HEADER LYASE 13-MAY-16 5G4J TITLE PHOSPHOLYASE A1RDF1 FROM ARTHROBACTER IN COMPLEX WITH TITLE 2 PHOSPHOETHANOLAMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE AMINOTRANSFERASE CLASS III PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 EC: 4.2.3.2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARTHROBACTER AURESCENS; SOURCE 3 ORGANISM_TAXID: 290340; SOURCE 4 STRAIN: TC1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-YSBLIC-3C KEYWDS LYASE, PYRIDOXAL PHOSPHATE, TRANSAMINASE, PHOSPHOLYASE EXPDTA X-RAY DIFFRACTION AUTHOR A.CUETOS,A.N.TUAN,J.MANGAS SANCHEZ,G.GROGAN REVDAT 3 10-JAN-24 5G4J 1 REMARK LINK REVDAT 2 01-MAR-17 5G4J 1 JRNL REVDAT 1 19-OCT-16 5G4J 0 JRNL AUTH A.CUETOS,F.STEFFEN-MUNSBERG,J.MANGAS SANCHEZ,A.FRESE, JRNL AUTH 2 U.T.BORNSCHEUER,M.HOHNE,G.GROGAN JRNL TITL STRUCTURAL BASIS FOR PHOSPHOLYASE ACTIVITY OF A CLASS III JRNL TITL 2 TRANSAMINASE HOMOLOGUE. JRNL REF CHEMBIOCHEM V. 17 2308 2016 JRNL REFN ESSN 1439-7633 JRNL PMID 27709756 JRNL DOI 10.1002/CBIC.201600482 REMARK 2 REMARK 2 RESOLUTION. 1.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 1.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 75.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 70978 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) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3636 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) : 1.87 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.92 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5226 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.84 REMARK 3 BIN R VALUE (WORKING SET) : 0.2420 REMARK 3 BIN FREE R VALUE SET COUNT : 240 REMARK 3 BIN FREE R VALUE : 0.2680 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6300 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 49 REMARK 3 SOLVENT ATOMS : 476 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.84000 REMARK 3 B22 (A**2) : 0.51000 REMARK 3 B33 (A**2) : 1.32000 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): 0.126 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.118 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.081 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.770 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6494 ; 0.021 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6175 ; 0.008 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8831 ; 1.915 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14127 ; 1.478 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 847 ; 6.287 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 259 ;32.885 ;23.282 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 998 ;14.118 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 47 ;18.596 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1015 ; 0.227 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7445 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1477 ; 0.006 ; 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): 3382 ; 2.382 ; 2.468 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3381 ; 2.381 ; 2.466 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4225 ; 3.081 ; 3.684 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3112 ; 3.127 ; 2.735 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 : 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 5G4J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1290066848. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-APR-16 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL 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 : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 74689 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.870 REMARK 200 RESOLUTION RANGE LOW (A) : 64.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.67000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 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: PDB ENTRY 5G4I REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% (W/V) PEG 3350, 0.2 M (NH4)2SO4 REMARK 280 AND 3% (V/V) 2-METHYL-2,4-PENTANEDIOL IN 0.1 M BIS-TRIS PROPANE REMARK 280 BUFFER AT PH 6.0 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 38.08300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.94850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.18550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.94850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.08300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.18550 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -90.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 THR A 2 REMARK 465 SER A 3 REMARK 465 GLU A 4 REMARK 465 THR A 5 REMARK 465 THR A 6 REMARK 465 THR A 7 REMARK 465 THR A 8 REMARK 465 PRO A 9 REMARK 465 SER A 10 REMARK 465 ARG A 11 REMARK 465 VAL A 12 REMARK 465 PRO A 13 REMARK 465 GLN A 14 REMARK 465 THR A 15 REMARK 465 ALA A 16 REMARK 465 ASN A 17 REMARK 465 PRO A 441 REMARK 465 GLY A 442 REMARK 465 ASN A 443 REMARK 465 LEU A 444 REMARK 465 VAL A 445 REMARK 465 LEU A 446 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 SER B 3 REMARK 465 GLU B 4 REMARK 465 THR B 5 REMARK 465 THR B 6 REMARK 465 THR B 7 REMARK 465 THR B 8 REMARK 465 PRO B 9 REMARK 465 SER B 10 REMARK 465 ARG B 11 REMARK 465 VAL B 12 REMARK 465 PRO B 13 REMARK 465 GLN B 14 REMARK 465 THR B 15 REMARK 465 ALA B 16 REMARK 465 ASN B 17 REMARK 465 GLN B 440 REMARK 465 PRO B 441 REMARK 465 GLY B 442 REMARK 465 ASN B 443 REMARK 465 LEU B 444 REMARK 465 VAL B 445 REMARK 465 LEU B 446 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP A 18 CG OD1 OD2 REMARK 470 ARG A 36 CD NE CZ NH1 NH2 REMARK 470 ARG A 175 NH1 NH2 REMARK 470 ILE A 182 CG2 CD1 REMARK 470 ALA A 183 CB REMARK 470 GLU A 184 CG CD OE1 OE2 REMARK 470 GLU A 192 CD OE1 OE2 REMARK 470 GLN A 193 NE2 REMARK 470 GLN A 228 CD OE1 NE2 REMARK 470 GLU A 297 CD OE1 OE2 REMARK 470 ARG A 327 NH2 REMARK 470 GLN A 331 CG CD OE1 NE2 REMARK 470 GLN A 340 OE1 NE2 REMARK 470 LYS A 347 CD CE NZ REMARK 470 GLN A 354 CD OE1 NE2 REMARK 470 ARG A 380 NE CZ NH1 NH2 REMARK 470 LYS A 388 CE NZ REMARK 470 ARG A 421 NH2 REMARK 470 GLU A 422 OE2 REMARK 470 GLN A 440 CG CD OE1 NE2 REMARK 470 ASP B 18 CG OD1 OD2 REMARK 470 LEU B 20 CD2 REMARK 470 ARG B 36 CD NE CZ NH1 NH2 REMARK 470 GLN B 37 CD OE1 NE2 REMARK 470 GLN B 53 CG CD OE1 NE2 REMARK 470 ARG B 175 NH1 NH2 REMARK 470 ILE B 182 CD1 REMARK 470 VAL B 189 CG1 REMARK 470 GLU B 192 CD OE1 OE2 REMARK 470 GLN B 193 CD OE1 NE2 REMARK 470 GLN B 228 CD OE1 NE2 REMARK 470 GLU B 235 CD OE1 OE2 REMARK 470 ASN B 271 ND2 REMARK 470 GLU B 297 CD OE1 OE2 REMARK 470 ARG B 327 NH2 REMARK 470 GLN B 331 NE2 REMARK 470 GLN B 340 CD OE1 NE2 REMARK 470 LYS B 343 CE NZ REMARK 470 LYS B 347 NZ REMARK 470 ASN B 351 OD1 ND2 REMARK 470 ILE B 352 CD1 REMARK 470 GLN B 354 CG CD OE1 NE2 REMARK 470 ARG B 355 CZ NH1 NH2 REMARK 470 ARG B 380 CG CD NE CZ NH1 NH2 REMARK 470 ASN B 381 CG OD1 ND2 REMARK 470 LYS B 388 CD CE NZ REMARK 470 GLU B 396 CG CD OE1 OE2 REMARK 470 GLU B 422 CG CD OE1 OE2 REMARK 470 PRO B 439 CG 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 OE1 GLU A 98 O HOH A 2088 2.13 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 ASP A 76 CB - CG - OD1 ANGL. DEV. = 7.2 DEGREES REMARK 500 ASP A 108 CB - CA - C ANGL. DEV. = -14.2 DEGREES REMARK 500 ASP A 108 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 LEU A 161 CA - CB - CG ANGL. DEV. = 16.2 DEGREES REMARK 500 LEU A 323 CA - CB - CG ANGL. DEV. = 15.6 DEGREES REMARK 500 ARG A 346 NE - CZ - NH1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ARG A 346 NE - CZ - NH2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ARG A 348 CG - CD - NE ANGL. DEV. = -14.1 DEGREES REMARK 500 ARG A 348 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 348 NE - CZ - NH2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG A 365 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 365 NE - CZ - NH2 ANGL. DEV. = -7.4 DEGREES REMARK 500 LEU B 161 CA - CB - CG ANGL. DEV. = 18.1 DEGREES REMARK 500 MET B 283 CG - SD - CE ANGL. DEV. = -10.3 DEGREES REMARK 500 ARG B 346 CG - CD - NE ANGL. DEV. = -13.1 DEGREES REMARK 500 ARG B 346 NE - CZ - NH1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG B 346 NE - CZ - NH2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ARG B 348 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG B 348 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG B 365 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG B 365 NE - CZ - NH2 ANGL. DEV. = -5.3 DEGREES REMARK 500 ARG B 395 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 ARG B 395 NE - CZ - NH2 ANGL. DEV. = -5.8 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 THR A 26 -62.38 -126.00 REMARK 500 TYR A 35 159.20 79.26 REMARK 500 TYR A 61 -35.16 -133.91 REMARK 500 THR A 84 -72.22 -114.29 REMARK 500 ASN A 86 52.30 -143.87 REMARK 500 GLU A 112 18.84 -144.66 REMARK 500 PHE A 145 70.14 -154.08 REMARK 500 LYS A 281 -94.49 4.53 REMARK 500 ALA A 383 76.64 -116.02 REMARK 500 ARG A 414 68.05 -159.40 REMARK 500 THR B 26 -64.63 -122.05 REMARK 500 TYR B 35 156.51 78.10 REMARK 500 TYR B 61 -39.24 -132.84 REMARK 500 THR B 84 -73.26 -115.51 REMARK 500 ASN B 86 56.64 -147.42 REMARK 500 GLU B 112 19.71 -144.44 REMARK 500 PHE B 145 71.41 -150.12 REMARK 500 LYS B 281 -96.42 7.23 REMARK 500 ALA B 383 78.98 -114.33 REMARK 500 ARG B 414 71.34 -160.98 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 NA A1443 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 353 O REMARK 620 2 SER A 356 O 87.8 REMARK 620 3 VAL A 359 O 117.8 97.2 REMARK 620 4 HOH A2285 O 93.4 174.6 77.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EXT B 1440 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EXT A 1441 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1442 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1441 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1443 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5G4I RELATED DB: PDB REMARK 900 PLP-DEPENDENT PHOSPHOLYASE A1RDF1 FROM ARTHROBACTER AURESCENS TC1 DBREF 5G4J A 1 446 UNP A1RDF1 A1RDF1_ARTAT 1 446 DBREF 5G4J B 1 446 UNP A1RDF1 A1RDF1_ARTAT 1 446 SEQRES 1 A 446 MET THR SER GLU THR THR THR THR PRO SER ARG VAL PRO SEQRES 2 A 446 GLN THR ALA ASN ASP LEU LEU ALA ARG ARG TYR ALA THR SEQRES 3 A 446 ILE GLY PRO HIS SER PRO LEU PHE TYR ARG GLN PRO LEU SEQRES 4 A 446 GLU LEU VAL SER GLY SER GLY VAL TRP LEU THR ASP ALA SEQRES 5 A 446 GLN GLY LYS VAL TYR LEU ASP GLY TYR ASN ASN VAL PRO SEQRES 6 A 446 HIS VAL GLY HIS ALA ASN PRO ALA VAL ALA ASP ALA ILE SEQRES 7 A 446 TYR GLN GLN LEU LEU THR VAL ASN LEU HIS THR ARG TYR SEQRES 8 A 446 LEU ASN SER ARG VAL VAL GLU TYR ALA GLU ALA LEU LEU SEQRES 9 A 446 SER LYS PHE ASP GLY ALA LEU GLU ARG LEU PHE LEU THR SEQRES 10 A 446 ASN SER GLY SER GLU ALA ASN GLU LEU ALA LEU ARG ILE SEQRES 11 A 446 ALA ARG GLN HIS THR GLY ASN THR GLY VAL LEU VAL SER SEQRES 12 A 446 ASP PHE SER TYR HIS GLY ASN THR THR SER LEU ALA GLU SEQRES 13 A 446 ILE THR THR GLY LEU THR VAL HIS GLU PRO LEU GLY ALA SEQRES 14 A 446 HIS VAL ARG ALA LEU ARG ILE PRO ASP VAL SER GLY ILE SEQRES 15 A 446 ALA GLU VAL ASP VAL PRO VAL LEU LEU GLU GLN SER LEU SEQRES 16 A 446 ALA ASP VAL ASP ALA ALA ILE ALA SER LEU GLN ALA ALA SEQRES 17 A 446 GLY HIS GLY VAL SER VAL PHE LEU PHE ASP PRO LEU PHE SEQRES 18 A 446 SER THR GLU GLY LEU LEU GLN LEU PRO SER GLY TYR ILE SEQRES 19 A 446 GLU GLY VAL ALA THR ARG VAL ARG ALA ALA GLY GLY LEU SEQRES 20 A 446 VAL ILE SER ASP GLU VAL GLN SER GLY PHE GLY ARG THR SEQRES 21 A 446 GLY SER GLY MET TRP GLY TYR GLN MET PHE ASN VAL GLU SEQRES 22 A 446 PRO GLU LEU VAL THR MET GLY LYS PRO MET GLY ASN GLY SEQRES 23 A 446 HIS PRO ILE GLY ALA VAL VAL THR THR ALA GLU LEU LEU SEQRES 24 A 446 ASP GLU PHE GLY ARG HIS ASN MET PHE PHE ASN THR PHE SEQRES 25 A 446 ALA GLY ASN PRO VAL SER SER ALA ALA GLY LEU ALA VAL SEQRES 26 A 446 LEU ARG TYR MET ASP GLN GLU ASP LEU MET ALA LYS ALA SEQRES 27 A 446 ASP GLN LEU GLY LYS TYR ILE ARG LYS ARG LEU GLU ASN SEQRES 28 A 446 ILE ALA GLN ARG SER GLY ASN VAL GLY SER VAL ARG GLY SEQRES 29 A 446 ARG GLY LEU PHE PHE GLY ILE ASP ILE ILE GLU SER ASP SEQRES 30 A 446 GLY SER ARG ASN PRO ALA PRO ALA LEU THR LYS ILE LEU SEQRES 31 A 446 ILE GLU ASP MET ARG GLU ARG GLY VAL LEU ILE SER ARG SEQRES 32 A 446 VAL GLY PRO HIS ASP ASN VAL LEU LYS MET ARG PRO PRO SEQRES 33 A 446 LEU VAL PHE GLY ARG GLU HIS ALA ASP ILE LEU LEU GLY SEQRES 34 A 446 GLN LEU GLU LEU SER LEU ALA SER LEU PRO GLN PRO GLY SEQRES 35 A 446 ASN LEU VAL LEU SEQRES 1 B 446 MET THR SER GLU THR THR THR THR PRO SER ARG VAL PRO SEQRES 2 B 446 GLN THR ALA ASN ASP LEU LEU ALA ARG ARG TYR ALA THR SEQRES 3 B 446 ILE GLY PRO HIS SER PRO LEU PHE TYR ARG GLN PRO LEU SEQRES 4 B 446 GLU LEU VAL SER GLY SER GLY VAL TRP LEU THR ASP ALA SEQRES 5 B 446 GLN GLY LYS VAL TYR LEU ASP GLY TYR ASN ASN VAL PRO SEQRES 6 B 446 HIS VAL GLY HIS ALA ASN PRO ALA VAL ALA ASP ALA ILE SEQRES 7 B 446 TYR GLN GLN LEU LEU THR VAL ASN LEU HIS THR ARG TYR SEQRES 8 B 446 LEU ASN SER ARG VAL VAL GLU TYR ALA GLU ALA LEU LEU SEQRES 9 B 446 SER LYS PHE ASP GLY ALA LEU GLU ARG LEU PHE LEU THR SEQRES 10 B 446 ASN SER GLY SER GLU ALA ASN GLU LEU ALA LEU ARG ILE SEQRES 11 B 446 ALA ARG GLN HIS THR GLY ASN THR GLY VAL LEU VAL SER SEQRES 12 B 446 ASP PHE SER TYR HIS GLY ASN THR THR SER LEU ALA GLU SEQRES 13 B 446 ILE THR THR GLY LEU THR VAL HIS GLU PRO LEU GLY ALA SEQRES 14 B 446 HIS VAL ARG ALA LEU ARG ILE PRO ASP VAL SER GLY ILE SEQRES 15 B 446 ALA GLU VAL ASP VAL PRO VAL LEU LEU GLU GLN SER LEU SEQRES 16 B 446 ALA ASP VAL ASP ALA ALA ILE ALA SER LEU GLN ALA ALA SEQRES 17 B 446 GLY HIS GLY VAL SER VAL PHE LEU PHE ASP PRO LEU PHE SEQRES 18 B 446 SER THR GLU GLY LEU LEU GLN LEU PRO SER GLY TYR ILE SEQRES 19 B 446 GLU GLY VAL ALA THR ARG VAL ARG ALA ALA GLY GLY LEU SEQRES 20 B 446 VAL ILE SER ASP GLU VAL GLN SER GLY PHE GLY ARG THR SEQRES 21 B 446 GLY SER GLY MET TRP GLY TYR GLN MET PHE ASN VAL GLU SEQRES 22 B 446 PRO GLU LEU VAL THR MET GLY LYS PRO MET GLY ASN GLY SEQRES 23 B 446 HIS PRO ILE GLY ALA VAL VAL THR THR ALA GLU LEU LEU SEQRES 24 B 446 ASP GLU PHE GLY ARG HIS ASN MET PHE PHE ASN THR PHE SEQRES 25 B 446 ALA GLY ASN PRO VAL SER SER ALA ALA GLY LEU ALA VAL SEQRES 26 B 446 LEU ARG TYR MET ASP GLN GLU ASP LEU MET ALA LYS ALA SEQRES 27 B 446 ASP GLN LEU GLY LYS TYR ILE ARG LYS ARG LEU GLU ASN SEQRES 28 B 446 ILE ALA GLN ARG SER GLY ASN VAL GLY SER VAL ARG GLY SEQRES 29 B 446 ARG GLY LEU PHE PHE GLY ILE ASP ILE ILE GLU SER ASP SEQRES 30 B 446 GLY SER ARG ASN PRO ALA PRO ALA LEU THR LYS ILE LEU SEQRES 31 B 446 ILE GLU ASP MET ARG GLU ARG GLY VAL LEU ILE SER ARG SEQRES 32 B 446 VAL GLY PRO HIS ASP ASN VAL LEU LYS MET ARG PRO PRO SEQRES 33 B 446 LEU VAL PHE GLY ARG GLU HIS ALA ASP ILE LEU LEU GLY SEQRES 34 B 446 GLN LEU GLU LEU SER LEU ALA SER LEU PRO GLN PRO GLY SEQRES 35 B 446 ASN LEU VAL LEU HET EXT A1441 23 HET NA A1442 1 HET NA A1443 1 HET EXT B1440 23 HET NA B1441 1 HETNAM EXT {5-HYDROXY-6-METHYL-4-[(E)-{[2-(PHOSPHONOOXY) HETNAM 2 EXT ETHYL]IMINO}METHYL]PYRIDIN-3-YL}METHYL DIHYDROGEN HETNAM 3 EXT PHOSPHATE HETNAM NA SODIUM ION FORMUL 3 EXT 2(C10 H16 N2 O9 P2) FORMUL 4 NA 3(NA 1+) FORMUL 8 HOH *476(H2 O) HELIX 1 1 ASP A 18 ALA A 25 1 8 HELIX 2 2 ASN A 71 LEU A 83 1 13 HELIX 3 3 ASN A 93 SER A 105 1 13 HELIX 4 4 SER A 119 GLY A 136 1 18 HELIX 5 5 THR A 151 GLU A 156 1 6 HELIX 6 6 ALA A 183 VAL A 185 5 3 HELIX 7 7 ASP A 186 ALA A 208 1 23 HELIX 8 8 GLY A 232 ALA A 244 1 13 HELIX 9 9 TRP A 265 PHE A 270 5 6 HELIX 10 10 GLY A 280 ASN A 285 5 6 HELIX 11 11 ALA A 296 ASN A 306 1 11 HELIX 12 12 ASN A 315 GLU A 332 1 18 HELIX 13 13 ASP A 333 SER A 356 1 24 HELIX 14 14 ALA A 383 ARG A 397 1 15 HELIX 15 15 GLY A 420 SER A 437 1 18 HELIX 16 16 ASP B 18 ALA B 25 1 8 HELIX 17 17 ASN B 71 LEU B 83 1 13 HELIX 18 18 ASN B 93 SER B 105 1 13 HELIX 19 19 SER B 119 GLY B 136 1 18 HELIX 20 20 THR B 151 GLU B 156 1 6 HELIX 21 21 ALA B 183 VAL B 185 5 3 HELIX 22 22 ASP B 186 ALA B 208 1 23 HELIX 23 23 GLY B 232 ALA B 244 1 13 HELIX 24 24 TRP B 265 PHE B 270 5 6 HELIX 25 25 GLY B 280 ASN B 285 5 6 HELIX 26 26 THR B 295 ASN B 306 1 12 HELIX 27 27 ASN B 315 GLU B 332 1 18 HELIX 28 28 ASP B 333 SER B 356 1 24 HELIX 29 29 ALA B 383 ARG B 397 1 15 HELIX 30 30 GLY B 420 SER B 437 1 18 SHEET 1 AA 4 LEU A 41 SER A 45 0 SHEET 2 AA 4 TRP A 48 ASP A 51 -1 O TRP A 48 N SER A 45 SHEET 3 AA 4 VAL A 56 ASP A 59 -1 O TYR A 57 N LEU A 49 SHEET 4 AA 4 VAL A 399 LEU A 400 1 N LEU A 400 O LEU A 58 SHEET 1 AB 7 LEU A 111 THR A 117 0 SHEET 2 AB 7 GLY A 290 THR A 295 -1 O GLY A 290 N THR A 117 SHEET 3 AB 7 LEU A 276 MET A 279 -1 O VAL A 277 N VAL A 293 SHEET 4 AB 7 LEU A 247 ASP A 251 1 O VAL A 248 N LEU A 276 SHEET 5 AB 7 VAL A 214 PHE A 217 1 O PHE A 215 N ILE A 249 SHEET 6 AB 7 VAL A 140 SER A 143 1 O LEU A 141 N LEU A 216 SHEET 7 AB 7 VAL A 171 LEU A 174 1 O ARG A 172 N VAL A 142 SHEET 1 AC 4 VAL A 359 ARG A 365 0 SHEET 2 AC 4 PHE A 368 ILE A 373 -1 O PHE A 368 N ARG A 365 SHEET 3 AC 4 VAL A 410 MET A 413 -1 O LEU A 411 N ILE A 371 SHEET 4 AC 4 SER A 402 VAL A 404 -1 O SER A 402 N LYS A 412 SHEET 1 BA 4 LEU B 41 SER B 45 0 SHEET 2 BA 4 TRP B 48 ASP B 51 -1 O TRP B 48 N SER B 45 SHEET 3 BA 4 VAL B 56 ASP B 59 -1 O TYR B 57 N LEU B 49 SHEET 4 BA 4 VAL B 399 LEU B 400 1 N LEU B 400 O LEU B 58 SHEET 1 BB 7 ARG B 113 THR B 117 0 SHEET 2 BB 7 GLY B 290 THR B 294 -1 O GLY B 290 N THR B 117 SHEET 3 BB 7 LEU B 276 MET B 279 -1 O VAL B 277 N VAL B 293 SHEET 4 BB 7 LEU B 247 ASP B 251 1 O VAL B 248 N LEU B 276 SHEET 5 BB 7 VAL B 214 PHE B 217 1 O PHE B 215 N ILE B 249 SHEET 6 BB 7 VAL B 140 SER B 143 1 O LEU B 141 N LEU B 216 SHEET 7 BB 7 VAL B 171 LEU B 174 1 O ARG B 172 N VAL B 142 SHEET 1 BC 4 VAL B 359 ARG B 365 0 SHEET 2 BC 4 PHE B 368 ILE B 373 -1 O PHE B 368 N ARG B 365 SHEET 3 BC 4 VAL B 410 MET B 413 -1 O LEU B 411 N ILE B 371 SHEET 4 BC 4 SER B 402 VAL B 404 -1 O SER B 402 N LYS B 412 LINK O ALA A 353 NA NA A1443 1555 1555 2.32 LINK O SER A 356 NA NA A1443 1555 1555 2.23 LINK O VAL A 359 NA NA A1443 1555 1555 2.24 LINK NA NA A1443 O HOH A2285 1555 1555 2.24 SITE 1 AC1 19 ARG A 90 THR A 311 HOH A2115 HOH A2121 SITE 2 AC1 19 HOH A2263 TYR B 61 GLY B 120 SER B 121 SITE 3 AC1 19 ASN B 124 TYR B 147 HIS B 148 ASP B 251 SITE 4 AC1 19 GLN B 254 LYS B 281 LYS B 412 ARG B 414 SITE 5 AC1 19 HOH B2015 HOH B2049 HOH B2073 SITE 1 AC2 20 TYR A 61 GLY A 120 SER A 121 ASN A 124 SITE 2 AC2 20 TYR A 147 HIS A 148 ASP A 251 GLN A 254 SITE 3 AC2 20 LYS A 281 LYS A 412 ARG A 414 HOH A2041 SITE 4 AC2 20 HOH A2044 HOH A2117 HOH A2118 HOH A2151 SITE 5 AC2 20 HOH A2152 HOH A2308 ARG B 90 THR B 311 SITE 1 AC3 3 GLY A 232 GLU A 235 ASN A 271 SITE 1 AC4 3 GLY B 232 GLU B 235 ASN B 271 SITE 1 AC5 4 ALA A 353 SER A 356 VAL A 359 HOH A2285 CRYST1 76.166 96.371 121.897 90.00 90.00 90.00 P 21 21 21 16 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 0.013129 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010377 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008204 0.00000 MTRIX1 1 0.230400 -0.473900 0.849900 26.18000 MTRIX2 1 -0.470400 -0.818800 -0.329000 -11.26000 MTRIX3 1 0.851900 -0.324000 -0.411600 -44.20000