEU B 116 O ARG B 138 SHEET 3 AA3 8 LEU B 37 ASP B 40 1 N TYR B 38 O SER B 113 SHEET 4 AA3 8 GLY B 159 ILE B 163 1 O LEU B 162 N LEU B 39 SHEET 5 AA3 8 THR B 191 VAL B 198 1 O THR B 191 N ILE B 161 SHEET 6 AA3 8 ALA B 237 ILE B 243 -1 O ALA B 237 N VAL B 198 SHEET 7 AA3 8 ILE B 219 ALA B 225 -1 N LEU B 220 O VAL B 242 SHEET 8 AA3 8 HIS B 271 VAL B 278 -1 O HIS B 271 N ALA B 225 SHEET 1 AA4 2 ARG B 47 GLN B 49 0 SHEET 2 AA4 2 TYR B 96 PRO B 98 -1 O TYR B 97 N TYR B 48 SHEET 1 AA5 8 ALA C 137 GLU C 140 0 SHEET 2 AA5 8 SER C 113 THR C 117 1 N LEU C 116 O ARG C 138 SHEET 3 AA5 8 LEU C 37 ASP C 40 1 N TYR C 38 O GLN C 115 SHEET 4 AA5 8 GLY C 159 ILE C 163 1 O LEU C 162 N LEU C 39 SHEET 5 AA5 8 THR C 191 VAL C 198 1 O THR C 191 N ILE C 161 SHEET 6 AA5 8 ALA C 237 ILE C 243 -1 O ALA C 237 N VAL C 198 SHEET 7 AA5 8 ILE C 219 ALA C 225 -1 N ILE C 222 O MET C 240 SHEET 8 AA5 8 HIS C 271 VAL C 278 -1 O VAL C 278 N ILE C 219 SHEET 1 AA6 2 ARG C 47 GLN C 49 0 SHEET 2 AA6 2 TYR C 96 PRO C 98 -1 O TYR C 97 N TYR C 48 SHEET 1 AA7 8 ALA D 137 GLU D 140 0 SHEET 2 AA7 8 SER D 113 THR D 117 1 N LEU D 116 O ARG D 138 SHEET 3 AA7 8 LEU D 37 ASP D 40 1 N TYR D 38 O GLN D 115 SHEET 4 AA7 8 GLY D 159 ILE D 163 1 O LEU D 162 N LEU D 39 SHEET 5 AA7 8 THR D 191 VAL D 198 1 O ALA D 193 N ILE D 161 SHEET 6 AA7 8 ALA D 237 ILE D 243 -1 O ALA D 237 N VAL D 198 SHEET 7 AA7 8 ILE D 219 ALA D 225 -1 N LEU D 220 O VAL D 242 SHEET 8 AA7 8 HIS D 271 VAL D 278 -1 O HIS D 271 N ALA D 225 SHEET 1 AA8 2 ARG D 47 GLN D 49 0 SHEET 2 AA8 2 TYR D 96 PRO D 98 -1 O TYR D 97 N TYR D 48 CISPEP 1 LEU A 152 PRO A 153 0 0.40 CISPEP 2 LEU B 152 PRO B 153 0 -3.94 CISPEP 3 LEU C 152 PRO C 153 0 1.47 CISPEP 4 LEU D 152 PRO D 153 0 3.78 SITE 1 AC1 23 HIS A 9 ALA A 10 ASP A 15 LYS A 18 SITE 2 AC1 23 HIS A 19 ASP A 40 HIS A 42 ALA A 43 SITE 3 AC1 23 GLY A 44 GLY A 99 SER A 100 ASP A 164 SITE 4 AC1 23 PRO A 166 TYR A 167 GLU A 168 MET A 235 SITE 5 AC1 23 HOH A 429 HOH A 431 HOH A 433 HOH A 434 SITE 6 AC1 23 HOH A 500 HOH A 541 HOH B 447 SITE 1 AC2 24 HIS B 9 ASN B 12 ALA B 14 ASP B 15 SITE 2 AC2 24 LYS B 18 HIS B 19 HIS B 42 ALA B 43 SITE 3 AC2 24 GLY B 44 ALA B 45 TYR B 48 LYS B 60 SITE 4 AC2 24 GLY B 99 SER B 100 HIS B 120 ASP B 123 SITE 5 AC2 24 ASP B 164 PRO B 165 PRO B 166 TRP B 195 SITE 6 AC2 24 HOH B 422 HOH B 460 HOH B 465 HOH B 502 SITE 1 AC3 21 HIS C 9 ALA C 10 ASP C 15 LYS C 18 SITE 2 AC3 21 HIS C 19 ASP C 40 HIS C 42 ALA C 43 SITE 3 AC3 21 GLY C 44 GLY C 99 SER C 100 ASP C 164 SITE 4 AC3 21 PRO C 166 GLU C 168 HOH C 402 HOH C 416 SITE 5 AC3 21 HOH C 423 HOH C 458 HOH C 494 HOH C 499 SITE 6 AC3 21 HOH C 524 SITE 1 AC4 17 HIS D 9 ALA D 10 ASP D 15 LYS D 18 SITE 2 AC4 17 HIS D 19 HIS D 42 ALA D 43 GLY D 44 SITE 3 AC4 17 GLY D 99 SER D 100 GLU D 118 HIS D 120 SITE 4 AC4 17 ASP D 123 ASP D 164 PRO D 166 HOH D 407 SITE 5 AC4 17 HOH D 409 CRYST1 66.420 170.730 66.590 90.00 118.32 90.00 P 1 21 1 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 0.015056 0.000000 0.008113 0.00000 SCALE2 0.000000 0.005857 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017059 0.00000