HEADER OXIDOREDUCTASE 27-OCT-22 8HAZ TITLE CRYSTAL STRUCTURE OF CAENORHABDITIS ELEGANS NMAD-1 IN COMPLEX WITH TITLE 2 LIGAND I COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA N6-METHYL ADENINE DEMETHYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: N6-METHYL ADENINE DEMETHYLASE 1; COMPND 5 EC: 1.14.11.51; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_TAXID: 6239; SOURCE 4 GENE: NMAD-1, F09F7.7; SOURCE 5 EXPRESSION_SYSTEM: PROKARYOTE COCULTURE; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 2746493 KEYWDS NMAD-1A, GENE REGULATION, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR G.SHANG,Z.CHEN REVDAT 1 07-FEB-24 8HAZ 0 JRNL AUTH G.SHANG,M.YANG,M.LI,L.MA,Y.LIU,J.MA,Y.CHEN,X.WANG,S.FAN, JRNL AUTH 2 M.XIE,W.WU,S.DAI,Z.CHEN JRNL TITL STRUCTURAL BASIS OF NUCLEIC ACID RECOGNITION AND 6MA JRNL TITL 2 DEMETHYLATION BY CAENORHABDITIS ELEGANS NMAD-1A. JRNL REF INT J MOL SCI V. 25 2024 JRNL REFN ESSN 1422-0067 JRNL PMID 38255759 JRNL DOI 10.3390/IJMS25020686 REMARK 2 REMARK 2 RESOLUTION. 2.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.18.2_3874: ???) 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) : 2.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 83.9 REMARK 3 NUMBER OF REFLECTIONS : 5265 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.250 REMARK 3 R VALUE (WORKING SET) : 0.249 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 264 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 37.5400 - 3.3500 0.89 2679 131 0.2294 0.2559 REMARK 3 2 2.7500 - 2.7000 0.79 2322 133 0.3020 0.3135 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.920 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 : 0.009 1757 REMARK 3 ANGLE : 0.989 2370 REMARK 3 CHIRALITY : 0.063 257 REMARK 3 PLANARITY : 0.004 304 REMARK 3 DIHEDRAL : 25.056 653 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 8HAZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1300033191. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-OCT-21 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6106 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.3 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.70 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: AB INITIO PHASING REMARK 200 SOFTWARE USED: BALBES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 200 MM, CH3COONH4, 100 REMARK 280 MM BIS-TRIS PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 289K 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 24.26400 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 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 GLY A 18 REMARK 465 SER A 19 REMARK 465 MET A 20 REMARK 465 THR A 21 REMARK 465 THR A 22 REMARK 465 GLU A 23 REMARK 465 ARG A 24 REMARK 465 VAL A 25 REMARK 465 LYS A 26 REMARK 465 LYS A 27 REMARK 465 LEU A 28 REMARK 465 ARG A 29 REMARK 465 VAL A 30 REMARK 465 VAL A 31 REMARK 465 GLU A 32 REMARK 465 GLY A 123 REMARK 465 PRO A 124 REMARK 465 LYS A 125 REMARK 465 VAL A 126 REMARK 465 ASN A 127 REMARK 465 PHE A 128 REMARK 465 LYS A 129 REMARK 465 HIS A 130 REMARK 465 LYS A 131 REMARK 465 LYS A 132 REMARK 465 VAL A 133 REMARK 465 LYS A 134 REMARK 465 THR A 135 REMARK 465 ASP A 136 REMARK 465 THR A 137 REMARK 465 PHE A 138 REMARK 465 VAL A 139 REMARK 465 ALA A 263 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 MET A 141 CG SD CE REMARK 470 ARG A 247 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 SER A 113 -151.72 -114.45 REMARK 500 ILE A 201 -60.72 74.02 REMARK 500 SER A 204 -158.17 -157.74 REMARK 500 ASP A 231 -125.60 53.77 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 471 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH A 472 DISTANCE = 6.47 ANGSTROMS REMARK 525 HOH A 473 DISTANCE = 7.55 ANGSTROMS DBREF 8HAZ A 21 263 UNP Q8MNT9 NMAD1_CAEEL 21 263 SEQADV 8HAZ GLY A 18 UNP Q8MNT9 EXPRESSION TAG SEQADV 8HAZ SER A 19 UNP Q8MNT9 EXPRESSION TAG SEQADV 8HAZ MET A 20 UNP Q8MNT9 EXPRESSION TAG SEQRES 1 A 246 GLY SER MET THR THR GLU ARG VAL LYS LYS LEU ARG VAL SEQRES 2 A 246 VAL GLU ASP LYS HIS VAL ASN TYR LYS VAL PHE ILE TYR SEQRES 3 A 246 ASP HIS ILE ARG GLN ILE ALA ILE PRO THR THR ASN LEU SEQRES 4 A 246 ASN SER GLN SER SER LEU GLU ASP ILE ILE ASP GLU SER SEQRES 5 A 246 THR SER CYS GLN SER VAL SER THR ASP GLY SER ILE GLU SEQRES 6 A 246 ILE ASP GLY LEU THR LEU ILE HIS ASN PHE LEU SER GLU SEQRES 7 A 246 SER GLU GLU SER LYS ILE LEU ASN MET ILE ASP THR VAL SEQRES 8 A 246 GLU TRP ALA GLN SER GLN SER GLY ARG ARG LYS GLN ASP SEQRES 9 A 246 TYR GLY PRO LYS VAL ASN PHE LYS HIS LYS LYS VAL LYS SEQRES 10 A 246 THR ASP THR PHE VAL GLY MET PRO GLU TYR ALA ASP MET SEQRES 11 A 246 LEU LEU ASN LYS MET SER GLU TYR ASP VAL LYS LYS LEU SEQRES 12 A 246 GLY ASN TYR GLN PRO PHE GLU MET CYS ASN LEU GLU TYR SEQRES 13 A 246 GLU GLU VAL LYS LYS SER ALA ILE GLU MET HIS GLN ASP SEQRES 14 A 246 ASP MET TRP ILE TRP GLY ASN ARG LEU ILE SER ILE ASN SEQRES 15 A 246 LEU ILE ASN GLY SER VAL MET THR LEU SER ASN ASP ASN SEQRES 16 A 246 LYS SER PHE LEU CYS TYR VAL HIS MET PRO HIS ARG SER SEQRES 17 A 246 LEU LEU CYS MET ALA ASP GLU CYS ARG TYR ASP TRP LYS SEQRES 18 A 246 HIS GLY VAL LEU ALA HIS HIS ILE ARG GLY ARG ARG ILE SEQRES 19 A 246 ALA LEU THR MET ARG GLU ALA ALA LYS ASP PHE ALA HET SO4 A 301 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *73(H2 O) HELIX 1 AA1 SER A 61 THR A 70 1 10 HELIX 2 AA2 SER A 94 ASP A 106 1 13 HELIX 3 AA3 GLU A 143 ASP A 156 1 14 HELIX 4 AA4 ALA A 230 ASP A 236 1 7 HELIX 5 AA5 LEU A 242 ILE A 246 5 5 SHEET 1 AA1 6 ILE A 49 PRO A 52 0 SHEET 2 AA1 6 LYS A 39 ASP A 44 -1 N ASP A 44 O ILE A 49 SHEET 3 AA1 6 PHE A 215 MET A 221 1 O LEU A 216 N LYS A 39 SHEET 4 AA1 6 SER A 204 ASN A 210 -1 N LEU A 208 O CYS A 217 SHEET 5 AA1 6 LYS A 238 VAL A 241 -1 O GLY A 240 N THR A 207 SHEET 6 AA1 6 ILE A 181 HIS A 184 -1 N HIS A 184 O HIS A 239 SHEET 1 AA2 7 LEU A 86 ILE A 89 0 SHEET 2 AA2 7 LEU A 226 MET A 229 -1 O CYS A 228 N THR A 87 SHEET 3 AA2 7 TRP A 191 LEU A 200 -1 N SER A 197 O LEU A 227 SHEET 4 AA2 7 ARG A 249 ALA A 258 -1 O GLU A 257 N GLY A 192 SHEET 5 AA2 7 GLU A 167 GLU A 174 -1 N TYR A 173 O ARG A 250 SHEET 6 AA2 7 ARG A 118 ASP A 121 -1 N ARG A 118 O GLU A 172 SHEET 7 AA2 7 ALA A 111 GLN A 112 -1 N ALA A 111 O LYS A 119 CRYST1 44.221 48.528 51.878 90.00 104.43 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 0.022614 0.000000 0.005821 0.00000 SCALE2 0.000000 0.020607 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019904 0.00000