HEADER HYDROLASE 22-AUG-17 5OTN TITLE CRYSTAL STRUCTURE OF ZEBRAFISH MTH1 IN COMPLEX WITH O6-METHYL-DGMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUDIX (NUCLEOSIDE DIPHOSPHATE LINKED MOIETY X)-TYPE MOTIF COMPND 3 1; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: NUDIX (NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X)-TYPE MOTIF 1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: NUDT1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS MTH1, INHIBITOR, COMPLEX, HYDROLASE, NUDIX, METHYLATED NUCLEOTIDE, KEYWDS 2 O6-METHYL-DGMP, ZEBRAFISH EXPDTA X-RAY DIFFRACTION AUTHOR R.GUSTAFSSON,L.HENRIKSSON,A.-S.JEMTH,L.BRAUTIGAM,J.CARRERAS PUIGVERT, AUTHOR 2 E.HOMAN,U.WARPMAN BERGLUND,T.HELLEDAY,P.STENMARK REVDAT 5 17-JAN-24 5OTN 1 LINK REVDAT 4 28-NOV-18 5OTN 1 JRNL REVDAT 3 24-OCT-18 5OTN 1 JRNL REVDAT 2 17-OCT-18 5OTN 1 JRNL REVDAT 1 05-SEP-18 5OTN 0 JRNL AUTH A.S.JEMTH,R.GUSTAFSSON,L.BRAUTIGAM,L.HENRIKSSON, JRNL AUTH 2 K.S.A.VALLIN,A.SARNO,I.ALMLOF,E.HOMAN,A.RASTI, JRNL AUTH 3 U.WARPMAN BERGLUND,P.STENMARK,T.HELLEDAY JRNL TITL MUTT HOMOLOGUE 1 (MTH1) CATALYZES THE HYDROLYSIS OF JRNL TITL 2 MUTAGENIC O6-METHYL-DGTP. JRNL REF NUCLEIC ACIDS RES. V. 46 10888 2018 JRNL REFN ESSN 1362-4962 JRNL PMID 30304478 JRNL DOI 10.1093/NAR/GKY896 REMARK 2 REMARK 2 RESOLUTION. 0.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 88256 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.121 REMARK 3 R VALUE (WORKING SET) : 0.121 REMARK 3 FREE R VALUE : 0.133 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.500 REMARK 3 FREE R VALUE TEST SET COUNT : 2217 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 0.99 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.02 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6133 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.45 REMARK 3 BIN R VALUE (WORKING SET) : 0.2960 REMARK 3 BIN FREE R VALUE SET COUNT : 146 REMARK 3 BIN FREE R VALUE : 0.3040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1272 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 94 REMARK 3 SOLVENT ATOMS : 163 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.17000 REMARK 3 B22 (A**2) : -0.07000 REMARK 3 B33 (A**2) : -0.10000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.018 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.018 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.013 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.556 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.983 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.981 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1534 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1443 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2068 ; 1.629 ; 1.999 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3362 ; 0.913 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 186 ; 6.845 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 72 ;36.558 ;24.306 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 274 ;11.760 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;21.924 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 216 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1698 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 320 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 702 ; 0.839 ; 0.837 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 701 ; 0.834 ; 0.834 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 902 ; 1.113 ; 1.266 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 903 ; 1.113 ; 1.270 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 832 ; 1.371 ; 1.152 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 832 ; 1.368 ; 1.152 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1167 ; 1.647 ; 1.618 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1531 ; 2.404 ;10.826 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1532 ; 2.404 ;10.843 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 2977 ; 1.263 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 106 ;23.271 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3002 ; 5.899 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5OTN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1200006327. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92819 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 90549 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.990 REMARK 200 RESOLUTION RANGE LOW (A) : 28.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.93000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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: 5HZX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M CACL2, 0.1 M MES PH 6.0, 20% REMARK 280 (W/V) PEG6000, 2.5 MM O6-METHYL-2'-DGTP, 6 MM MGCL2, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 22.26400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.96000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.68950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.96000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.26400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.68950 REMARK 290 SMTRY3 4 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: 3330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL 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 -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 318 O HOH A 381 2.05 REMARK 500 OD1 ASN A 90 O HOH A 301 2.13 REMARK 500 OD1 ASP A 143 O HOH A 302 2.15 REMARK 500 ND2 ASN A 90 O HOH A 303 2.18 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 ASP A 62 -85.12 -91.05 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 CA A 211 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 36 O REMARK 620 2 GLU A 56 OE1 81.5 REMARK 620 3 GLU A 56 OE2 87.9 49.6 REMARK 620 4 GLU A 100 OE2 170.9 91.0 83.2 REMARK 620 5 6OG A 201 OP1 96.8 154.2 156.2 92.2 REMARK 620 6 HOH A 426 O 93.0 71.0 119.8 89.5 83.4 REMARK 620 7 HOH A 428 O 93.7 125.2 75.8 86.3 80.5 163.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 212 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 52 OE1 REMARK 620 2 GLU A 52 OE2 51.8 REMARK 620 3 GLU A 55 OE1 77.6 129.2 REMARK 620 4 ASP A 62 OD2 25.0 75.9 53.3 REMARK 620 5 GLU A 92 OE2 31.8 82.3 46.9 6.8 REMARK 620 6 HOH A 331 O 89.6 75.1 103.5 90.3 89.9 REMARK 620 7 HOH A 397 O 93.3 96.6 89.7 97.8 99.3 166.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 213 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 62 OD1 REMARK 620 2 GLU A 92 OE1 87.4 REMARK 620 3 GLU A 92 OE2 77.1 51.6 REMARK 620 4 GLU A 100 OE1 103.8 41.9 93.1 REMARK 620 5 GOL A 205 O2 99.0 45.3 96.9 6.8 REMARK 620 6 GOL A 205 O3 105.2 46.4 97.6 4.5 6.3 REMARK 620 7 HOH A 331 O 104.6 46.9 98.2 5.1 5.6 1.0 REMARK 620 8 HOH A 428 O 97.5 47.9 99.5 10.1 3.3 8.5 7.6 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6OG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 212 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 214 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 216 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 217 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5OTM RELATED DB: PDB DBREF 5OTN A 1 156 UNP Q7ZWC3 Q7ZWC3_DANRE 1 156 SEQADV 5OTN GLY A -2 UNP Q7ZWC3 EXPRESSION TAG SEQADV 5OTN SER A -1 UNP Q7ZWC3 EXPRESSION TAG SEQADV 5OTN HIS A 0 UNP Q7ZWC3 EXPRESSION TAG SEQRES 1 A 159 GLY SER HIS MET PHE THR SER LYS LEU LEU THR LEU VAL SEQRES 2 A 159 LEU VAL VAL GLN PRO GLY ARG VAL LEU LEU GLY MET LYS SEQRES 3 A 159 LYS ARG GLY PHE GLY ALA GLY LYS TRP ASN GLY PHE GLY SEQRES 4 A 159 GLY LYS VAL GLN THR GLY GLU THR ILE GLU GLN ALA ALA SEQRES 5 A 159 ARG ARG GLU LEU LEU GLU GLU SER GLY LEU THR VAL ASP SEQRES 6 A 159 THR LEU HIS LYS ILE GLY ASN ILE LYS PHE GLU PHE ILE SEQRES 7 A 159 GLY GLU THR GLU LEU MET ASP VAL HIS ILE PHE ARG ALA SEQRES 8 A 159 ASP ASN TYR GLU GLY GLU PRO ALA GLU SER ASP GLU MET SEQRES 9 A 159 ARG PRO GLN TRP PHE ASP ILE ASP LYS ILE PRO PHE SER SEQRES 10 A 159 GLN MET TRP ALA ASP ASP ILE LEU TRP PHE PRO LEU MET SEQRES 11 A 159 LEU GLN LYS LYS ARG PHE LEU GLY TYR PHE LYS PHE GLN SEQRES 12 A 159 GLY HIS ASP VAL ILE VAL GLU HIS LYS LEU ASP GLU VAL SEQRES 13 A 159 GLU ASP LEU HET 6OG A 201 24 HET GOL A 202 6 HET GOL A 203 6 HET GOL A 204 6 HET GOL A 205 6 HET GOL A 206 6 HET GOL A 207 6 HET GOL A 208 6 HET GOL A 209 6 HET GOL A 210 6 HET CA A 211 1 HET CA A 212 1 HET CA A 213 1 HET EDO A 214 4 HET EDO A 215 4 HET EDO A 216 4 HET CL A 217 1 HETNAM 6OG 6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE HETNAM GOL GLYCEROL HETNAM CA CALCIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 6OG C11 H16 N5 O7 P FORMUL 3 GOL 9(C3 H8 O3) FORMUL 12 CA 3(CA 2+) FORMUL 15 EDO 3(C2 H6 O2) FORMUL 18 CL CL 1- FORMUL 19 HOH *163(H2 O) HELIX 1 AA1 THR A 44 GLY A 58 1 15 HELIX 2 AA2 ASP A 109 ILE A 111 5 3 HELIX 3 AA3 PRO A 112 MET A 116 5 5 HELIX 4 AA4 ASP A 119 GLN A 129 1 11 SHEET 1 AA1 3 TRP A 32 ASN A 33 0 SHEET 2 AA1 3 ARG A 17 LYS A 23 -1 N GLY A 21 O ASN A 33 SHEET 3 AA1 3 MET A 101 ASP A 107 -1 O GLN A 104 N LEU A 20 SHEET 1 AA2 7 TRP A 32 ASN A 33 0 SHEET 2 AA2 7 ARG A 17 LYS A 23 -1 N GLY A 21 O ASN A 33 SHEET 3 AA2 7 THR A 3 GLN A 14 -1 N VAL A 12 O LEU A 19 SHEET 4 AA2 7 GLU A 79 ALA A 88 1 O LEU A 80 N THR A 3 SHEET 5 AA2 7 HIS A 65 PHE A 74 -1 N ILE A 67 O ILE A 85 SHEET 6 AA2 7 ARG A 132 GLN A 140 1 O PHE A 139 N GLU A 73 SHEET 7 AA2 7 VAL A 144 VAL A 153 -1 O VAL A 146 N LYS A 138 LINK O GLY A 36 CA CA A 211 1555 1555 2.30 LINK OE1 GLU A 52 CA CA A 212 1555 1555 2.47 LINK OE2 GLU A 52 CA CA A 212 1555 1555 2.57 LINK OE1 GLU A 55 CA CA A 212 1555 1555 2.37 LINK OE1 GLU A 56 CA CA A 211 1555 1555 2.85 LINK OE2 GLU A 56 CA CA A 211 1555 1555 2.39 LINK OD2 ASP A 62 CA CA A 212 1555 4544 2.40 LINK OD1 ASP A 62 CA CA A 213 1555 4544 2.40 LINK OE2 GLU A 92 CA CA A 212 1555 4544 2.35 LINK OE1 GLU A 92 CA CA A 213 1555 4544 2.55 LINK OE2 GLU A 92 CA CA A 213 1555 4544 2.48 LINK OE2 GLU A 100 CA CA A 211 1555 1555 2.29 LINK OE1 GLU A 100 CA CA A 213 1555 1555 2.38 LINK OP1 6OG A 201 CA CA A 211 1555 1555 2.38 LINK O2 GOL A 205 CA CA A 213 1555 1555 2.48 LINK O3 GOL A 205 CA CA A 213 1555 1555 2.53 LINK CA CA A 211 O HOH A 426 1555 1555 2.40 LINK CA CA A 211 O HOH A 428 1555 4444 2.52 LINK CA CA A 212 O HOH A 331 1555 1555 2.45 LINK CA CA A 212 O HOH A 397 1555 1555 2.40 LINK CA CA A 213 O HOH A 331 1555 1555 2.60 LINK CA CA A 213 O HOH A 428 1555 4444 2.54 SITE 1 AC1 19 THR A 8 LEU A 9 LYS A 23 ASN A 33 SITE 2 AC1 19 GLY A 36 GLY A 37 LYS A 38 PHE A 72 SITE 3 AC1 19 MET A 81 GLU A 100 TRP A 117 ASP A 119 SITE 4 AC1 19 ASP A 120 GOL A 202 GOL A 205 CA A 211 SITE 5 AC1 19 HOH A 344 HOH A 387 HOH A 428 SITE 1 AC2 6 LYS A 5 LYS A 38 LEU A 54 6OG A 201 SITE 2 AC2 6 HOH A 357 HOH A 376 SITE 1 AC3 8 VAL A 39 THR A 41 LEU A 122 LEU A 126 SITE 2 AC3 8 LEU A 150 GOL A 204 HOH A 352 HOH A 360 SITE 1 AC4 10 SER A 4 GLU A 79 PRO A 125 LEU A 126 SITE 2 AC4 10 GLN A 129 LYS A 131 GOL A 203 HOH A 352 SITE 3 AC4 10 HOH A 353 HOH A 389 SITE 1 AC5 12 LYS A 23 ARG A 25 GLY A 26 PHE A 27 SITE 2 AC5 12 VAL A 61 ASP A 62 GLU A 92 GLU A 100 SITE 3 AC5 12 6OG A 201 CA A 213 CL A 217 HOH A 428 SITE 1 AC6 5 PHE A 2 GLN A 14 GLY A 16 LEU A 128 SITE 2 AC6 5 LYS A 130 SITE 1 AC7 8 GLN A 14 GLN A 40 ARG A 51 ASN A 90 SITE 2 AC7 8 TYR A 91 HOH A 307 HOH A 309 HOH A 410 SITE 1 AC8 7 THR A 44 ILE A 45 ALA A 118 ILE A 121 SITE 2 AC8 7 HOH A 361 HOH A 377 HOH A 416 SITE 1 AC9 4 SER A 114 ASP A 155 LEU A 156 HOH A 340 SITE 1 AD1 6 PRO A 95 PRO A 103 GLU A 152 HOH A 398 SITE 2 AD1 6 HOH A 403 HOH A 413 SITE 1 AD2 6 GLY A 36 GLU A 56 GLU A 100 6OG A 201 SITE 2 AD2 6 HOH A 426 HOH A 428 SITE 1 AD3 6 GLU A 52 GLU A 55 ASP A 62 GLU A 92 SITE 2 AD3 6 HOH A 331 HOH A 397 SITE 1 AD4 6 ASP A 62 GLU A 92 GLU A 100 GOL A 205 SITE 2 AD4 6 HOH A 331 HOH A 428 SITE 1 AD5 3 LEU A 128 GLN A 129 HOH A 355 SITE 1 AD6 7 LYS A 66 ASN A 69 SER A 114 LEU A 134 SITE 2 AD6 7 LEU A 156 EDO A 216 HOH A 439 SITE 1 AD7 6 PRO A 112 PHE A 113 SER A 114 GLN A 115 SITE 2 AD7 6 EDO A 215 HOH A 439 SITE 1 AD8 4 GLY A 26 ARG A 50 GOL A 205 HOH A 444 CRYST1 44.528 55.379 65.920 90.00 90.00 90.00 P 21 21 21 4 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 0.022458 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018057 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015170 0.00000