HEADER DNA BINDING PROTEIN 05-NOV-19 6TC9 TITLE CRYSTAL STRUCTURE OF MUTM FROM NEISSERIA MENINGITIDIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA CONTAINING ABASIC SITE ANALOGUE; COMPND 3 CHAIN: D, G; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE; COMPND 7 CHAIN: A, C; COMPND 8 SYNONYM: FAPY-DNA GLYCOSYLASE,DNA-(APURINIC OR APYRIMIDINIC SITE) COMPND 9 LYASE MUTM,AP LYASE MUTM; COMPND 10 EC: 3.2.2.23,4.2.99.18; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA; COMPND 14 CHAIN: B, F; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS ALPHA522; SOURCE 7 ORGANISM_TAXID: 996307; SOURCE 8 GENE: MUTM, FPG, NMALPHA522_0971; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS MUTM, FPG/NEI, NEISSERIA MENINGITIDIS, BER, DNA REPAIR, DNA BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.SILHAN,B.LANDOVA,E.BOURA REVDAT 3 24-JAN-24 6TC9 1 REMARK REVDAT 2 16-DEC-20 6TC9 1 JRNL REVDAT 1 16-SEP-20 6TC9 0 JRNL AUTH B.LANDOVA,J.SILHAN JRNL TITL CONFORMATIONAL CHANGES OF DNA REPAIR GLYCOSYLASE MUTM JRNL TITL 2 TRIGGERED BY DNA BINDING. JRNL REF FEBS LETT. V. 594 3032 2020 JRNL REFN ISSN 0014-5793 JRNL PMID 32598485 JRNL DOI 10.1002/1873-3468.13876 REMARK 2 REMARK 2 RESOLUTION. 2.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2-3472 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) : 2.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 44909 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.240 REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.281 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2246 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE 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) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.300 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 72.45 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 42.6938 1.1627 20.8958 REMARK 3 T TENSOR REMARK 3 T11: 0.2815 T22: 0.4497 REMARK 3 T33: 0.2819 T12: 0.0008 REMARK 3 T13: -0.0002 T23: 0.0064 REMARK 3 L TENSOR REMARK 3 L11: 0.9088 L22: 0.8358 REMARK 3 L33: 4.2576 L12: 0.0157 REMARK 3 L13: -0.0030 L23: 0.3036 REMARK 3 S TENSOR REMARK 3 S11: 0.3026 S12: 0.0075 S13: -0.0081 REMARK 3 S21: -0.0118 S22: -0.4264 S23: -0.1751 REMARK 3 S31: -0.0236 S32: -0.6413 S33: 0.0472 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 3 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN A AND (RESID 2 THROUGH 123 OR REMARK 3 RESID 126 THROUGH 236 OR (RESID 237 AND REMARK 3 (NAME N OR NAME CA OR NAME C OR NAME O OR REMARK 3 NAME CB )) OR RESID 238 THROUGH 275)) REMARK 3 SELECTION : (CHAIN C AND (RESID 2 THROUGH 31 OR RESID REMARK 3 33 THROUGH 62 OR (RESID 63 AND (NAME N OR REMARK 3 NAME CA OR NAME C OR NAME O OR NAME CB )) REMARK 3 OR RESID 64 THROUGH 219 OR RESID 234 REMARK 3 THROUGH 275)) REMARK 3 ATOM PAIRS NUMBER : 1562 REMARK 3 RMSD : NULL REMARK 3 NCS GROUP : 2 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN B REMARK 3 SELECTION : CHAIN F REMARK 3 ATOM PAIRS NUMBER : 272 REMARK 3 RMSD : NULL REMARK 3 NCS GROUP : 3 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN D REMARK 3 SELECTION : CHAIN G REMARK 3 ATOM PAIRS NUMBER : 236 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6TC9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1292105232. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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, 1.0389 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44999 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.175 REMARK 200 RESOLUTION RANGE LOW (A) : 36.223 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.6300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.60500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.950 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: 6TC6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS-HCL PH = 8.5, 200 MM REMARK 280 MAGNESIUM ACETATE,, PH 8.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 65.38500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.19000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 65.38500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 40.19000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, C, F 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 DT D 1 REMARK 465 DG D 2 REMARK 465 DT G 1 REMARK 465 DG G 2 REMARK 465 MET A 1 REMARK 465 LYS A 32 REMARK 465 GLY A 220 REMARK 465 SER A 221 REMARK 465 THR A 222 REMARK 465 LEU A 223 REMARK 465 ARG A 224 REMARK 465 ASP A 225 REMARK 465 PHE A 226 REMARK 465 VAL A 227 REMARK 465 ASP A 228 REMARK 465 SER A 229 REMARK 465 ASP A 230 REMARK 465 GLY A 231 REMARK 465 LYS A 232 REMARK 465 SER A 233 REMARK 465 MET C 1 REMARK 465 GLY C 124 REMARK 465 ILE C 125 REMARK 465 GLY C 220 REMARK 465 SER C 221 REMARK 465 THR C 222 REMARK 465 LEU C 223 REMARK 465 ARG C 224 REMARK 465 ASP C 225 REMARK 465 PHE C 226 REMARK 465 VAL C 227 REMARK 465 ASP C 228 REMARK 465 SER C 229 REMARK 465 ASP C 230 REMARK 465 GLY C 231 REMARK 465 LYS C 232 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 ASP A 40 CG OD1 OD2 REMARK 470 GLU A 43 CG CD OE1 OE2 REMARK 470 ARG A 63 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 32 CG CD CE NZ REMARK 470 ASP C 40 CG OD1 OD2 REMARK 470 GLU C 43 CG CD OE1 OE2 REMARK 470 GLN C 237 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 3DR D 7 O3' - P - OP1 ANGL. DEV. = -13.9 DEGREES REMARK 500 DT D 9 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC D 13 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT G 9 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 LEU C 33 CA - CB - CG ANGL. DEV. = 14.9 DEGREES 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 ALA A 57 -130.58 58.29 REMARK 500 SER A 76 21.93 -145.94 REMARK 500 ASP A 112 88.11 -166.19 REMARK 500 GLN A 238 96.16 -160.63 REMARK 500 LEU C 31 14.56 -155.88 REMARK 500 LEU C 33 70.60 -116.31 REMARK 500 ARG C 34 -50.53 65.51 REMARK 500 ALA C 57 -129.80 60.60 REMARK 500 SER C 76 22.35 -146.10 REMARK 500 ASP C 112 87.94 -165.74 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 440 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH C 441 DISTANCE = 7.47 ANGSTROMS 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 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 250 SG REMARK 620 2 CYS A 253 SG 112.2 REMARK 620 3 CYS A 270 SG 114.4 99.1 REMARK 620 4 CYS A 273 SG 110.3 108.6 111.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 250 SG REMARK 620 2 CYS C 253 SG 115.0 REMARK 620 3 CYS C 270 SG 117.9 101.0 REMARK 620 4 CYS C 273 SG 104.7 109.2 108.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN C 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6TC6 RELATED DB: PDB DBREF 6TC9 D 1 14 PDB 6TC9 6TC9 1 14 DBREF 6TC9 G 1 14 PDB 6TC9 6TC9 1 14 DBREF 6TC9 A 1 275 UNP I4E596 I4E596_NEIME 1 275 DBREF 6TC9 B 1 14 PDB 6TC9 6TC9 1 14 DBREF 6TC9 C 1 275 UNP I4E596 I4E596_NEIME 1 275 DBREF 6TC9 F 1 14 PDB 6TC9 6TC9 1 14 SEQRES 1 D 14 DT DG DT DC DC DA 3DR DG DT DC DT DA DC SEQRES 2 D 14 DC SEQRES 1 G 14 DT DG DT DC DC DA 3DR DG DT DC DT DA DC SEQRES 2 G 14 DC SEQRES 1 A 275 MET PRO GLU LEU PRO GLU VAL GLU THR THR LEU ARG GLY SEQRES 2 A 275 ILE ALA PRO HIS ILE GLU GLY LYS THR VAL GLU ALA VAL SEQRES 3 A 275 VAL LEU ARG GLN LEU LYS LEU ARG TRP GLN ILE ASN PRO SEQRES 4 A 275 ASP LEU GLY GLU ILE LEU SER GLY ARG GLN VAL LEU SER SEQRES 5 A 275 CYS GLY ARG ARG ALA LYS TYR LEU LEU ILE ARG PHE GLN SEQRES 6 A 275 THR GLY VAL LEU LEU ILE HIS LEU GLY MET SER GLY SER SEQRES 7 A 275 LEU ARG ILE PHE THR PRO SER ASP GLY ARG ILE GLY ARG SEQRES 8 A 275 PRO ASP ARG HIS ASP HIS VAL ASP ILE VAL PHE SER ASP SEQRES 9 A 275 GLY THR VAL MET ARG TYR ARG ASP PRO ARG LYS PHE GLY SEQRES 10 A 275 ALA ILE LEU TRP TYR GLU GLY ILE GLU GLU HIS HIS PRO SEQRES 11 A 275 LEU LEU GLU LYS LEU GLY PRO GLU PRO LEU SER GLU ALA SEQRES 12 A 275 PHE CYS ALA ASP TYR LEU TYR ALA ARG LEU LYS ALA GLN SEQRES 13 A 275 LYS ARG ALA VAL LYS LEU ALA LEU MET ASP ASN ALA VAL SEQRES 14 A 275 VAL VAL GLY VAL GLY ASN ILE TYR ALA ASN GLU SER LEU SEQRES 15 A 275 PHE ARG ALA GLY ILE SER PRO HIS ARG PRO ALA ASN ARG SEQRES 16 A 275 LEU LYS LYS LYS GLU CYS ALA LEU LEU VAL GLU THR VAL SEQRES 17 A 275 LYS ALA VAL LEU GLN ARG ALA ILE GLU THR GLY GLY SER SEQRES 18 A 275 THR LEU ARG ASP PHE VAL ASP SER ASP GLY LYS SER GLY SEQRES 19 A 275 TYR PHE GLN GLN GLU TYR THR VAL TYR GLY ARG HIS ASN SEQRES 20 A 275 GLN PRO CYS PRO ARG CYS GLY GLY LEU VAL VAL LYS GLU SEQRES 21 A 275 THR LEU GLY GLN ARG GLY THR PHE TYR CYS PRO ASN CYS SEQRES 22 A 275 GLN LYS SEQRES 1 B 14 DA DG DG DT DA DG DA DC DC DT DG DG DA SEQRES 2 B 14 DC SEQRES 1 C 275 MET PRO GLU LEU PRO GLU VAL GLU THR THR LEU ARG GLY SEQRES 2 C 275 ILE ALA PRO HIS ILE GLU GLY LYS THR VAL GLU ALA VAL SEQRES 3 C 275 VAL LEU ARG GLN LEU LYS LEU ARG TRP GLN ILE ASN PRO SEQRES 4 C 275 ASP LEU GLY GLU ILE LEU SER GLY ARG GLN VAL LEU SER SEQRES 5 C 275 CYS GLY ARG ARG ALA LYS TYR LEU LEU ILE ARG PHE GLN SEQRES 6 C 275 THR GLY VAL LEU LEU ILE HIS LEU GLY MET SER GLY SER SEQRES 7 C 275 LEU ARG ILE PHE THR PRO SER ASP GLY ARG ILE GLY ARG SEQRES 8 C 275 PRO ASP ARG HIS ASP HIS VAL ASP ILE VAL PHE SER ASP SEQRES 9 C 275 GLY THR VAL MET ARG TYR ARG ASP PRO ARG LYS PHE GLY SEQRES 10 C 275 ALA ILE LEU TRP TYR GLU GLY ILE GLU GLU HIS HIS PRO SEQRES 11 C 275 LEU LEU GLU LYS LEU GLY PRO GLU PRO LEU SER GLU ALA SEQRES 12 C 275 PHE CYS ALA ASP TYR LEU TYR ALA ARG LEU LYS ALA GLN SEQRES 13 C 275 LYS ARG ALA VAL LYS LEU ALA LEU MET ASP ASN ALA VAL SEQRES 14 C 275 VAL VAL GLY VAL GLY ASN ILE TYR ALA ASN GLU SER LEU SEQRES 15 C 275 PHE ARG ALA GLY ILE SER PRO HIS ARG PRO ALA ASN ARG SEQRES 16 C 275 LEU LYS LYS LYS GLU CYS ALA LEU LEU VAL GLU THR VAL SEQRES 17 C 275 LYS ALA VAL LEU GLN ARG ALA ILE GLU THR GLY GLY SER SEQRES 18 C 275 THR LEU ARG ASP PHE VAL ASP SER ASP GLY LYS SER GLY SEQRES 19 C 275 TYR PHE GLN GLN GLU TYR THR VAL TYR GLY ARG HIS ASN SEQRES 20 C 275 GLN PRO CYS PRO ARG CYS GLY GLY LEU VAL VAL LYS GLU SEQRES 21 C 275 THR LEU GLY GLN ARG GLY THR PHE TYR CYS PRO ASN CYS SEQRES 22 C 275 GLN LYS SEQRES 1 F 14 DA DG DG DT DA DG DA DC DC DT DG DG DA SEQRES 2 F 14 DC HET 3DR D 7 11 HET 3DR G 7 11 HET ZN A 301 1 HET ZN C 301 1 HET MG C 302 1 HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETSYN 3DR ABASIC DIDEOXYRIBOSE FORMUL 1 3DR 2(C5 H11 O6 P) FORMUL 7 ZN 2(ZN 2+) FORMUL 9 MG MG 2+ FORMUL 10 HOH *59(H2 O) HELIX 1 AA1 GLU A 3 GLU A 19 1 17 HELIX 2 AA2 ASP A 40 SER A 46 1 7 HELIX 3 AA3 ASP A 86 ARG A 91 5 6 HELIX 4 AA4 ILE A 125 HIS A 129 5 5 HELIX 5 AA5 CYS A 145 LEU A 153 1 9 HELIX 6 AA6 ALA A 159 MET A 165 1 7 HELIX 7 AA7 GLY A 174 ALA A 185 1 12 HELIX 8 AA8 PRO A 192 LEU A 196 5 5 HELIX 9 AA9 LYS A 197 GLY A 219 1 23 HELIX 10 AB1 GLU C 3 GLU C 19 1 17 HELIX 11 AB2 ASP C 40 SER C 46 1 7 HELIX 12 AB3 ASP C 86 ARG C 91 5 6 HELIX 13 AB4 CYS C 145 LEU C 153 1 9 HELIX 14 AB5 ALA C 159 MET C 165 1 7 HELIX 15 AB6 GLY C 174 ALA C 185 1 12 HELIX 16 AB7 PRO C 192 LEU C 196 5 5 HELIX 17 AB8 LYS C 197 GLY C 219 1 23 SHEET 1 AA1 4 VAL A 23 LEU A 28 0 SHEET 2 AA1 4 ASP A 96 PHE A 102 -1 O ASP A 99 N VAL A 27 SHEET 3 AA1 4 VAL A 107 ARG A 111 -1 O TYR A 110 N VAL A 98 SHEET 4 AA1 4 SER A 78 PHE A 82 -1 N ARG A 80 O ARG A 109 SHEET 1 AA2 4 SER A 52 ARG A 56 0 SHEET 2 AA2 4 TYR A 59 ARG A 63 -1 O ARG A 63 N SER A 52 SHEET 3 AA2 4 VAL A 68 HIS A 72 -1 O LEU A 69 N ILE A 62 SHEET 4 AA2 4 ALA A 118 TYR A 122 -1 O LEU A 120 N LEU A 70 SHEET 1 AA3 2 VAL A 258 LEU A 262 0 SHEET 2 AA3 2 ARG A 265 TYR A 269 -1 O THR A 267 N GLU A 260 SHEET 1 AA4 4 VAL C 23 LEU C 28 0 SHEET 2 AA4 4 ASP C 96 PHE C 102 -1 O ASP C 99 N VAL C 27 SHEET 3 AA4 4 VAL C 107 ARG C 111 -1 O TYR C 110 N VAL C 98 SHEET 4 AA4 4 SER C 78 PHE C 82 -1 N ARG C 80 O ARG C 109 SHEET 1 AA5 4 SER C 52 ARG C 56 0 SHEET 2 AA5 4 TYR C 59 ARG C 63 -1 O LEU C 61 N GLY C 54 SHEET 3 AA5 4 VAL C 68 HIS C 72 -1 O LEU C 69 N ILE C 62 SHEET 4 AA5 4 ALA C 118 TYR C 122 -1 O LEU C 120 N LEU C 70 SHEET 1 AA6 2 VAL C 258 LEU C 262 0 SHEET 2 AA6 2 ARG C 265 TYR C 269 -1 O THR C 267 N GLU C 260 LINK O3' DA D 6 P 3DR D 7 1555 1555 1.61 LINK O3' 3DR D 7 P DG D 8 1555 1555 1.61 LINK O3' DA G 6 P 3DR G 7 1555 1555 1.61 LINK O3' 3DR G 7 P DG G 8 1555 1555 1.61 LINK SG CYS A 250 ZN ZN A 301 1555 1555 2.28 LINK SG CYS A 253 ZN ZN A 301 1555 1555 2.23 LINK SG CYS A 270 ZN ZN A 301 1555 1555 2.34 LINK SG CYS A 273 ZN ZN A 301 1555 1555 2.28 LINK SG CYS C 250 ZN ZN C 301 1555 1555 2.31 LINK SG CYS C 253 ZN ZN C 301 1555 1555 2.26 LINK SG CYS C 270 ZN ZN C 301 1555 1555 2.39 LINK SG CYS C 273 ZN ZN C 301 1555 1555 2.38 SITE 1 AC1 4 CYS A 250 CYS A 253 CYS A 270 CYS A 273 SITE 1 AC2 4 CYS C 250 CYS C 253 CYS C 270 CYS C 273 CRYST1 130.770 80.380 83.620 90.00 89.95 90.00 C 1 2 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 0.007647 0.000000 -0.000007 0.00000 SCALE2 0.000000 0.012441 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011959 0.00000