HEADER HYDROLASE 09-APR-14 4CXV TITLE STRUCTURE OF BIFUNCTIONAL ENDONUCLEASE (ATBFN2) IN COMPLEX WITH TITLE 2 PHOSPHATE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDONUCLEASE 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ATENDO2, DEOXYRIBONUCLEASE ENDO2, SINGLE-STRANDED-NUCLEATE COMPND 5 ENDONUCLEASE ENDO2, BIFUNCTIONAL ENDONUCLEASE ATBFN2; COMPND 6 EC: 3.1.30.1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: THALE CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 EXPRESSION_SYSTEM: ARABIDOPSIS THALIANA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: THALE CRESS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 3702; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: A. TUMEFACIENS KEYWDS HYDROLASE, SSDNA BINDING EXPDTA X-RAY DIFFRACTION AUTHOR T.-F.YU,M.MAESTRE-REYNA,C.-Y.KO,T.-P.KO,Y.-J.SUN,T.-Y.LIN,J.-F.SHAW, AUTHOR 2 A.H.-J.WANG REVDAT 5 20-DEC-23 4CXV 1 HETSYN REVDAT 4 29-JUL-20 4CXV 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 23-MAY-18 4CXV 1 REMARK REVDAT 2 28-JAN-15 4CXV 1 JRNL REMARK REVDAT 1 23-JUL-14 4CXV 0 JRNL AUTH T.YU,M.MAESTRE-REYNA,C.KO,T.KO,Y.SUN,T.LIN,J.SHAW,A.H.WANG JRNL TITL STRUCTURAL INSIGHTS OF THE SSDNA BINDING SITE IN THE JRNL TITL 2 MULTIFUNCTIONAL ENDONUCLEASE ATBFN2 FROM ARABIDOPSIS JRNL TITL 3 THALIANA. JRNL REF PLOS ONE V. 9 05821 2014 JRNL REFN ESSN 1932-6203 JRNL PMID 25157844 JRNL DOI 10.1371/JOURNAL.PONE.0105821 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.43 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 31321 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) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1659 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2356 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE SET COUNT : 114 REMARK 3 BIN FREE R VALUE : 0.3480 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4064 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 247 REMARK 3 SOLVENT ATOMS : 426 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -17.54000 REMARK 3 B22 (A**2) : 26.73000 REMARK 3 B33 (A**2) : -9.19000 REMARK 3 B12 (A**2) : 11.00000 REMARK 3 B13 (A**2) : 0.19000 REMARK 3 B23 (A**2) : 15.70000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.055 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.043 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.132 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.660 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4455 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3967 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6092 ; 1.563 ; 1.994 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9049 ; 0.915 ; 3.004 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 519 ; 5.848 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 199 ;35.733 ;24.171 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 670 ;15.369 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;10.685 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 702 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4871 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1007 ; 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): 2064 ; 1.677 ; 2.714 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2063 ; 1.676 ; 2.713 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2572 ; 2.459 ; 4.054 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2391 ; 1.945 ; 2.967 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 : MASK 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. U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 4CXV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-APR-14. REMARK 100 THE DEPOSITION ID IS D_1290060231. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-SEP-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL15A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : HORIZONTALLY FOCUSING SINGLE REMARK 200 CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34563 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.26000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: PDB ENTRY 4CWM REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, PH 7.5 0.2 M NA2HPO4 30% REMARK 280 (W/V) PEG3350 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, E, F, G 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 SER A 104 REMARK 465 SER A 105 REMARK 465 GLN A 106 REMARK 465 SER A 107 REMARK 465 LYS A 202 REMARK 465 HIS A 265 REMARK 465 HIS A 266 REMARK 465 HIS A 267 REMARK 465 HIS A 268 REMARK 465 HIS A 269 REMARK 465 ALA B 102 REMARK 465 ALA B 103 REMARK 465 SER B 104 REMARK 465 SER B 105 REMARK 465 GLN B 106 REMARK 465 LYS B 202 REMARK 465 HIS B 265 REMARK 465 HIS B 266 REMARK 465 HIS B 267 REMARK 465 HIS B 268 REMARK 465 HIS B 269 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 26 NZ REMARK 470 LYS A 100 NZ REMARK 470 GLN A 108 CG CD OE1 NE2 REMARK 470 LYS A 137 CE NZ REMARK 470 ASP A 191 CG OD1 OD2 REMARK 470 THR A 203 OG1 CG2 REMARK 470 HIS A 264 CA C O CB CG ND1 CD2 REMARK 470 HIS A 264 CE1 NE2 REMARK 470 LYS B 3 CD CE NZ REMARK 470 LYS B 26 CG CD CE NZ REMARK 470 GLU B 27 CG CD OE1 OE2 REMARK 470 GLU B 34 CG CD OE1 OE2 REMARK 470 ARG B 46 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 50 CD NE CZ NH1 NH2 REMARK 470 LYS B 150 CE NZ REMARK 470 GLU B 175 CG CD OE1 OE2 REMARK 470 THR B 203 OG1 CG2 REMARK 470 LYS B 223 NZ REMARK 470 GLU B 232 CG CD OE1 OE2 REMARK 470 HIS B 264 CA C O CB CG ND1 CD2 REMARK 470 HIS B 264 CE1 NE2 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 OE2 GLU B 4 OE2 GLU B 163 1.91 REMARK 500 OE1 GLU B 77 O HOH B 2065 1.99 REMARK 500 O2 MAN C 4 O HOH A 2208 2.00 REMARK 500 O6 BMA C 3 O HOH A 2206 2.03 REMARK 500 O HOH A 2070 O HOH A 2085 2.19 REMARK 500 O LYS B 201 N THR B 203 2.19 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 CYS A 66 55.72 -110.68 REMARK 500 TYR A 147 -118.75 48.77 REMARK 500 SER A 159 -48.09 -136.19 REMARK 500 SER A 159 -48.19 -136.33 REMARK 500 GLU A 232 -147.41 -140.76 REMARK 500 CYS B 66 54.62 -110.33 REMARK 500 TYR B 147 -118.75 49.62 REMARK 500 SER B 159 -49.84 -135.58 REMARK 500 THR B 200 49.66 -90.92 REMARK 500 GLU B 232 -147.38 -139.00 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 A2002 DISTANCE = 6.58 ANGSTROMS REMARK 525 HOH A2052 DISTANCE = 6.89 ANGSTROMS REMARK 525 HOH A2053 DISTANCE = 8.02 ANGSTROMS REMARK 525 HOH A2087 DISTANCE = 6.33 ANGSTROMS REMARK 525 HOH B2001 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH B2084 DISTANCE = 6.23 ANGSTROMS REMARK 525 HOH B2196 DISTANCE = 6.14 ANGSTROMS REMARK 525 HOH B2198 DISTANCE = 6.72 ANGSTROMS REMARK 525 HOH B2199 DISTANCE = 7.35 ANGSTROMS REMARK 525 HOH B2200 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH B2201 DISTANCE = 7.97 ANGSTROMS REMARK 525 HOH B2202 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH B2204 DISTANCE = 7.25 ANGSTROMS REMARK 525 HOH B2205 DISTANCE = 7.48 ANGSTROMS REMARK 525 HOH B2208 DISTANCE = 6.66 ANGSTROMS REMARK 525 HOH B2209 DISTANCE = 7.46 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 ALPHA-D-MANNOSE (MAN): PART OF THE N-GLYCAN REMARK 600 ZINC ION (ZN2): TRIMETALIC METL CLUSTER IN THE ACTIVE SITE REMARK 600 N-ACETYL-D-GLUCOSAMINE (NAG): PART OF THE N-GLYCANS 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 433 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TRP A 1 O REMARK 620 2 HIS A 6 NE2 94.6 REMARK 620 3 ASP A 124 OD1 166.9 91.7 REMARK 620 4 PO4 A 401 O2 94.9 117.8 92.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 431 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 45 OD1 REMARK 620 2 HIS A 58 ND1 83.1 REMARK 620 3 HIS A 120 NE2 80.7 95.0 REMARK 620 4 ASP A 124 OD2 174.1 99.5 93.7 REMARK 620 5 PO4 A 401 O3 82.0 99.1 156.1 102.8 REMARK 620 6 PO4 A 401 O2 90.1 163.8 98.4 88.7 65.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 432 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 130 NE2 REMARK 620 2 HIS A 154 NE2 95.8 REMARK 620 3 ASP A 158 OD1 89.3 96.1 REMARK 620 4 ASP A 158 OD2 143.1 90.1 53.8 REMARK 620 5 PO4 A 401 O4 87.1 168.5 95.0 94.2 REMARK 620 6 HOH A2117 O 110.1 79.4 160.3 106.7 89.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 433 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TRP B 1 O REMARK 620 2 HIS B 6 NE2 95.3 REMARK 620 3 ASP B 124 OD1 166.5 90.6 REMARK 620 4 PO4 B 401 O3 92.9 117.7 95.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 431 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 45 OD1 REMARK 620 2 HIS B 58 ND1 85.6 REMARK 620 3 HIS B 120 NE2 81.3 95.2 REMARK 620 4 ASP B 124 OD2 174.0 97.8 93.5 REMARK 620 5 PO4 B 401 O3 88.1 161.3 101.1 90.2 REMARK 620 6 PO4 B 401 O2 85.0 101.7 157.3 99.1 60.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 432 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 130 NE2 REMARK 620 2 HIS B 154 NE2 96.0 REMARK 620 3 ASP B 158 OD2 144.9 88.4 REMARK 620 4 ASP B 158 OD1 90.3 95.3 54.6 REMARK 620 5 PO4 B 401 O1 87.9 168.9 94.4 95.1 REMARK 620 6 HOH B2102 O 114.2 78.6 100.8 155.1 90.3 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4CWM RELATED DB: PDB REMARK 900 HIGH-GLYCOSYLATION CRYSTAL STRUCTURE OF THE BIFUNCTIONAL REMARK 900 ENDONUCLEASE (ATBFN2) FROM ARABIDOPSIS THALIANA REMARK 900 RELATED ID: 4CXO RELATED DB: PDB REMARK 900 BIFUNCTIONAL ENDONUCLEASE IN COMPLEX WITH SSDNA REMARK 900 RELATED ID: 4CXP RELATED DB: PDB REMARK 900 STRUCTURE OF BIFUNCTIONAL ENDONUCLEASE (ATBFN2) FROM ARABIDOPSIS REMARK 900 THALIANA IN COMPLEX WITH SULFATE REMARK 999 REMARK 999 SEQUENCE REMARK 999 OUR SEQUENCE CONTAINS A C-TERMINAL HISTIDINE TAG DBREF 4CXV A 1 263 UNP Q9C9G4 ENDO2_ARATH 28 290 DBREF 4CXV B 1 263 UNP Q9C9G4 ENDO2_ARATH 28 290 SEQADV 4CXV HIS A 264 UNP Q9C9G4 EXPRESSION TAG SEQADV 4CXV HIS A 265 UNP Q9C9G4 EXPRESSION TAG SEQADV 4CXV HIS A 266 UNP Q9C9G4 EXPRESSION TAG SEQADV 4CXV HIS A 267 UNP Q9C9G4 EXPRESSION TAG SEQADV 4CXV HIS A 268 UNP Q9C9G4 EXPRESSION TAG SEQADV 4CXV HIS A 269 UNP Q9C9G4 EXPRESSION TAG SEQADV 4CXV HIS B 264 UNP Q9C9G4 EXPRESSION TAG SEQADV 4CXV HIS B 265 UNP Q9C9G4 EXPRESSION TAG SEQADV 4CXV HIS B 266 UNP Q9C9G4 EXPRESSION TAG SEQADV 4CXV HIS B 267 UNP Q9C9G4 EXPRESSION TAG SEQADV 4CXV HIS B 268 UNP Q9C9G4 EXPRESSION TAG SEQADV 4CXV HIS B 269 UNP Q9C9G4 EXPRESSION TAG SEQRES 1 A 269 TRP GLY LYS GLU GLY HIS GLU ILE ILE CYS LYS ILE ALA SEQRES 2 A 269 GLN THR ARG LEU ASP GLU THR ALA ALA LYS ALA VAL LYS SEQRES 3 A 269 GLU LEU LEU PRO GLU SER ALA GLU GLY ASP LEU SER SER SEQRES 4 A 269 LEU CYS LEU TRP ALA ASP ARG VAL LYS PHE ARG TYR HIS SEQRES 5 A 269 TRP SER SER PRO LEU HIS TYR ILE ASN THR PRO ASP ALA SEQRES 6 A 269 CYS SER TYR GLN TYR ASN ARG ASP CYS LYS ASP GLU SER SEQRES 7 A 269 GLY GLU LYS GLY ARG CYS VAL ALA GLY ALA ILE TYR ASN SEQRES 8 A 269 TYR THR THR GLN LEU LEU SER TYR LYS THR ALA ALA SER SEQRES 9 A 269 SER GLN SER GLN TYR ASN LEU THR GLU ALA LEU LEU PHE SEQRES 10 A 269 VAL SER HIS PHE MET GLY ASP ILE HIS GLN PRO LEU HIS SEQRES 11 A 269 VAL SER TYR ALA SER ASP LYS GLY GLY ASN THR ILE GLU SEQRES 12 A 269 VAL HIS TRP TYR THR ARG LYS ALA ASN LEU HIS HIS ILE SEQRES 13 A 269 TRP ASP SER ASN ILE ILE GLU THR ALA GLU ALA ASP LEU SEQRES 14 A 269 TYR ASN SER ALA LEU GLU GLY MET VAL ASP ALA LEU LYS SEQRES 15 A 269 LYS ASN ILE THR THR GLU TRP ALA ASP GLN VAL LYS ARG SEQRES 16 A 269 TRP GLU THR CYS THR LYS LYS THR ALA CYS PRO ASP ILE SEQRES 17 A 269 TYR ALA SER GLU GLY ILE GLN ALA ALA CYS ASP TRP ALA SEQRES 18 A 269 TYR LYS GLY VAL THR GLU GLY ASP THR LEU GLU ASP GLU SEQRES 19 A 269 TYR PHE TYR SER ARG LEU PRO ILE VAL TYR GLN ARG LEU SEQRES 20 A 269 ALA GLN GLY GLY VAL ARG LEU ALA ALA THR LEU ASN ARG SEQRES 21 A 269 ILE PHE GLY HIS HIS HIS HIS HIS HIS SEQRES 1 B 269 TRP GLY LYS GLU GLY HIS GLU ILE ILE CYS LYS ILE ALA SEQRES 2 B 269 GLN THR ARG LEU ASP GLU THR ALA ALA LYS ALA VAL LYS SEQRES 3 B 269 GLU LEU LEU PRO GLU SER ALA GLU GLY ASP LEU SER SER SEQRES 4 B 269 LEU CYS LEU TRP ALA ASP ARG VAL LYS PHE ARG TYR HIS SEQRES 5 B 269 TRP SER SER PRO LEU HIS TYR ILE ASN THR PRO ASP ALA SEQRES 6 B 269 CYS SER TYR GLN TYR ASN ARG ASP CYS LYS ASP GLU SER SEQRES 7 B 269 GLY GLU LYS GLY ARG CYS VAL ALA GLY ALA ILE TYR ASN SEQRES 8 B 269 TYR THR THR GLN LEU LEU SER TYR LYS THR ALA ALA SER SEQRES 9 B 269 SER GLN SER GLN TYR ASN LEU THR GLU ALA LEU LEU PHE SEQRES 10 B 269 VAL SER HIS PHE MET GLY ASP ILE HIS GLN PRO LEU HIS SEQRES 11 B 269 VAL SER TYR ALA SER ASP LYS GLY GLY ASN THR ILE GLU SEQRES 12 B 269 VAL HIS TRP TYR THR ARG LYS ALA ASN LEU HIS HIS ILE SEQRES 13 B 269 TRP ASP SER ASN ILE ILE GLU THR ALA GLU ALA ASP LEU SEQRES 14 B 269 TYR ASN SER ALA LEU GLU GLY MET VAL ASP ALA LEU LYS SEQRES 15 B 269 LYS ASN ILE THR THR GLU TRP ALA ASP GLN VAL LYS ARG SEQRES 16 B 269 TRP GLU THR CYS THR LYS LYS THR ALA CYS PRO ASP ILE SEQRES 17 B 269 TYR ALA SER GLU GLY ILE GLN ALA ALA CYS ASP TRP ALA SEQRES 18 B 269 TYR LYS GLY VAL THR GLU GLY ASP THR LEU GLU ASP GLU SEQRES 19 B 269 TYR PHE TYR SER ARG LEU PRO ILE VAL TYR GLN ARG LEU SEQRES 20 B 269 ALA GLN GLY GLY VAL ARG LEU ALA ALA THR LEU ASN ARG SEQRES 21 B 269 ILE PHE GLY HIS HIS HIS HIS HIS HIS MODRES 4CXV ASN A 91 ASN GLYCOSYLATION SITE MODRES 4CXV ASN A 110 ASN GLYCOSYLATION SITE MODRES 4CXV ASN A 184 ASN GLYCOSYLATION SITE MODRES 4CXV ASN B 91 ASN GLYCOSYLATION SITE MODRES 4CXV ASN B 110 ASN GLYCOSYLATION SITE MODRES 4CXV ASN B 184 ASN GLYCOSYLATION SITE HET NAG C 1 14 HET NAG C 2 14 HET BMA C 3 11 HET MAN C 4 11 HET NAG D 1 14 HET NAG D 2 14 HET NAG E 1 14 HET NAG E 2 14 HET BMA E 3 11 HET MAN E 4 11 HET MAN E 5 11 HET MAN E 6 11 HET NAG F 1 14 HET NAG F 2 14 HET NAG G 1 14 HET NAG G 2 14 HET BMA G 3 11 HET NAG A 361 14 HET PO4 A 401 5 HET ZN A 431 1 HET ZN A 432 1 HET ZN A 433 1 HET PO4 B 401 5 HET ZN B 431 1 HET ZN B 432 1 HET ZN B 433 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM PO4 PHOSPHATE ION HETNAM ZN ZINC ION HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 3 NAG 11(C8 H15 N O6) FORMUL 3 BMA 3(C6 H12 O6) FORMUL 3 MAN 4(C6 H12 O6) FORMUL 9 PO4 2(O4 P 3-) FORMUL 10 ZN 6(ZN 2+) FORMUL 17 HOH *426(H2 O) HELIX 1 1 GLY A 2 ARG A 16 1 15 HELIX 2 2 ASP A 18 LEU A 29 1 12 HELIX 3 3 PRO A 30 GLU A 34 5 5 HELIX 4 4 ASP A 36 CYS A 41 5 6 HELIX 5 5 LEU A 42 VAL A 47 1 6 HELIX 6 6 TYR A 51 TYR A 59 5 9 HELIX 7 7 GLN A 69 CYS A 74 1 6 HELIX 8 8 CYS A 84 LEU A 97 1 14 HELIX 9 9 ASN A 110 ILE A 125 1 16 HELIX 10 10 HIS A 126 LEU A 129 5 4 HELIX 11 11 SER A 135 LYS A 137 5 3 HELIX 12 12 LEU A 153 SER A 159 1 7 HELIX 13 13 SER A 159 TYR A 170 1 12 HELIX 14 14 ALA A 173 GLU A 188 1 16 HELIX 15 15 TRP A 189 THR A 198 1 10 HELIX 16 16 CYS A 205 TRP A 220 1 16 HELIX 17 17 GLU A 232 GLY A 263 1 32 HELIX 18 18 GLY B 2 ARG B 16 1 15 HELIX 19 19 ASP B 18 LEU B 29 1 12 HELIX 20 20 PRO B 30 GLU B 34 5 5 HELIX 21 21 ASP B 36 CYS B 41 5 6 HELIX 22 22 LEU B 42 VAL B 47 1 6 HELIX 23 23 TYR B 51 TYR B 59 5 9 HELIX 24 24 GLN B 69 CYS B 74 1 6 HELIX 25 25 CYS B 84 LEU B 97 1 14 HELIX 26 26 ASN B 110 ILE B 125 1 16 HELIX 27 27 HIS B 126 LEU B 129 5 4 HELIX 28 28 SER B 135 LYS B 137 5 3 HELIX 29 29 LEU B 153 SER B 159 1 7 HELIX 30 30 SER B 159 TYR B 170 1 12 HELIX 31 31 ALA B 173 GLU B 188 1 16 HELIX 32 32 TRP B 189 THR B 198 1 10 HELIX 33 33 CYS B 205 TRP B 220 1 16 HELIX 34 34 GLU B 232 GLY B 263 1 32 SHEET 1 AA 2 ILE A 60 THR A 62 0 SHEET 2 AA 2 VAL A 131 TYR A 133 1 O SER A 132 N THR A 62 SHEET 1 AB 3 ARG A 149 ASN A 152 0 SHEET 2 AB 3 GLU A 143 TRP A 146 -1 O VAL A 144 N ALA A 151 SHEET 3 AB 3 THR A 230 LEU A 231 1 N LEU A 231 O HIS A 145 SHEET 1 BA 2 ILE B 60 THR B 62 0 SHEET 2 BA 2 VAL B 131 TYR B 133 1 O SER B 132 N THR B 62 SHEET 1 BB 3 ARG B 149 ASN B 152 0 SHEET 2 BB 3 GLU B 143 TRP B 146 -1 O VAL B 144 N ALA B 151 SHEET 3 BB 3 THR B 230 LEU B 231 1 N LEU B 231 O HIS B 145 SSBOND 1 CYS A 10 CYS A 41 1555 1555 2.04 SSBOND 2 CYS A 66 CYS A 218 1555 1555 2.07 SSBOND 3 CYS A 74 CYS A 84 1555 1555 2.07 SSBOND 4 CYS A 199 CYS A 205 1555 1555 2.08 SSBOND 5 CYS B 10 CYS B 41 1555 1555 2.04 SSBOND 6 CYS B 66 CYS B 218 1555 1555 2.06 SSBOND 7 CYS B 74 CYS B 84 1555 1555 2.08 SSBOND 8 CYS B 199 CYS B 205 1555 1555 2.08 LINK ND2 ASN A 91 C1 NAG C 1 1555 1555 1.45 LINK ND2 ASN A 110 C1 NAG D 1 1555 1555 1.44 LINK ND2 ASN A 184 C1 NAG A 361 1555 1555 1.44 LINK ND2 ASN B 91 C1 NAG E 1 1555 1555 1.44 LINK ND2 ASN B 110 C1 NAG F 1 1555 1555 1.46 LINK ND2 ASN B 184 C1 NAG G 1 1555 1555 1.44 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.43 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.44 LINK O3 BMA C 3 C1 MAN C 4 1555 1555 1.44 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.44 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.43 LINK O4 NAG E 2 C1 BMA E 3 1555 1555 1.44 LINK O6 BMA E 3 C1 MAN E 4 1555 1555 1.43 LINK O3 BMA E 3 C1 MAN E 6 1555 1555 1.45 LINK O6 MAN E 4 C1 MAN E 5 1555 1555 1.45 LINK O4 NAG F 1 C1 NAG F 2 1555 1555 1.44 LINK O4 NAG G 1 C1 NAG G 2 1555 1555 1.44 LINK O4 NAG G 2 C1 BMA G 3 1555 1555 1.44 LINK O TRP A 1 ZN ZN A 433 1555 1555 2.17 LINK NE2 HIS A 6 ZN ZN A 433 1555 1555 1.99 LINK OD1 ASP A 45 ZN ZN A 431 1555 1555 2.48 LINK ND1 HIS A 58 ZN ZN A 431 1555 1555 2.25 LINK NE2 HIS A 120 ZN ZN A 431 1555 1555 2.15 LINK OD2 ASP A 124 ZN ZN A 431 1555 1555 2.18 LINK OD1 ASP A 124 ZN ZN A 433 1555 1555 2.05 LINK NE2 HIS A 130 ZN ZN A 432 1555 1555 2.15 LINK NE2 HIS A 154 ZN ZN A 432 1555 1555 2.28 LINK OD1 ASP A 158 ZN ZN A 432 1555 1555 2.62 LINK OD2 ASP A 158 ZN ZN A 432 1555 1555 2.10 LINK O3 PO4 A 401 ZN ZN A 431 1555 1555 2.07 LINK O2 PO4 A 401 ZN ZN A 431 1555 1555 2.17 LINK O4 PO4 A 401 ZN ZN A 432 1555 1555 2.12 LINK O2 PO4 A 401 ZN ZN A 433 1555 1555 1.80 LINK ZN ZN A 432 O HOH A2117 1555 1555 1.80 LINK O TRP B 1 ZN ZN B 433 1555 1555 2.16 LINK NE2 HIS B 6 ZN ZN B 433 1555 1555 2.00 LINK OD1 ASP B 45 ZN ZN B 431 1555 1555 2.36 LINK ND1 HIS B 58 ZN ZN B 431 1555 1555 2.24 LINK NE2 HIS B 120 ZN ZN B 431 1555 1555 2.14 LINK OD2 ASP B 124 ZN ZN B 431 1555 1555 2.22 LINK OD1 ASP B 124 ZN ZN B 433 1555 1555 2.05 LINK NE2 HIS B 130 ZN ZN B 432 1555 1555 2.15 LINK NE2 HIS B 154 ZN ZN B 432 1555 1555 2.30 LINK OD2 ASP B 158 ZN ZN B 432 1555 1555 2.09 LINK OD1 ASP B 158 ZN ZN B 432 1555 1555 2.59 LINK O3 PO4 B 401 ZN ZN B 431 1555 1555 2.20 LINK O2 PO4 B 401 ZN ZN B 431 1555 1555 2.44 LINK O1 PO4 B 401 ZN ZN B 432 1555 1555 1.95 LINK O3 PO4 B 401 ZN ZN B 433 1555 1555 1.91 LINK ZN ZN B 432 O HOH B2102 1555 1555 1.98 CRYST1 45.524 52.870 60.841 71.34 78.63 76.62 P 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 0.021966 -0.005225 -0.003043 0.00000 SCALE2 0.000000 0.019442 -0.005839 0.00000 SCALE3 0.000000 0.000000 0.017505 0.00000