HEADER OXIDOREDUCTASE 07-FEB-23 8CH4 TITLE CRYSTAL STRUCTURE OF THE RING CLEAVING DIOXYGENASE 5-NITROSALICYLATE TITLE 2 1,2-DIOXYGENASE FROM BRADYRHIZOBIUM SP. COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5-NITROSALICYLIC ACID 1,2-DIOXYGENASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: 5NSA 1,2-DIOXYGENASE,5-NITROANTHRANILIC ACID DEGRADATION COMPND 5 PROTEIN B; COMPND 6 EC: 1.13.11.64; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BRADYRHIZOBIUM SP. JS329; SOURCE 3 ORGANISM_TAXID: 722413; SOURCE 4 GENE: NAAB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PJS804 KEYWDS OXIDASE, CUPIN FOLD, BETA-BARREL, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.FERRARONI,A.STOLZ,E.EPPINGER REVDAT 2 12-JUL-23 8CH4 1 JRNL REVDAT 1 05-JUL-23 8CH4 0 JRNL AUTH E.EPPINGER,A.STOLZ,M.FERRARONI JRNL TITL CRYSTAL STRUCTURE OF THE MONOCUPIN RING-CLEAVING DIOXYGENASE JRNL TITL 2 5-NITROSALICYLATE 1,2-DIOXYGENASE FROM BRADYRHIZOBIUM SP. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 79 632 2023 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 37326584 JRNL DOI 10.1107/S2059798323004199 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 44632 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) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2241 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3222 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.4160 REMARK 3 BIN FREE R VALUE SET COUNT : 150 REMARK 3 BIN FREE R VALUE : 0.4130 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5689 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 157 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.31000 REMARK 3 B22 (A**2) : -4.88000 REMARK 3 B33 (A**2) : -1.74000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.63000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.243 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.214 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.287 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.090 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5857 ; 0.006 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7960 ; 1.364 ; 1.628 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 723 ; 7.811 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 293 ;32.673 ;22.628 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 907 ;17.105 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ; 9.717 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 740 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4505 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2898 ; 3.197 ; 4.596 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3616 ; 4.710 ; 6.881 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2959 ; 4.258 ; 4.752 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): 9377 ; 8.458 ;62.595 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: NULL REMARK 4 REMARK 4 8CH4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1292128503. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAR-19 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 : ELETTRA REMARK 200 BEAMLINE : 11.2C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MANOCHROMATOR REMARK 200 OPTICS : LN2 CLOSED LOOP COOLING REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46889 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 48.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.16600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0900 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) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.58700 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% MPD, 5% PEG 400, 100 MM TRIS-HCL REMARK 280 PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 296K 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 71.58650 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 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 180 REMARK 465 SER A 181 REMARK 465 THR A 182 REMARK 465 HIS A 183 REMARK 465 THR A 184 REMARK 465 TRP A 185 REMARK 465 SER A 186 REMARK 465 ASN A 187 REMARK 465 THR A 188 REMARK 465 LYS A 189 REMARK 465 ALA A 190 REMARK 465 PRO A 191 REMARK 465 GLU A 192 REMARK 465 VAL A 193 REMARK 465 SER A 194 REMARK 465 LYS A 195 REMARK 465 THR A 196 REMARK 465 GLN A 197 REMARK 465 ALA A 198 REMARK 465 ALA A 199 REMARK 465 LYS A 200 REMARK 465 GLU A 201 REMARK 465 LEU A 202 REMARK 465 LEU A 203 REMARK 465 LYS A 204 REMARK 465 GLN A 205 REMARK 465 GLY A 206 REMARK 465 GLU A 207 REMARK 465 THR B 182 REMARK 465 HIS B 183 REMARK 465 THR B 184 REMARK 465 TRP B 185 REMARK 465 SER B 186 REMARK 465 ASN B 187 REMARK 465 THR B 188 REMARK 465 LYS B 189 REMARK 465 ALA B 190 REMARK 465 PRO B 191 REMARK 465 GLU B 192 REMARK 465 VAL B 193 REMARK 465 SER B 194 REMARK 465 LYS B 195 REMARK 465 THR B 196 REMARK 465 GLN B 197 REMARK 465 ALA B 198 REMARK 465 ALA B 199 REMARK 465 LYS B 200 REMARK 465 GLU B 201 REMARK 465 LEU B 202 REMARK 465 LEU B 203 REMARK 465 LYS B 204 REMARK 465 GLN B 205 REMARK 465 GLY B 206 REMARK 465 GLU B 207 REMARK 465 GLY C 180 REMARK 465 SER C 181 REMARK 465 THR C 182 REMARK 465 HIS C 183 REMARK 465 THR C 184 REMARK 465 TRP C 185 REMARK 465 SER C 186 REMARK 465 ASN C 187 REMARK 465 THR C 188 REMARK 465 LYS C 189 REMARK 465 ALA C 190 REMARK 465 PRO C 191 REMARK 465 GLU C 192 REMARK 465 VAL C 193 REMARK 465 SER C 194 REMARK 465 LYS C 195 REMARK 465 THR C 196 REMARK 465 GLN C 197 REMARK 465 ALA C 198 REMARK 465 ALA C 199 REMARK 465 LYS C 200 REMARK 465 GLU C 201 REMARK 465 LEU C 202 REMARK 465 LEU C 203 REMARK 465 LYS C 204 REMARK 465 GLN C 205 REMARK 465 GLY C 206 REMARK 465 GLU C 207 REMARK 465 HIS D 183 REMARK 465 THR D 184 REMARK 465 TRP D 185 REMARK 465 SER D 186 REMARK 465 ASN D 187 REMARK 465 THR D 188 REMARK 465 LYS D 189 REMARK 465 ALA D 190 REMARK 465 PRO D 191 REMARK 465 GLU D 192 REMARK 465 VAL D 193 REMARK 465 SER D 194 REMARK 465 LYS D 195 REMARK 465 THR D 196 REMARK 465 GLN D 197 REMARK 465 ALA D 198 REMARK 465 ALA D 199 REMARK 465 LYS D 200 REMARK 465 GLU D 201 REMARK 465 LEU D 202 REMARK 465 LEU D 203 REMARK 465 LYS D 204 REMARK 465 GLN D 205 REMARK 465 GLY D 206 REMARK 465 GLU D 207 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 2 CG CD CE NZ REMARK 470 LYS A 6 CG CD CE NZ REMARK 470 GLU A 18 CG CD OE1 OE2 REMARK 470 ASP A 49 CG OD1 OD2 REMARK 470 ARG A 51 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 56 CG CD NE CZ NH1 NH2 REMARK 470 TYR A 58 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 70 CG CD OE1 OE2 REMARK 470 LYS B 2 CG CD CE NZ REMARK 470 LYS B 6 CG CD CE NZ REMARK 470 GLU B 18 CG CD OE1 OE2 REMARK 470 ASP B 22 CG OD1 OD2 REMARK 470 LYS B 48 CG CD CE NZ REMARK 470 ARG B 51 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 56 CG CD NE CZ NH1 NH2 REMARK 470 TYR B 58 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU B 70 CG CD OE1 OE2 REMARK 470 LYS B 72 CG CD CE NZ REMARK 470 LYS C 2 CG CD CE NZ REMARK 470 LYS C 6 CG CD CE NZ REMARK 470 ASP C 7 CG OD1 OD2 REMARK 470 LYS C 19 CG CD CE NZ REMARK 470 ARG C 44 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 48 CG CD CE NZ REMARK 470 ARG C 51 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 56 CG CD NE CZ NH1 NH2 REMARK 470 TYR C 58 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS C 72 CG CD CE NZ REMARK 470 ARG C 139 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 179 CG CD CE NZ REMARK 470 LYS D 2 CG CD CE NZ REMARK 470 GLU D 18 CG CD OE1 OE2 REMARK 470 ARG D 51 CG CD NE CZ NH1 NH2 REMARK 470 ARG D 56 CZ NH1 NH2 REMARK 470 TYR D 58 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU D 70 CG CD OE1 OE2 REMARK 470 ARG D 139 CG CD NE CZ NH1 NH2 REMARK 470 LYS D 179 CG CD CE NZ REMARK 470 THR D 182 OG1 CG2 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 B 403 O HOH B 435 2.11 REMARK 500 O HOH A 410 O HOH A 436 2.15 REMARK 500 O HOH B 431 O HOH B 432 2.17 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 ARG A 57 61.64 -103.19 REMARK 500 ARG B 51 47.78 -88.10 REMARK 500 ARG B 57 69.02 -102.16 REMARK 500 SER B 95 122.17 -39.54 REMARK 500 THR B 141 -168.21 -118.64 REMARK 500 MET D 1 114.09 -162.30 REMARK 500 PRO D 131 154.25 -49.53 REMARK 500 PRO D 168 -179.65 -66.13 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 FE A 301 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 96 NE2 REMARK 620 2 HIS A 98 NE2 98.5 REMARK 620 3 HIS A 136 NE2 83.9 98.5 REMARK 620 4 HOH A 410 O 163.8 85.1 111.4 REMARK 620 5 HOH A 415 O 75.9 167.3 92.3 97.3 REMARK 620 6 HOH A 432 O 88.9 97.3 163.5 74.9 71.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 301 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 96 NE2 REMARK 620 2 HIS B 98 NE2 98.6 REMARK 620 3 HIS B 136 NE2 93.3 102.0 REMARK 620 4 HOH B 403 O 152.2 91.4 109.9 REMARK 620 5 HOH B 416 O 79.5 175.0 82.8 88.3 REMARK 620 6 HOH B 425 O 84.9 82.4 175.5 70.7 92.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE C 301 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 96 NE2 REMARK 620 2 HIS C 98 NE2 110.1 REMARK 620 3 HIS C 136 NE2 84.9 97.5 REMARK 620 4 HOH C 404 O 159.1 90.8 93.5 REMARK 620 5 HOH C 407 O 78.2 171.4 84.7 80.8 REMARK 620 6 HOH C 430 O 91.3 89.3 173.0 87.9 88.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE D 301 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS D 96 NE2 REMARK 620 2 HIS D 98 NE2 98.7 REMARK 620 3 HIS D 136 NE2 89.8 95.6 REMARK 620 4 HOH D 406 O 170.5 87.7 96.6 REMARK 620 5 HOH D 431 O 88.2 98.3 166.1 83.9 REMARK 620 N 1 2 3 4 DBREF 8CH4 A 1 207 UNP D3WZ86 NAAB_BRASZ 1 207 DBREF 8CH4 B 1 207 UNP D3WZ86 NAAB_BRASZ 1 207 DBREF 8CH4 C 1 207 UNP D3WZ86 NAAB_BRASZ 1 207 DBREF 8CH4 D 1 207 UNP D3WZ86 NAAB_BRASZ 1 207 SEQADV 8CH4 FME A 0 UNP D3WZ86 EXPRESSION TAG SEQADV 8CH4 FME B 0 UNP D3WZ86 EXPRESSION TAG SEQADV 8CH4 FME C 0 UNP D3WZ86 EXPRESSION TAG SEQADV 8CH4 FME D 0 UNP D3WZ86 EXPRESSION TAG SEQRES 1 A 208 FME MET LYS TRP SER ASN LYS ASP GLY TYR PRO TRP SER SEQRES 2 A 208 LYS ILE ILE HIS ALA GLU LYS PHE PHE ASP LYS VAL ILE SEQRES 3 A 208 GLN ASN ASP THR ARG PRO GLY LYS TRP GLU TRP ALA ASP SEQRES 4 A 208 VAL VAL SER GLY LEU ARG ASP LEU ASP LYS ASP PRO ARG SEQRES 5 A 208 MET ASN SER GLU ARG ARG TYR VAL ALA ILE VAL ASN GLU SEQRES 6 A 208 ASP VAL GLY LEU GLY GLU THR LYS GLY ILE GLY ILE THR SEQRES 7 A 208 PRO GLY LEU PHE CYS GLY CYS GLN LEU ILE HIS PRO GLY SEQRES 8 A 208 GLU GLU VAL THR SER HIS ARG HIS ASN SER VAL ALA LEU SEQRES 9 A 208 TYR PHE ILE VAL GLU GLY THR GLY GLU LEU GLU VAL GLU SEQRES 10 A 208 GLY GLU VAL TYR SER TYR LYS PRO PHE ASP ILE MET THR SEQRES 11 A 208 CYS PRO ALA TRP SER TYR HIS ALA TRP ARG ALA THR GLY SEQRES 12 A 208 ASP LYS ASP THR LEU MET TYR VAL ILE HIS ASP MET ALA SEQRES 13 A 208 LEU LEU ALA TYR MET ARG ALA LEU PHE TRP GLU GLU PRO SEQRES 14 A 208 LYS GLY SER GLU ASN ILE ARG HIS MET VAL LYS GLY SER SEQRES 15 A 208 THR HIS THR TRP SER ASN THR LYS ALA PRO GLU VAL SER SEQRES 16 A 208 LYS THR GLN ALA ALA LYS GLU LEU LEU LYS GLN GLY GLU SEQRES 1 B 208 FME MET LYS TRP SER ASN LYS ASP GLY TYR PRO TRP SER SEQRES 2 B 208 LYS ILE ILE HIS ALA GLU LYS PHE PHE ASP LYS VAL ILE SEQRES 3 B 208 GLN ASN ASP THR ARG PRO GLY LYS TRP GLU TRP ALA ASP SEQRES 4 B 208 VAL VAL SER GLY LEU ARG ASP LEU ASP LYS ASP PRO ARG SEQRES 5 B 208 MET ASN SER GLU ARG ARG TYR VAL ALA ILE VAL ASN GLU SEQRES 6 B 208 ASP VAL GLY LEU GLY GLU THR LYS GLY ILE GLY ILE THR SEQRES 7 B 208 PRO GLY LEU PHE CYS GLY CYS GLN LEU ILE HIS PRO GLY SEQRES 8 B 208 GLU GLU VAL THR SER HIS ARG HIS ASN SER VAL ALA LEU SEQRES 9 B 208 TYR PHE ILE VAL GLU GLY THR GLY GLU LEU GLU VAL GLU SEQRES 10 B 208 GLY GLU VAL TYR SER TYR LYS PRO PHE ASP ILE MET THR SEQRES 11 B 208 CYS PRO ALA TRP SER TYR HIS ALA TRP ARG ALA THR GLY SEQRES 12 B 208 ASP LYS ASP THR LEU MET TYR VAL ILE HIS ASP MET ALA SEQRES 13 B 208 LEU LEU ALA TYR MET ARG ALA LEU PHE TRP GLU GLU PRO SEQRES 14 B 208 LYS GLY SER GLU ASN ILE ARG HIS MET VAL LYS GLY SER SEQRES 15 B 208 THR HIS THR TRP SER ASN THR LYS ALA PRO GLU VAL SER SEQRES 16 B 208 LYS THR GLN ALA ALA LYS GLU LEU LEU LYS GLN GLY GLU SEQRES 1 C 208 FME MET LYS TRP SER ASN LYS ASP GLY TYR PRO TRP SER SEQRES 2 C 208 LYS ILE ILE HIS ALA GLU LYS PHE PHE ASP LYS VAL ILE SEQRES 3 C 208 GLN ASN ASP THR ARG PRO GLY LYS TRP GLU TRP ALA ASP SEQRES 4 C 208 VAL VAL SER GLY LEU ARG ASP LEU ASP LYS ASP PRO ARG SEQRES 5 C 208 MET ASN SER GLU ARG ARG TYR VAL ALA ILE VAL ASN GLU SEQRES 6 C 208 ASP VAL GLY LEU GLY GLU THR LYS GLY ILE GLY ILE THR SEQRES 7 C 208 PRO GLY LEU PHE CYS GLY CYS GLN LEU ILE HIS PRO GLY SEQRES 8 C 208 GLU GLU VAL THR SER HIS ARG HIS ASN SER VAL ALA LEU SEQRES 9 C 208 TYR PHE ILE VAL GLU GLY THR GLY GLU LEU GLU VAL GLU SEQRES 10 C 208 GLY GLU VAL TYR SER TYR LYS PRO PHE ASP ILE MET THR SEQRES 11 C 208 CYS PRO ALA TRP SER TYR HIS ALA TRP ARG ALA THR GLY SEQRES 12 C 208 ASP LYS ASP THR LEU MET TYR VAL ILE HIS ASP MET ALA SEQRES 13 C 208 LEU LEU ALA TYR MET ARG ALA LEU PHE TRP GLU GLU PRO SEQRES 14 C 208 LYS GLY SER GLU ASN ILE ARG HIS MET VAL LYS GLY SER SEQRES 15 C 208 THR HIS THR TRP SER ASN THR LYS ALA PRO GLU VAL SER SEQRES 16 C 208 LYS THR GLN ALA ALA LYS GLU LEU LEU LYS GLN GLY GLU SEQRES 1 D 208 FME MET LYS TRP SER ASN LYS ASP GLY TYR PRO TRP SER SEQRES 2 D 208 LYS ILE ILE HIS ALA GLU LYS PHE PHE ASP LYS VAL ILE SEQRES 3 D 208 GLN ASN ASP THR ARG PRO GLY LYS TRP GLU TRP ALA ASP SEQRES 4 D 208 VAL VAL SER GLY LEU ARG ASP LEU ASP LYS ASP PRO ARG SEQRES 5 D 208 MET ASN SER GLU ARG ARG TYR VAL ALA ILE VAL ASN GLU SEQRES 6 D 208 ASP VAL GLY LEU GLY GLU THR LYS GLY ILE GLY ILE THR SEQRES 7 D 208 PRO GLY LEU PHE CYS GLY CYS GLN LEU ILE HIS PRO GLY SEQRES 8 D 208 GLU GLU VAL THR SER HIS ARG HIS ASN SER VAL ALA LEU SEQRES 9 D 208 TYR PHE ILE VAL GLU GLY THR GLY GLU LEU GLU VAL GLU SEQRES 10 D 208 GLY GLU VAL TYR SER TYR LYS PRO PHE ASP ILE MET THR SEQRES 11 D 208 CYS PRO ALA TRP SER TYR HIS ALA TRP ARG ALA THR GLY SEQRES 12 D 208 ASP LYS ASP THR LEU MET TYR VAL ILE HIS ASP MET ALA SEQRES 13 D 208 LEU LEU ALA TYR MET ARG ALA LEU PHE TRP GLU GLU PRO SEQRES 14 D 208 LYS GLY SER GLU ASN ILE ARG HIS MET VAL LYS GLY SER SEQRES 15 D 208 THR HIS THR TRP SER ASN THR LYS ALA PRO GLU VAL SER SEQRES 16 D 208 LYS THR GLN ALA ALA LYS GLU LEU LEU LYS GLN GLY GLU HET FME A 0 10 HET FME B 0 10 HET FME C 0 10 HET FME D 0 10 HET FE A 301 1 HET FE B 301 1 HET FE C 301 1 HET FE D 301 1 HETNAM FME N-FORMYLMETHIONINE HETNAM FE FE (III) ION FORMUL 1 FME 4(C6 H11 N O3 S) FORMUL 5 FE 4(FE 3+) FORMUL 9 HOH *157(H2 O) HELIX 1 AA1 ALA A 17 ILE A 25 1 9 HELIX 2 AA2 GLU A 35 LEU A 46 1 12 HELIX 3 AA3 ASP A 47 ASP A 49 5 3 HELIX 4 AA4 ASN A 53 ARG A 56 5 4 HELIX 5 AA5 ASP A 65 GLY A 67 5 3 HELIX 6 AA6 ASP A 153 MET A 160 1 8 HELIX 7 AA7 GLY A 170 GLU A 172 5 3 HELIX 8 AA8 ALA B 17 ILE B 25 1 9 HELIX 9 AA9 GLU B 35 LEU B 46 1 12 HELIX 10 AB1 ASP B 47 ASP B 49 5 3 HELIX 11 AB2 ASN B 53 ARG B 56 5 4 HELIX 12 AB3 ASP B 65 GLY B 67 5 3 HELIX 13 AB4 ASP B 153 MET B 160 1 8 HELIX 14 AB5 GLY B 170 GLU B 172 5 3 HELIX 15 AB6 ALA C 17 ILE C 25 1 9 HELIX 16 AB7 GLU C 35 ASP C 47 1 13 HELIX 17 AB8 ASN C 53 ARG C 56 5 4 HELIX 18 AB9 ASP C 65 GLY C 67 5 3 HELIX 19 AC1 ASP C 153 MET C 160 1 8 HELIX 20 AC2 GLY C 170 GLU C 172 5 3 HELIX 21 AC3 ALA D 17 ILE D 25 1 9 HELIX 22 AC4 TRP D 36 LEU D 46 1 11 HELIX 23 AC5 ASP D 47 ASP D 49 5 3 HELIX 24 AC6 ASP D 65 GLY D 67 5 3 HELIX 25 AC7 ASP D 153 ARG D 161 1 9 HELIX 26 AC8 GLY D 170 GLU D 172 5 3 SHEET 1 AA1 7 SER A 12 HIS A 16 0 SHEET 2 AA1 7 TYR C 58 ASN C 63 -1 O ALA C 60 N ILE A 15 SHEET 3 AA1 7 PHE C 81 ILE C 87 -1 O CYS C 82 N ILE C 61 SHEET 4 AA1 7 THR C 146 HIS C 152 -1 O VAL C 150 N GLY C 83 SHEET 5 AA1 7 ALA C 102 GLU C 108 -1 N LEU C 103 O ILE C 151 SHEET 6 AA1 7 ASP C 126 CYS C 130 -1 O MET C 128 N TYR C 104 SHEET 7 AA1 7 LYS D 33 GLU D 35 -1 O TRP D 34 N ILE C 127 SHEET 1 AA2 7 LYS A 33 TRP A 34 0 SHEET 2 AA2 7 ILE B 127 CYS B 130 -1 O ILE B 127 N TRP A 34 SHEET 3 AA2 7 ALA B 102 GLU B 108 -1 N TYR B 104 O MET B 128 SHEET 4 AA2 7 THR B 146 HIS B 152 -1 O ILE B 151 N LEU B 103 SHEET 5 AA2 7 PHE B 81 ILE B 87 -1 N GLY B 83 O VAL B 150 SHEET 6 AA2 7 TYR B 58 ASN B 63 -1 N VAL B 59 O CYS B 84 SHEET 7 AA2 7 SER D 12 HIS D 16 -1 O ILE D 15 N ALA B 60 SHEET 1 AA3 7 LYS B 33 TRP B 34 0 SHEET 2 AA3 7 ILE A 127 CYS A 130 -1 N ILE A 127 O TRP B 34 SHEET 3 AA3 7 ALA A 102 GLU A 108 -1 N TYR A 104 O MET A 128 SHEET 4 AA3 7 THR A 146 HIS A 152 -1 O ILE A 151 N LEU A 103 SHEET 5 AA3 7 PHE A 81 ILE A 87 -1 N ILE A 87 O THR A 146 SHEET 6 AA3 7 TYR A 58 ASN A 63 -1 N ILE A 61 O CYS A 82 SHEET 7 AA3 7 SER C 12 HIS C 16 -1 O LYS C 13 N VAL A 62 SHEET 1 AA4 6 GLU A 118 TYR A 122 0 SHEET 2 AA4 6 THR A 110 VAL A 115 -1 N LEU A 113 O TYR A 120 SHEET 3 AA4 6 HIS A 136 THR A 141 -1 O ALA A 137 N GLU A 114 SHEET 4 AA4 6 GLU A 92 HIS A 98 -1 N VAL A 93 O TRP A 138 SHEET 5 AA4 6 PHE A 164 GLU A 166 -1 O GLU A 166 N ARG A 97 SHEET 6 AA4 6 ILE A 174 HIS A 176 -1 O ARG A 175 N TRP A 165 SHEET 1 AA5 7 SER B 12 HIS B 16 0 SHEET 2 AA5 7 TYR D 58 ASN D 63 -1 O ALA D 60 N ILE B 15 SHEET 3 AA5 7 PHE D 81 ILE D 87 -1 O CYS D 82 N ILE D 61 SHEET 4 AA5 7 THR D 146 HIS D 152 -1 O THR D 146 N ILE D 87 SHEET 5 AA5 7 ALA D 102 GLU D 108 -1 N LEU D 103 O ILE D 151 SHEET 6 AA5 7 ILE D 127 CYS D 130 -1 O MET D 128 N TYR D 104 SHEET 7 AA5 7 LYS C 33 TRP C 34 -1 N TRP C 34 O ILE D 127 SHEET 1 AA6 6 GLU B 118 TYR B 122 0 SHEET 2 AA6 6 THR B 110 VAL B 115 -1 N LEU B 113 O TYR B 120 SHEET 3 AA6 6 HIS B 136 THR B 141 -1 O ALA B 137 N GLU B 114 SHEET 4 AA6 6 GLU B 92 HIS B 98 -1 N VAL B 93 O TRP B 138 SHEET 5 AA6 6 PHE B 164 GLU B 166 -1 O GLU B 166 N ARG B 97 SHEET 6 AA6 6 ILE B 174 HIS B 176 -1 O ARG B 175 N TRP B 165 SHEET 1 AA7 6 GLU C 118 TYR C 122 0 SHEET 2 AA7 6 THR C 110 VAL C 115 -1 N LEU C 113 O TYR C 120 SHEET 3 AA7 6 HIS C 136 THR C 141 -1 O ARG C 139 N GLU C 112 SHEET 4 AA7 6 GLU C 92 HIS C 98 -1 N VAL C 93 O TRP C 138 SHEET 5 AA7 6 PHE C 164 GLU C 166 -1 O GLU C 166 N ARG C 97 SHEET 6 AA7 6 ILE C 174 HIS C 176 -1 O ARG C 175 N TRP C 165 SHEET 1 AA8 6 GLU D 118 TYR D 122 0 SHEET 2 AA8 6 THR D 110 VAL D 115 -1 N LEU D 113 O TYR D 120 SHEET 3 AA8 6 HIS D 136 THR D 141 -1 O ALA D 137 N GLU D 114 SHEET 4 AA8 6 GLU D 92 HIS D 98 -1 N VAL D 93 O TRP D 138 SHEET 5 AA8 6 PHE D 164 GLU D 166 -1 O GLU D 166 N ARG D 97 SHEET 6 AA8 6 ILE D 174 HIS D 176 -1 O ARG D 175 N TRP D 165 LINK C FME A 0 N MET A 1 1555 1555 1.35 LINK C FME B 0 N MET B 1 1555 1555 1.33 LINK C FME C 0 N MET C 1 1555 1555 1.33 LINK C FME D 0 N MET D 1 1555 1555 1.35 LINK NE2 HIS A 96 FE FE A 301 1555 1555 2.11 LINK NE2 HIS A 98 FE FE A 301 1555 1555 2.25 LINK NE2 HIS A 136 FE FE A 301 1555 1555 2.07 LINK FE FE A 301 O HOH A 410 1555 1555 1.99 LINK FE FE A 301 O HOH A 415 1555 1555 2.17 LINK FE FE A 301 O HOH A 432 1555 1555 2.22 LINK NE2 HIS B 96 FE FE B 301 1555 1555 2.06 LINK NE2 HIS B 98 FE FE B 301 1555 1555 2.26 LINK NE2 HIS B 136 FE FE B 301 1555 1555 2.07 LINK FE FE B 301 O HOH B 403 1555 1555 1.83 LINK FE FE B 301 O HOH B 416 1555 1555 2.22 LINK FE FE B 301 O HOH B 425 1555 1555 2.34 LINK NE2 HIS C 96 FE FE C 301 1555 1555 1.97 LINK NE2 HIS C 98 FE FE C 301 1555 1555 2.14 LINK NE2 HIS C 136 FE FE C 301 1555 1555 2.07 LINK FE FE C 301 O HOH C 404 1555 1555 1.93 LINK FE FE C 301 O HOH C 407 1555 1555 2.10 LINK FE FE C 301 O HOH C 430 1555 1555 2.39 LINK NE2 HIS D 96 FE FE D 301 1555 1555 1.90 LINK NE2 HIS D 98 FE FE D 301 1555 1555 2.22 LINK NE2 HIS D 136 FE FE D 301 1555 1555 2.11 LINK FE FE D 301 O HOH D 406 1555 1555 1.96 LINK FE FE D 301 O HOH D 431 1555 1555 2.19 CISPEP 1 GLU A 167 PRO A 168 0 -15.24 CISPEP 2 GLU B 167 PRO B 168 0 -5.42 CISPEP 3 GLU C 167 PRO C 168 0 -8.19 CISPEP 4 GLU D 167 PRO D 168 0 -10.85 CRYST1 50.427 143.173 60.076 90.00 107.33 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 0.019831 0.000000 0.006189 0.00000 SCALE2 0.000000 0.006985 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017438 0.00000 HETATM 1 N FME A 0 4.912 -24.675 6.890 1.00 69.39 N HETATM 2 CN FME A 0 4.791 -25.601 5.922 1.00 83.26 C HETATM 3 O1 FME A 0 4.433 -25.396 4.758 1.00 81.06 O HETATM 4 CA FME A 0 4.976 -25.006 8.307 1.00 65.32 C HETATM 5 CB FME A 0 3.671 -25.649 8.808 1.00 67.30 C HETATM 6 CG FME A 0 3.670 -25.976 10.283 1.00 70.78 C HETATM 7 SD FME A 0 2.415 -25.000 11.152 1.00 91.56 S HETATM 8 CE FME A 0 2.407 -23.525 10.134 1.00 97.72 C HETATM 9 C FME A 0 6.267 -25.725 8.714 1.00 63.34 C HETATM 10 O FME A 0 7.213 -25.045 9.102 1.00 64.04 O