HEADER TRANSFERASE 25-MAY-16 5B6A TITLE STRUCTURE OF PYRIDOXAL KINASEFROM PSEUDOMONAS AERUGINOSA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRIDOXAL KINASE PDXY; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PL KINASE; COMPND 5 EC: 2.7.1.35; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA (STRAIN ATCC 15692 / SOURCE 3 PAO1 / 1C / PRS 101 / LMG 12228); SOURCE 4 ORGANISM_TAXID: 208964; SOURCE 5 STRAIN: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228; SOURCE 6 GENE: PDXY, PA5516; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS PSEUDOMONAS AERUGINOSA, PDXK, PYRIDOXAL KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.I.KIM,M.HONG REVDAT 4 08-NOV-23 5B6A 1 REMARK REVDAT 3 04-DEC-19 5B6A 1 JRNL REMARK REVDAT 2 17-AUG-16 5B6A 1 JRNL REVDAT 1 10-AUG-16 5B6A 0 JRNL AUTH M.I.KIM,M.HONG JRNL TITL CRYSTAL STRUCTURE AND CATALYTIC MECHANISM OF PYRIDOXAL JRNL TITL 2 KINASE FROM PSEUDOMONAS AERUGINOSA JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 478 300 2016 JRNL REFN ESSN 1090-2104 JRNL PMID 27425248 JRNL DOI 10.1016/J.BBRC.2016.07.007 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 3 NUMBER OF REFLECTIONS : 22725 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1238 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) : 1693 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.65 REMARK 3 BIN R VALUE (WORKING SET) : 0.2690 REMARK 3 BIN FREE R VALUE SET COUNT : 96 REMARK 3 BIN FREE R VALUE : 0.2610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2191 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 75 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.59000 REMARK 3 B22 (A**2) : -1.59000 REMARK 3 B33 (A**2) : 5.16000 REMARK 3 B12 (A**2) : -0.79000 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): 0.167 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.148 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.112 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.454 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2267 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3093 ; 1.619 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 291 ; 6.105 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 102 ;38.295 ;23.627 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 345 ;17.297 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;18.508 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 347 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1759 ; 0.006 ; 0.021 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): 1162 ; 1.212 ; 2.987 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1453 ; 2.021 ; 4.468 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1105 ; 1.473 ; 3.198 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 5 A 56 REMARK 3 ORIGIN FOR THE GROUP (A): -13.8030 -35.9400 0.8950 REMARK 3 T TENSOR REMARK 3 T11: 0.0784 T22: 0.0753 REMARK 3 T33: 0.1202 T12: 0.0196 REMARK 3 T13: 0.0188 T23: -0.0493 REMARK 3 L TENSOR REMARK 3 L11: 2.2275 L22: 0.8459 REMARK 3 L33: 1.8000 L12: -0.6023 REMARK 3 L13: -0.7025 L23: -0.1895 REMARK 3 S TENSOR REMARK 3 S11: -0.0930 S12: 0.0325 S13: 0.0940 REMARK 3 S21: 0.1705 S22: 0.0985 S23: -0.1753 REMARK 3 S31: 0.0092 S32: 0.1840 S33: -0.0056 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 57 A 115 REMARK 3 ORIGIN FOR THE GROUP (A): -14.9220 -40.8330 -13.9340 REMARK 3 T TENSOR REMARK 3 T11: 0.0247 T22: 0.2144 REMARK 3 T33: 0.0465 T12: 0.0000 REMARK 3 T13: 0.0224 T23: -0.0601 REMARK 3 L TENSOR REMARK 3 L11: 3.6103 L22: 2.6139 REMARK 3 L33: 1.6536 L12: -1.0754 REMARK 3 L13: 0.5356 L23: -0.3136 REMARK 3 S TENSOR REMARK 3 S11: 0.0951 S12: 0.5705 S13: -0.1492 REMARK 3 S21: -0.0915 S22: -0.1138 S23: -0.0008 REMARK 3 S31: -0.0371 S32: -0.0288 S33: 0.0186 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 116 A 142 REMARK 3 RESIDUE RANGE : A 143 A 213 REMARK 3 ORIGIN FOR THE GROUP (A): 6.5670 -43.3740 -6.3190 REMARK 3 T TENSOR REMARK 3 T11: 0.0281 T22: 0.2264 REMARK 3 T33: 0.1114 T12: -0.0052 REMARK 3 T13: 0.0191 T23: -0.0610 REMARK 3 L TENSOR REMARK 3 L11: 3.9620 L22: 2.0857 REMARK 3 L33: 0.7242 L12: -0.5357 REMARK 3 L13: 0.0238 L23: 0.2127 REMARK 3 S TENSOR REMARK 3 S11: 0.0187 S12: 0.0561 S13: 0.2324 REMARK 3 S21: 0.1302 S22: -0.0062 S23: -0.2454 REMARK 3 S31: 0.0285 S32: 0.2733 S33: -0.0126 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 214 A 288 REMARK 3 ORIGIN FOR THE GROUP (A): 0.9120 -27.7550 0.9450 REMARK 3 T TENSOR REMARK 3 T11: 0.0638 T22: 0.1884 REMARK 3 T33: 0.3674 T12: -0.0629 REMARK 3 T13: -0.0235 T23: -0.1005 REMARK 3 L TENSOR REMARK 3 L11: 2.8669 L22: 1.9891 REMARK 3 L33: 2.2318 L12: -0.6839 REMARK 3 L13: -0.8548 L23: -0.3001 REMARK 3 S TENSOR REMARK 3 S11: -0.0313 S12: -0.1457 S13: 0.5935 REMARK 3 S21: 0.1612 S22: 0.1156 S23: -0.6148 REMARK 3 S31: -0.2039 S32: 0.4136 S33: -0.0843 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: U VALUES : WITH TLS ADDED HYDROGENS REMARK 3 HAVE BEEN USED IF PRESENT IN THE INPUT REMARK 4 REMARK 4 5B6A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1300000609. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-14 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 : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00002 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24013 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.7000 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) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.39200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PHASER, PHASER REMARK 200 STARTING MODEL: 3PZS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS, PH 8.5, 1M LITHIUM REMARK 280 CHLORIDE, 13% (W/V) POLYETHYLENE GLYCOL 6000, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 20.49733 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 40.99467 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 40.99467 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 20.49733 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: 4990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 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 GLU A 121 CG CD OE1 OE2 REMARK 470 ARG A 282 CG CD NE CZ NH1 NH2 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 LEU A 112 CA - CB - CG ANGL. DEV. = 16.1 DEGREES REMARK 500 LEU A 257 CA - CB - CG ANGL. DEV. = 14.8 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 LYS A 122 -138.48 -103.78 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 MG A 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 225 OD1 REMARK 620 2 HOH A 441 O 80.1 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRS A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 303 DBREF 5B6A A 1 288 UNP Q9HT57 PDXY_PSEAE 1 288 SEQRES 1 A 288 MET PRO ARG THR PRO HIS LEU LEU ALA ILE GLN SER HIS SEQRES 2 A 288 VAL VAL PHE GLY HIS ALA GLY ASN ALA ALA ALA VAL PHE SEQRES 3 A 288 PRO MET GLN ARG ILE GLY ILE ASN VAL TRP PRO LEU ASN SEQRES 4 A 288 THR VAL GLN PHE SER ASN HIS THR GLN TYR GLY ARG TRP SEQRES 5 A 288 THR GLY GLN VAL LEU PRO PRO GLU GLN ILE PRO ALA LEU SEQRES 6 A 288 VAL ASP GLY ILE ALA GLY ILE GLY GLU LEU GLY ASN CYS SEQRES 7 A 288 ASP ALA VAL LEU SER GLY TYR LEU GLY SER ALA ALA GLN SEQRES 8 A 288 GLY ARG ALA ILE LEU ASP VAL VAL ALA ARG ILE LYS GLN SEQRES 9 A 288 ALA ASN PRO ARG ALA LEU TYR LEU CYS ASP PRO VAL MET SEQRES 10 A 288 GLY HIS PRO GLU LYS GLY CYS ILE VAL ALA PRO GLU VAL SEQRES 11 A 288 SER ASP PHE LEU LEU GLU GLU ALA ALA ALA VAL ALA ASP SEQRES 12 A 288 TYR LEU CYS PRO ASN GLN LEU GLU LEU ASP SER PHE CYS SEQRES 13 A 288 ASP ARG GLN PRO ASN SER LEU ALA ASP CYS VAL GLU MET SEQRES 14 A 288 ALA ARG SER LEU LEU ALA ARG GLY PRO ARG ALA ILE LEU SEQRES 15 A 288 VAL LYS HIS LEU ASN TYR PRO GLY LYS ALA GLY ASP THR SEQRES 16 A 288 PHE GLU MET LEU LEU VAL ALA ALA ASP GLN ALA TRP HIS SEQRES 17 A 288 LEU GLN ARG PRO LEU LEU ALA PHE PRO ARG GLN PRO VAL SEQRES 18 A 288 GLY VAL GLY ASP LEU ALA SER GLY LEU PHE LEU SER ARG SEQRES 19 A 288 LEU LEU LEU GLY ASP ASP LEU ARG ASN ALA PHE GLU PHE SEQRES 20 A 288 THR GLY ALA ALA VAL HIS GLU VAL LEU LEU GLU THR GLN SEQRES 21 A 288 ALA CYS GLY SER TYR GLU LEU GLU LEU VAL ARG ALA GLN SEQRES 22 A 288 ASP ARG ILE ALA HIS PRO ARG VAL ARG PHE ASP ALA VAL SEQRES 23 A 288 ARG LEU HET TRS A 301 8 HET MG A 302 1 HET PO4 A 303 5 HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM MG MAGNESIUM ION HETNAM PO4 PHOSPHATE ION HETSYN TRS TRIS BUFFER FORMUL 2 TRS C4 H12 N O3 1+ FORMUL 3 MG MG 2+ FORMUL 4 PO4 O4 P 3- FORMUL 5 HOH *75(H2 O) HELIX 1 AA1 GLY A 20 ILE A 31 1 12 HELIX 2 AA2 HIS A 46 GLY A 50 5 5 HELIX 3 AA3 GLU A 60 ILE A 72 1 13 HELIX 4 AA4 GLY A 73 CYS A 78 5 6 HELIX 5 AA5 SER A 88 ASN A 106 1 19 HELIX 6 AA6 ALA A 127 GLU A 137 1 11 HELIX 7 AA7 ASN A 148 ASP A 157 1 10 HELIX 8 AA8 SER A 162 LEU A 174 1 13 HELIX 9 AA9 ALA A 175 GLY A 177 5 3 HELIX 10 AB1 GLY A 222 LEU A 237 1 16 HELIX 11 AB2 ASP A 240 GLY A 263 1 24 HELIX 12 AB3 ALA A 272 HIS A 278 1 7 SHEET 1 AA110 GLY A 54 VAL A 56 0 SHEET 2 AA110 ASN A 34 PHE A 43 -1 N GLN A 42 O GLN A 55 SHEET 3 AA110 HIS A 6 VAL A 14 1 N LEU A 7 O TRP A 36 SHEET 4 AA110 ALA A 80 SER A 83 1 O LEU A 82 N ILE A 10 SHEET 5 AA110 LEU A 110 CYS A 113 1 O LEU A 110 N VAL A 81 SHEET 6 AA110 TYR A 144 LEU A 145 1 O TYR A 144 N CYS A 113 SHEET 7 AA110 ALA A 180 VAL A 183 1 O LEU A 182 N LEU A 145 SHEET 8 AA110 THR A 195 VAL A 201 -1 O VAL A 201 N ILE A 181 SHEET 9 AA110 ALA A 206 PRO A 212 -1 O ARG A 211 N PHE A 196 SHEET 10 AA110 VAL A 286 ARG A 287 -1 O VAL A 286 N HIS A 208 LINK OD1 ASP A 225 MG MG A 302 1555 1555 2.77 LINK MG MG A 302 O HOH A 441 1555 1555 2.49 SITE 1 AC1 5 SER A 12 HIS A 46 THR A 47 TYR A 85 SITE 2 AC1 5 HOH A 470 SITE 1 AC2 4 VAL A 116 ASP A 225 PO4 A 303 HOH A 441 SITE 1 AC3 5 ASN A 148 GLY A 224 MG A 302 HOH A 429 SITE 2 AC3 5 HOH A 441 CRYST1 102.547 102.547 61.492 90.00 90.00 120.00 P 31 2 1 6 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 0.009752 0.005630 0.000000 0.00000 SCALE2 0.000000 0.011260 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016262 0.00000