HEADER LYASE 13-APR-15 4ZA9 TITLE STRUCTURE OF A. NIGER FDC1 IN COMPLEX WITH A PHENYLPYRUVATE DERIVED TITLE 2 ADDUCT TO THE PRENYLATED FLAVIN COFACTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: FDC1; COMPND 3 CHAIN: A; COMPND 4 EC: 4.1.1.61; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ASPERGILLUS NIGER; SOURCE 3 ORGANISM_TAXID: 425011; SOURCE 4 GENE: AN03G06590; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS UBID-ENZYME, PRENYLATED FLAVIN, (DE)CARBOXYLASE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR K.A.P.PAYNE,D.LEYS REVDAT 2 01-JUL-15 4ZA9 1 JRNL REVDAT 1 17-JUN-15 4ZA9 0 JRNL AUTH K.A.PAYNE,M.D.WHITE,K.FISHER,B.KHARA,S.S.BAILEY,D.PARKER, JRNL AUTH 2 N.J.RATTRAY,D.K.TRIVEDI,R.GOODACRE,R.BEVERIDGE,P.BARRAN, JRNL AUTH 3 S.E.RIGBY,N.S.SCRUTTON,S.HAY,D.LEYS JRNL TITL NEW COFACTOR SUPPORTS ALPHA , BETA-UNSATURATED ACID JRNL TITL 2 DECARBOXYLATION VIA 1,3-DIPOLAR CYCLOADDITION. JRNL REF NATURE V. 522 502 2015 JRNL REFN ESSN 1476-4687 JRNL PMID 26083754 JRNL DOI 10.1038/NATURE14560 REMARK 2 REMARK 2 RESOLUTION. 1.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 63.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 264342 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) : 0.131 REMARK 3 R VALUE (WORKING SET) : 0.130 REMARK 3 FREE R VALUE : 0.145 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 13893 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) : 1.01 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.04 REMARK 3 REFLECTION IN BIN (WORKING SET) : 18314 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.99 REMARK 3 BIN R VALUE (WORKING SET) : 0.2460 REMARK 3 BIN FREE R VALUE SET COUNT : 893 REMARK 3 BIN FREE R VALUE : 0.2600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3807 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 465 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.38 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.96000 REMARK 3 B22 (A**2) : -1.97000 REMARK 3 B33 (A**2) : 1.01000 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): 0.019 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.020 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.014 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.602 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.978 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.972 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4216 ; 0.029 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2824 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5783 ; 2.250 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6923 ; 4.353 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 552 ; 6.408 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 171 ;33.731 ;23.743 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 685 ;11.400 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;20.328 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 629 ; 0.198 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4827 ; 0.026 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 840 ; 0.023 ; 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): 2649 ; 1.980 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1055 ; 6.899 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4318 ; 2.715 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1567 ; 4.309 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1465 ; 5.787 ; 4.500 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): 7039 ; 4.631 ; 3.000 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 : 1.40 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 4ZA9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000208925. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 264342 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.010 REMARK 200 RESOLUTION RANGE LOW (A) : 63.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.02700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.31400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M POTASSIUM THIOCYANATE, BIS-TRIS REMARK 280 PROPANE 6.5, 20 % W/V PEG 3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 48.02500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.92500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 48.02500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.92500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 727 LIES ON A SPECIAL POSITION. 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 MET A 1 REMARK 465 SER A 2 REMARK 465 ASN A 500 REMARK 465 LEU A 501 REMARK 465 GLU A 502 REMARK 465 HIS A 503 REMARK 465 HIS A 504 REMARK 465 HIS A 505 REMARK 465 HIS A 506 REMARK 465 HIS A 507 REMARK 465 HIS A 508 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 ALA A 3 N CB REMARK 470 LYS A 60 CG CD CE NZ REMARK 470 LYS A 75 CD CE NZ REMARK 470 ASP A 129 OD1 OD2 REMARK 470 GLU A 136 CD OE1 OE2 REMARK 470 LYS A 179 CE NZ REMARK 470 ARG A 204 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 273 CG CD OE1 OE2 REMARK 470 GLU A 410 CG CD OE1 OE2 REMARK 470 LYS A 412 CG CD CE NZ REMARK 470 ASP A 433 CG OD1 OD2 REMARK 470 ARG A 470 CZ NH1 NH2 REMARK 470 LYS A 495 CG CD CE NZ REMARK 470 SER A 499 CB OG 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 984 O HOH A 1047 1.74 REMARK 500 O HOH A 947 O HOH A 1132 1.99 REMARK 500 O HOH A 1038 O HOH A 1045 2.04 REMARK 500 O HOH A 748 O HOH A 1069 2.11 REMARK 500 CE MET A 59 O HOH A 971 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 785 O HOH A 785 2655 1.08 REMARK 500 O HOH A 742 O HOH A 944 2655 1.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 15 CG GLU A 15 CD 0.095 REMARK 500 GLU A 15 CD GLU A 15 OE2 0.069 REMARK 500 LYS A 18 CE LYS A 18 NZ 0.156 REMARK 500 LYS A 18 CE LYS A 18 NZ 0.179 REMARK 500 GLU A 202 CD GLU A 202 OE1 0.071 REMARK 500 GLU A 202 CD GLU A 202 OE2 0.108 REMARK 500 MET A 221 CG MET A 221 SD -0.174 REMARK 500 SER A 243 CA SER A 243 CB 0.097 REMARK 500 GLU A 282 CD GLU A 282 OE1 0.080 REMARK 500 ARG A 370 CZ ARG A 370 NH2 0.126 REMARK 500 GLU A 377 CD GLU A 377 OE2 0.083 REMARK 500 ARG A 380 CA ARG A 380 CB 0.325 REMARK 500 LYS A 381 CE LYS A 381 NZ 0.215 REMARK 500 ARG A 382 CD ARG A 382 NE -0.102 REMARK 500 ASN A 389 CG ASN A 389 ND2 -0.213 REMARK 500 ARG A 452 CG ARG A 452 CD 0.168 REMARK 500 GLU A 473 CA GLU A 473 CB 0.208 REMARK 500 LYS A 486 CD LYS A 486 CE -0.222 REMARK 500 REMARK 500 REMARK: NULL 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 LYS A 18 CD - CE - NZ ANGL. DEV. = 14.8 DEGREES REMARK 500 ARG A 42 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 83 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 MET A 156 CG - SD - CE ANGL. DEV. = -11.9 DEGREES REMARK 500 GLU A 202 OE1 - CD - OE2 ANGL. DEV. = 7.7 DEGREES REMARK 500 MET A 221 CG - SD - CE ANGL. DEV. = -18.0 DEGREES REMARK 500 ASP A 254 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 GLU A 377 CG - CD - OE2 ANGL. DEV. = -17.9 DEGREES REMARK 500 ARG A 380 CG - CD - NE ANGL. DEV. = 18.8 DEGREES REMARK 500 ARG A 380 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 398 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ASP A 404 CB - CG - OD1 ANGL. DEV. = -6.8 DEGREES REMARK 500 ASP A 404 CB - CG - OD2 ANGL. DEV. = 11.7 DEGREES REMARK 500 ARG A 435 NE - CZ - NH1 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG A 452 CG - CD - NE ANGL. DEV. = -16.3 DEGREES REMARK 500 ASP A 484 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 491 CB - CG - OD2 ANGL. DEV. = -6.2 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 LEU A 34 -37.04 70.60 REMARK 500 MET A 59 172.38 -50.99 REMARK 500 LYS A 60 138.36 -179.77 REMARK 500 TYR A 154 17.63 -151.21 REMARK 500 ASP A 433 49.26 -109.13 REMARK 500 MET A 443 -77.02 -94.12 REMARK 500 THR A 467 -82.57 -119.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 83 0.10 SIDE CHAIN REMARK 500 GLU A 377 0.09 SIDE CHAIN REMARK 500 ARG A 380 0.08 SIDE CHAIN 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 A1164 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A1165 DISTANCE = 7.08 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 MN A 602 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 168 OD1 REMARK 620 2 HIS A 191 ND1 91.3 REMARK 620 3 GLU A 233 OE2 96.1 172.3 REMARK 620 4 4MJ A 601 O2 95.2 88.8 92.9 REMARK 620 5 HOH A 733 O 177.8 86.5 86.1 84.2 REMARK 620 6 HOH A 823 O 90.3 85.9 91.7 172.4 90.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 603 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TRP A 169 O REMARK 620 2 ALA A 222 O 97.3 REMARK 620 3 SER A 223 O 75.7 75.7 REMARK 620 4 MET A 225 O 170.1 72.8 101.2 REMARK 620 5 GLU A 233 OE2 69.5 106.6 145.2 112.8 REMARK 620 6 4MJ A 601 O2 80.7 174.7 108.4 109.1 68.1 REMARK 620 7 4MJ A 601 O4 95.5 136.9 67.9 92.0 116.5 48.4 REMARK 620 8 HOH A 733 O 120.9 120.9 151.0 66.1 57.9 57.0 86.0 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 604 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 421 O REMARK 620 2 ASP A 427 OD2 85.7 REMARK 620 3 ASP A 459 O 86.8 98.2 REMARK 620 4 LEU A 461 O 103.9 160.3 99.5 REMARK 620 5 HOH A1083 O 74.0 78.4 160.7 87.7 REMARK 620 6 HOH A1014 O 145.4 110.0 119.5 53.1 79.1 REMARK 620 7 HOH A1019 O 165.0 81.5 87.3 90.7 110.7 48.2 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 4MJ A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 604 DBREF 4ZA9 A 1 500 UNP A2QHE5 A2QHE5_ASPNC 1 500 SEQADV 4ZA9 LEU A 501 UNP A2QHE5 EXPRESSION TAG SEQADV 4ZA9 GLU A 502 UNP A2QHE5 EXPRESSION TAG SEQADV 4ZA9 HIS A 503 UNP A2QHE5 EXPRESSION TAG SEQADV 4ZA9 HIS A 504 UNP A2QHE5 EXPRESSION TAG SEQADV 4ZA9 HIS A 505 UNP A2QHE5 EXPRESSION TAG SEQADV 4ZA9 HIS A 506 UNP A2QHE5 EXPRESSION TAG SEQADV 4ZA9 HIS A 507 UNP A2QHE5 EXPRESSION TAG SEQADV 4ZA9 HIS A 508 UNP A2QHE5 EXPRESSION TAG SEQRES 1 A 508 MET SER ALA GLN PRO ALA HIS LEU CYS PHE ARG SER PHE SEQRES 2 A 508 VAL GLU ALA LEU LYS VAL ASP ASN ASP LEU VAL GLU ILE SEQRES 3 A 508 ASN THR PRO ILE ASP PRO ASN LEU GLU ALA ALA ALA ILE SEQRES 4 A 508 THR ARG ARG VAL CYS GLU THR ASN ASP LYS ALA PRO LEU SEQRES 5 A 508 PHE ASN ASN LEU ILE GLY MET LYS ASN GLY LEU PHE ARG SEQRES 6 A 508 ILE LEU GLY ALA PRO GLY SER LEU ARG LYS SER SER ALA SEQRES 7 A 508 ASP ARG TYR GLY ARG LEU ALA ARG HIS LEU ALA LEU PRO SEQRES 8 A 508 PRO THR ALA SER MET ARG GLU ILE LEU ASP LYS MET LEU SEQRES 9 A 508 SER ALA SER ASP MET PRO PRO ILE PRO PRO THR ILE VAL SEQRES 10 A 508 PRO THR GLY PRO CYS LYS GLU ASN SER LEU ASP ASP SER SEQRES 11 A 508 GLU PHE ASP LEU THR GLU LEU PRO VAL PRO LEU ILE HIS SEQRES 12 A 508 LYS SER ASP GLY GLY LYS TYR ILE GLN THR TYR GLY MET SEQRES 13 A 508 HIS ILE VAL GLN SER PRO ASP GLY THR TRP THR ASN TRP SEQRES 14 A 508 SER ILE ALA ARG ALA MET VAL HIS ASP LYS ASN HIS LEU SEQRES 15 A 508 THR GLY LEU VAL ILE PRO PRO GLN HIS ILE TRP GLN ILE SEQRES 16 A 508 HIS GLN MET TRP LYS LYS GLU GLY ARG SER ASP VAL PRO SEQRES 17 A 508 TRP ALA LEU ALA PHE GLY VAL PRO PRO ALA ALA ILE MET SEQRES 18 A 508 ALA SER SER MET PRO ILE PRO ASP GLY VAL THR GLU ALA SEQRES 19 A 508 GLY TYR VAL GLY ALA MET THR GLY SER SER LEU GLU LEU SEQRES 20 A 508 VAL LYS CYS ASP THR ASN ASP LEU TYR VAL PRO ALA THR SEQRES 21 A 508 SER GLU ILE VAL LEU GLU GLY THR LEU SER ILE SER GLU SEQRES 22 A 508 THR GLY PRO GLU GLY PRO PHE GLY GLU MET HIS GLY TYR SEQRES 23 A 508 ILE PHE PRO GLY ASP THR HIS LEU GLY ALA LYS TYR LYS SEQRES 24 A 508 VAL ASN ARG ILE THR TYR ARG ASN ASN ALA ILE MET PRO SEQRES 25 A 508 MET SER SER CYS GLY ARG LEU THR ASP GLU THR HIS THR SEQRES 26 A 508 MET ILE GLY SER LEU ALA ALA ALA GLU ILE ARG LYS LEU SEQRES 27 A 508 CYS GLN GLN ASN ASP LEU PRO ILE THR ASP ALA PHE ALA SEQRES 28 A 508 PRO PHE GLU SER GLN VAL THR TRP VAL ALA LEU ARG VAL SEQRES 29 A 508 ASP THR GLU LYS LEU ARG ALA MET LYS THR THR SER GLU SEQRES 30 A 508 GLY PHE ARG LYS ARG VAL GLY ASP VAL VAL PHE ASN HIS SEQRES 31 A 508 LYS ALA GLY TYR THR ILE HIS ARG LEU VAL LEU VAL GLY SEQRES 32 A 508 ASP ASP ILE ASP VAL TYR GLU GLY LYS ASP VAL LEU TRP SEQRES 33 A 508 ALA PHE SER THR ARG CYS ARG PRO GLY MET ASP GLU THR SEQRES 34 A 508 LEU PHE GLU ASP VAL ARG GLY PHE PRO LEU ILE PRO TYR SEQRES 35 A 508 MET GLY HIS GLY ASN GLY PRO ALA HIS ARG GLY GLY LYS SEQRES 36 A 508 VAL VAL SER ASP ALA LEU MET PRO THR GLU TYR THR THR SEQRES 37 A 508 GLY ARG ASN TRP GLU ALA ALA ASP PHE ASN GLN SER TYR SEQRES 38 A 508 PRO GLU ASP LEU LYS GLN LYS VAL LEU ASP ASN TRP THR SEQRES 39 A 508 LYS MET GLY PHE SER ASN LEU GLU HIS HIS HIS HIS HIS SEQRES 40 A 508 HIS HET 4MJ A 601 45 HET MN A 602 1 HET K A 603 1 HET K A 604 1 HETNAM 4MJ 1-DEOXY-5-O-PHOSPHONO-1-[(1S)-3,3,4,5-TETRAMETHYL-9,11- HETNAM 2 4MJ DIOXO-1-(PHENYLACETYL)-2,3,8,9,10,11-HEXAHYDRO-1H,7H- HETNAM 3 4MJ QUINOLINO[1,8-FG]PTERIDIN-7-YL]-D-RIBITOL HETNAM MN MANGANESE (II) ION HETNAM K POTASSIUM ION HETSYN 4MJ PHENYLPYRUVATE DERIVED ADDUCT TO PRENYLATED FMN HETSYN 2 4MJ COFACTOR FORMUL 2 4MJ C30 H37 N4 O10 P FORMUL 3 MN MN 2+ FORMUL 4 K 2(K 1+) FORMUL 6 HOH *465(H2 O) HELIX 1 AA1 PRO A 5 LEU A 8 5 4 HELIX 2 AA2 CYS A 9 ASP A 20 1 12 HELIX 3 AA3 LEU A 34 ASN A 47 1 14 HELIX 4 AA4 TYR A 81 ARG A 86 1 6 HELIX 5 AA5 SER A 95 SER A 105 1 11 HELIX 6 AA6 ALA A 106 MET A 109 5 4 HELIX 7 AA7 GLY A 120 GLU A 124 5 5 HELIX 8 AA8 ASP A 133 LEU A 137 5 5 HELIX 9 AA9 GLN A 190 GLY A 203 1 14 HELIX 10 AB1 PRO A 216 SER A 224 1 9 HELIX 11 AB2 THR A 232 GLY A 242 1 11 HELIX 12 AB3 ASP A 321 MET A 326 1 6 HELIX 13 AB4 MET A 326 ASN A 342 1 17 HELIX 14 AB5 PRO A 352 GLN A 356 5 5 HELIX 15 AB6 ASP A 365 LYS A 373 1 9 HELIX 16 AB7 THR A 375 ASN A 389 1 15 HELIX 17 AB8 HIS A 390 TYR A 394 5 5 HELIX 18 AB9 GLU A 410 CYS A 422 1 13 HELIX 19 AC1 ILE A 440 HIS A 445 1 6 HELIX 20 AC2 MET A 462 THR A 467 5 6 HELIX 21 AC3 ASP A 476 TYR A 481 1 6 HELIX 22 AC4 PRO A 482 GLY A 497 1 16 SHEET 1 AA1 4 LEU A 23 ILE A 26 0 SHEET 2 AA1 4 ALA A 50 PHE A 53 1 O LEU A 52 N ILE A 26 SHEET 3 AA1 4 ARG A 65 GLY A 68 -1 O ILE A 66 N PHE A 53 SHEET 4 AA1 4 ILE A 310 MET A 313 1 O MET A 311 N ARG A 65 SHEET 1 AA2 3 THR A 115 ILE A 116 0 SHEET 2 AA2 3 GLU A 246 LYS A 249 1 O LEU A 247 N THR A 115 SHEET 3 AA2 3 TYR A 256 PRO A 258 -1 O VAL A 257 N VAL A 248 SHEET 1 AA3 6 ASN A 125 LEU A 127 0 SHEET 2 AA3 6 HIS A 293 TYR A 305 -1 O ILE A 303 N LEU A 127 SHEET 3 AA3 6 ILE A 263 GLU A 277 -1 N GLU A 266 O ASN A 301 SHEET 4 AA3 6 VAL A 207 PHE A 213 -1 N PHE A 213 O ILE A 263 SHEET 5 AA3 6 MET A 156 GLN A 160 -1 N ILE A 158 O ALA A 210 SHEET 6 AA3 6 THR A 167 SER A 170 -1 O SER A 170 N HIS A 157 SHEET 1 AA4 4 ASN A 125 LEU A 127 0 SHEET 2 AA4 4 HIS A 293 TYR A 305 -1 O ILE A 303 N LEU A 127 SHEET 3 AA4 4 HIS A 181 GLY A 184 -1 N LEU A 182 O TYR A 298 SHEET 4 AA4 4 ALA A 174 ASP A 178 -1 N MET A 175 O THR A 183 SHEET 1 AA5 5 ILE A 346 PHE A 350 0 SHEET 2 AA5 5 TRP A 359 VAL A 364 -1 O ALA A 361 N PHE A 350 SHEET 3 AA5 5 ARG A 398 VAL A 402 1 O VAL A 402 N VAL A 364 SHEET 4 AA5 5 LYS A 455 ASP A 459 1 O SER A 458 N LEU A 399 SHEET 5 AA5 5 GLU A 428 PHE A 431 -1 N PHE A 431 O LYS A 455 LINK OD1 ASN A 168 MN MN A 602 1555 1555 2.14 LINK O TRP A 169 K K A 603 1555 1555 3.11 LINK ND1 HIS A 191 MN MN A 602 1555 1555 2.27 LINK O ALA A 222 K K A 603 1555 1555 2.81 LINK O SER A 223 K K A 603 1555 1555 3.14 LINK O MET A 225 K K A 603 1555 1555 2.80 LINK OE2 GLU A 233 MN MN A 602 1555 1555 2.14 LINK OE2 GLU A 233 K K A 603 1555 1555 2.76 LINK O ARG A 421 K K A 604 1555 1555 2.65 LINK OD2 ASP A 427 K K A 604 1555 1555 2.79 LINK O ASP A 459 K K A 604 1555 1555 2.69 LINK O LEU A 461 K K A 604 1555 1555 2.69 LINK O2 4MJ A 601 MN MN A 602 1555 1555 2.21 LINK O2 4MJ A 601 K K A 603 1555 1555 2.85 LINK O4 4MJ A 601 K K A 603 1555 1555 2.99 LINK MN MN A 602 O HOH A 733 1555 1555 2.20 LINK MN MN A 602 O HOH A 823 1555 1555 2.20 LINK K K A 603 O HOH A 733 1555 1555 3.28 LINK K K A 604 O HOH A1083 1555 2555 2.78 LINK K K A 604 O HOH A1014 1555 2555 3.42 LINK K K A 604 O HOH A1019 1555 2555 2.72 CISPEP 1 LEU A 63 PHE A 64 0 -4.63 CISPEP 2 PRO A 188 PRO A 189 0 7.48 CISPEP 3 GLY A 278 PRO A 279 0 -0.84 CISPEP 4 LEU A 319 THR A 320 0 -1.25 SITE 1 AC1 27 THR A 153 ASN A 168 SER A 170 ILE A 171 SITE 2 AC1 27 ALA A 172 ARG A 173 LEU A 185 GLN A 190 SITE 3 AC1 27 HIS A 191 SER A 223 SER A 224 MET A 225 SITE 4 AC1 27 PRO A 226 GLU A 233 ILE A 327 LYS A 391 SITE 5 AC1 27 PHE A 437 LEU A 439 MN A 602 K A 603 SITE 6 AC1 27 HOH A 733 HOH A 743 HOH A 749 HOH A 755 SITE 7 AC1 27 HOH A 844 HOH A 900 HOH A 937 SITE 1 AC2 7 ASN A 168 HIS A 191 GLU A 233 4MJ A 601 SITE 2 AC2 7 K A 603 HOH A 733 HOH A 823 SITE 1 AC3 7 TRP A 169 ALA A 222 SER A 223 MET A 225 SITE 2 AC3 7 GLU A 233 4MJ A 601 MN A 602 SITE 1 AC4 6 ARG A 421 ASP A 427 ASP A 459 LEU A 461 SITE 2 AC4 6 HOH A1019 HOH A1083 CRYST1 96.050 63.850 87.680 90.00 90.00 90.00 P 21 21 2 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 0.010411 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015662 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011405 0.00000