HEADER TRANSFERASE 23-OCT-09 3KE3 TITLE CRYSTAL STRUCTURE OF PUTATIVE SERINE-PYRUVATE AMINOTRANSFERASE TITLE 2 (YP_263484.1) FROM PSYCHROBACTER ARCTICUM 273-4 AT 2.20 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE SERINE-PYRUVATE AMINOTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSYCHROBACTER ARCTICUS 273-4; SOURCE 3 ORGANISM_TAXID: 259536; SOURCE 4 STRAIN: DSM 17307 / 273-4; SOURCE 5 GENE: AGXT, PSYC_0177; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS PUTATIVE SERINE-PYRUVATE AMINOTRANSFERASE, STRUCTURAL GENOMICS, JOINT KEYWDS 2 CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, KEYWDS 3 PSI-2, AMINOTRANSFERASE, PYRUVATE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 5 01-FEB-23 3KE3 1 REMARK SEQADV REVDAT 4 17-JUL-19 3KE3 1 REMARK LINK REVDAT 3 25-OCT-17 3KE3 1 REMARK REVDAT 2 13-JUL-11 3KE3 1 VERSN REVDAT 1 03-NOV-09 3KE3 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF PUTATIVE SERINE-PYRUVATE JRNL TITL 2 AMINOTRANSFERASE (YP_263484.1) FROM PSYCHROBACTER ARCTICUM JRNL TITL 3 273-4 AT 2.20 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.87 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 19024 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 : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 983 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1291 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.85 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE SET COUNT : 84 REMARK 3 BIN FREE R VALUE : 0.3040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2847 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 170 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 32.16 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.67000 REMARK 3 B22 (A**2) : 1.80000 REMARK 3 B33 (A**2) : -0.14000 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): 0.279 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.196 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.138 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.433 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2995 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1979 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4067 ; 1.543 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4861 ; 1.139 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 388 ; 4.756 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 126 ;35.330 ;24.841 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 513 ;14.128 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;17.055 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 462 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3345 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 574 ; 0.001 ; 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): 1884 ; 1.069 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 765 ; 0.204 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3018 ; 2.100 ; 4.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1111 ; 3.935 ; 6.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1040 ; 5.506 ; 8.000 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 : 3 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 7 A 21 REMARK 3 ORIGIN FOR THE GROUP (A): -15.2860 56.1950 35.3110 REMARK 3 T TENSOR REMARK 3 T11: 0.1903 T22: 0.1563 REMARK 3 T33: 0.3399 T12: 0.1106 REMARK 3 T13: -0.0172 T23: 0.0149 REMARK 3 L TENSOR REMARK 3 L11: 8.7027 L22: 2.3850 REMARK 3 L33: 11.7080 L12: -2.7625 REMARK 3 L13: -4.0977 L23: -0.5048 REMARK 3 S TENSOR REMARK 3 S11: 0.4870 S12: 0.4561 S13: 0.8304 REMARK 3 S21: -0.1792 S22: -0.1268 S23: 0.1108 REMARK 3 S31: -1.1009 S32: -0.3443 S33: -0.3602 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 22 A 268 REMARK 3 ORIGIN FOR THE GROUP (A): 1.5270 37.0360 16.2640 REMARK 3 T TENSOR REMARK 3 T11: 0.0635 T22: 0.0712 REMARK 3 T33: 0.0726 T12: -0.0539 REMARK 3 T13: -0.0181 T23: -0.0061 REMARK 3 L TENSOR REMARK 3 L11: 1.6047 L22: 1.6324 REMARK 3 L33: 2.0865 L12: -0.1028 REMARK 3 L13: -0.3723 L23: 0.1262 REMARK 3 S TENSOR REMARK 3 S11: -0.1123 S12: 0.2073 S13: -0.1233 REMARK 3 S21: -0.1915 S22: 0.1088 S23: -0.0032 REMARK 3 S31: 0.1458 S32: -0.0474 S33: 0.0035 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 269 A 377 REMARK 3 ORIGIN FOR THE GROUP (A): 22.3280 49.3780 14.0280 REMARK 3 T TENSOR REMARK 3 T11: 0.0972 T22: 0.2550 REMARK 3 T33: 0.2037 T12: -0.1248 REMARK 3 T13: 0.0345 T23: 0.0261 REMARK 3 L TENSOR REMARK 3 L11: 2.9919 L22: 1.7642 REMARK 3 L33: 1.7941 L12: -0.6406 REMARK 3 L13: -0.0157 L23: 0.0333 REMARK 3 S TENSOR REMARK 3 S11: -0.0658 S12: 0.2281 S13: 0.2127 REMARK 3 S21: -0.1900 S22: 0.0365 S23: -0.4131 REMARK 3 S31: -0.2431 S32: 0.5122 S33: 0.0292 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: 1. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS REMARK 3 ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE REMARK 3 INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE REMARK 3 ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REMARK 3 REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. REMARK 3 ELECTRON DENSITY REVEALS RESIDUE LYS-198 TO BE COVALENTLY REMARK 3 ATTACHED TO PYRIDOXAL-5'-PHOSPHATE (PLP) VIA A SCHIFF-BASE REMARK 3 LINKAGE. THIS COVALENTLY MODIFIED RESIDUE HAS BEEN MODELED AS 2- REMARK 3 LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL- PYRIDIN-4- REMARK 3 YLMETHANE) (LLP). 5. ALTHOUGH CYS 205 HAS BEEN FLAGGED AS A REMARK 3 RAMACHANDRAN OUTLIER ITS CURRENT MODELING IS IN AGREEMENT WITH REMARK 3 THE ELECTRON DENSITY. 6. ACETATE (ACT), 1,2-ETHANEDIOL (EDO), REMARK 3 AND SULFATE (SO4) FROM THE CRYSTALLIZATION/CRYOPROTECTANT REMARK 3 SOLUTIONS HAVE BEEN MODELED INTO THE SOLVENT STRUCTURE. 7. TLS REMARK 3 GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD SERVER. REMARK 4 REMARK 4 3KE3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000055876. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91162,0.97956,0.97938 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : FLAT MIRROR, VERTICAL AND REMARK 200 HORIZONTAL FOCUSSING MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.2.5 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19035 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 29.867 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.12500 REMARK 200 R SYM (I) : 0.12500 REMARK 200 FOR THE DATA SET : 8.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.65200 REMARK 200 R SYM FOR SHELL (I) : 0.65200 REMARK 200 FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX, SHELXD, AUTOSHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25.0000% POLYETHYLENE GLYCOL 4000, REMARK 280 0.2000M AMMONIUM SULFATE, 0.1M SODIUM ACETATE PH 4.6, ADDITIVE: REMARK 280 0.001M PYRIDOXAL-5'-PHOSPATE (PLP), NANODROP', VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 60.53600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.53600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 30.82250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.17600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 30.82250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.17600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 60.53600 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 30.82250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.17600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 60.53600 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 30.82250 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.17600 REMARK 290 SMTRY3 8 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 300 REMARK: CRYSTAL PACKING ANALYSIS AND ANALYTICAL SIZE EXCLUSION REMARK 300 CHROMATOGRAPHY COUPLED WITH STATIC LIGHT SCATTERING SUPPORT THE REMARK 300 ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN REMARK 300 SOLUTION. 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: 10150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -73.0 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 60.53600 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 0 REMARK 465 MSE A 1 REMARK 465 THR A 2 REMARK 465 ALA A 3 REMARK 465 LEU A 4 REMARK 465 ARG A 5 REMARK 465 GLN A 6 REMARK 465 LYS A 378 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 7 CG OD1 OD2 REMARK 470 GLU A 110 CG CD OE1 OE2 REMARK 470 ASP A 111 OD1 OD2 REMARK 470 GLU A 113 CG CD OE1 OE2 REMARK 470 GLU A 124 CD OE1 OE2 REMARK 470 LYS A 134 CE NZ REMARK 470 LYS A 293 CE NZ REMARK 470 LYS A 320 NZ 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 183 CB - CG - OD1 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 LLP A 198 -100.05 -91.48 REMARK 500 CYS A 205 -18.64 -171.48 REMARK 500 HIS A 249 -56.66 -122.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 379 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 380 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 381 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 382 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 383 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 384 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 385 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 386 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 387 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 388 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 391141 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 SEQUENCE THIS CONSTRUCT WAS EXPRESSED WITH THE PURIFICATION TAG REMARK 999 MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING REMARK 999 ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DBREF 3KE3 A 1 378 UNP Q4FVA8 Q4FVA8_PSYA2 1 378 SEQADV 3KE3 GLY A 0 UNP Q4FVA8 EXPRESSION TAG SEQRES 1 A 379 GLY MSE THR ALA LEU ARG GLN ASP ILE ASP PRO ASN GLY SEQRES 2 A 379 LEU LEU GLU TYR SER VAL VAL TYR THR ASP ARG ALA LEU SEQRES 3 A 379 ASN HIS MSE SER LYS ALA PHE GLN GLU VAL MSE ASN ASP SEQRES 4 A 379 LEU LEU SER ASN LEU LYS THR VAL TYR ASN ALA GLU ALA SEQRES 5 A 379 ALA VAL ILE ILE PRO GLY SER GLY THR TYR GLY MSE GLU SEQRES 6 A 379 ALA VAL ALA ARG GLN LEU THR ILE ASP GLU ASP CYS LEU SEQRES 7 A 379 ILE ILE ARG ASN GLY TRP PHE SER TYR ARG TRP THR GLN SEQRES 8 A 379 ILE LEU GLU LYS GLY LYS PHE ALA LYS SER SER THR VAL SEQRES 9 A 379 LEU THR ALA GLU ARG THR GLU ASP THR GLU ALA PRO LYS SEQRES 10 A 379 PRO PHE ALA PRO VAL ASP ILE GLU THR ALA VAL ALA LYS SEQRES 11 A 379 ILE LYS GLU ASP LYS SER ALA ILE VAL TYR ALA PRO HIS SEQRES 12 A 379 VAL GLU THR SER SER GLY ILE ILE LEU SER GLU GLU TYR SEQRES 13 A 379 ILE LYS ALA LEU SER GLU ALA VAL HIS SER VAL GLY GLY SEQRES 14 A 379 LEU LEU VAL ILE ASP CYS ILE ALA SER GLY CYS VAL TRP SEQRES 15 A 379 LEU ASP MSE LYS GLU LEU GLY ILE ASP VAL LEU ILE SER SEQRES 16 A 379 ALA PRO GLN LLP GLY TRP SER SER THR PRO CYS ALA GLY SEQRES 17 A 379 LEU VAL MSE LEU SER ALA ALA ALA ILE LYS LYS VAL GLU SEQRES 18 A 379 SER THR GLU SER ASN CYS PHE SER LEU ASP LEU LYS GLN SEQRES 19 A 379 TRP LEU THR ILE MSE ARG ALA TYR GLU ASN GLY GLY HIS SEQRES 20 A 379 ALA TYR HIS ALA THR MSE PRO THR ASP SER LEU ARG GLN SEQRES 21 A 379 PHE ARG ASP ALA ILE LEU GLU ALA LYS GLU ILE GLY PHE SEQRES 22 A 379 ASP ILE LEU ARG ASP ALA GLN TRP GLU LEU GLY ASN ARG SEQRES 23 A 379 VAL ARG LYS VAL LEU THR ASP LYS GLY ILE GLU SER VAL SEQRES 24 A 379 ALA ALA GLU GLY PHE GLU ALA PRO GLY VAL VAL VAL SER SEQRES 25 A 379 TYR THR GLU ARG ASP ASP MSE HIS LYS GLY SER ALA PHE SEQRES 26 A 379 ALA GLU ALA GLY LEU GLN ILE ALA ALA GLY VAL PRO LEU SEQRES 27 A 379 LYS VAL GLY GLU PRO ASP ASN PHE LYS THR PHE ARG LEU SEQRES 28 A 379 GLY LEU PHE GLY LEU ASP LYS LEU THR ASP ILE ASP GLY SEQRES 29 A 379 THR VAL GLU ARG PHE GLU LYS ALA LEU ASP GLU VAL LEU SEQRES 30 A 379 ALA LYS MODRES 3KE3 MSE A 28 MET SELENOMETHIONINE MODRES 3KE3 MSE A 36 MET SELENOMETHIONINE MODRES 3KE3 MSE A 63 MET SELENOMETHIONINE MODRES 3KE3 MSE A 184 MET SELENOMETHIONINE MODRES 3KE3 LLP A 198 LYS MODRES 3KE3 MSE A 210 MET SELENOMETHIONINE MODRES 3KE3 MSE A 238 MET SELENOMETHIONINE MODRES 3KE3 MSE A 252 MET SELENOMETHIONINE MODRES 3KE3 MSE A 318 MET SELENOMETHIONINE HET MSE A 28 8 HET MSE A 36 8 HET MSE A 63 8 HET MSE A 184 8 HET LLP A 198 24 HET MSE A 210 8 HET MSE A 238 8 HET MSE A 252 8 HET MSE A 318 8 HET ACT A 379 4 HET ACT A 380 4 HET ACT A 381 4 HET ACT A 382 4 HET ACT A 383 4 HET ACT A 384 4 HET EDO A 385 4 HET EDO A 386 4 HET SO4 A 387 5 HET SO4 A 388 5 HETNAM MSE SELENOMETHIONINE HETNAM LLP (2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5- HETNAM 2 LLP (PHOSPHONOOXYMETHYL)PYRIDIN-4- HETNAM 3 LLP YL]METHYLIDENEAMINO]HEXANOIC ACID HETNAM ACT ACETATE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETSYN LLP N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MSE 8(C5 H11 N O2 SE) FORMUL 1 LLP C14 H22 N3 O7 P FORMUL 2 ACT 6(C2 H3 O2 1-) FORMUL 8 EDO 2(C2 H6 O2) FORMUL 10 SO4 2(O4 S 2-) FORMUL 12 HOH *170(H2 O) HELIX 1 1 SER A 29 ASN A 48 1 20 HELIX 2 2 SER A 58 THR A 71 1 14 HELIX 3 3 GLY A 82 LYS A 96 1 15 HELIX 4 4 ASP A 122 LYS A 134 1 13 HELIX 5 5 SER A 152 VAL A 166 1 15 HELIX 6 6 ASP A 183 GLY A 188 1 6 HELIX 7 7 SER A 212 SER A 221 1 10 HELIX 8 8 ASP A 230 ASN A 243 1 14 HELIX 9 9 PRO A 253 GLY A 271 1 19 HELIX 10 10 GLY A 271 LYS A 293 1 23 HELIX 11 11 ARG A 315 LYS A 320 1 6 HELIX 12 12 GLY A 321 ALA A 327 1 7 HELIX 13 13 GLY A 354 THR A 359 1 6 HELIX 14 14 ASP A 360 ALA A 377 1 18 SHEET 1 A 7 ALA A 51 PRO A 56 0 SHEET 2 A 7 ALA A 206 LEU A 211 -1 O VAL A 209 N VAL A 53 SHEET 3 A 7 VAL A 191 SER A 194 -1 N LEU A 192 O MSE A 210 SHEET 4 A 7 LEU A 169 ASP A 173 1 N ILE A 172 O VAL A 191 SHEET 5 A 7 ILE A 137 PRO A 141 1 N VAL A 138 O VAL A 171 SHEET 6 A 7 ASP A 75 ARG A 80 1 N ILE A 79 O TYR A 139 SHEET 7 A 7 SER A 100 THR A 105 1 O THR A 102 N ILE A 78 SHEET 1 B 2 GLU A 107 ARG A 108 0 SHEET 2 B 2 PHE A 118 ALA A 119 -1 O ALA A 119 N GLU A 107 SHEET 1 C 2 VAL A 143 GLU A 144 0 SHEET 2 C 2 ILE A 149 ILE A 150 -1 O ILE A 149 N GLU A 144 SHEET 1 D 3 VAL A 308 TYR A 312 0 SHEET 2 D 3 THR A 347 GLY A 351 -1 O PHE A 348 N SER A 311 SHEET 3 D 3 ALA A 332 ALA A 333 -1 N ALA A 332 O ARG A 349 LINK C HIS A 27 N MSE A 28 1555 1555 1.32 LINK C MSE A 28 N SER A 29 1555 1555 1.33 LINK C VAL A 35 N MSE A 36 1555 1555 1.33 LINK C MSE A 36 N ASN A 37 1555 1555 1.33 LINK C GLY A 62 N MSE A 63 1555 1555 1.34 LINK C MSE A 63 N GLU A 64 1555 1555 1.33 LINK C ASP A 183 N MSE A 184 1555 1555 1.32 LINK C MSE A 184 N LYS A 185 1555 1555 1.32 LINK C GLN A 197 N LLP A 198 1555 1555 1.33 LINK C LLP A 198 N GLY A 199 1555 1555 1.32 LINK C VAL A 209 N MSE A 210 1555 1555 1.33 LINK C MSE A 210 N LEU A 211 1555 1555 1.33 LINK C ILE A 237 N MSE A 238 1555 1555 1.33 LINK C MSE A 238 N ARG A 239 1555 1555 1.33 LINK C THR A 251 N MSE A 252 1555 1555 1.34 LINK C MSE A 252 N PRO A 253 1555 1555 1.34 LINK C ASP A 317 N MSE A 318 1555 1555 1.34 LINK C MSE A 318 N HIS A 319 1555 1555 1.33 SITE 1 AC1 4 TRP A 83 ARG A 87 GLN A 90 HIS A 249 SITE 1 AC2 7 VAL A 18 VAL A 19 PHE A 84 THR A 145 SITE 2 AC2 7 LLP A 198 TYR A 248 ARG A 349 SITE 1 AC3 5 GLY A 245 HIS A 246 GLU A 314 HOH A 538 SITE 2 AC3 5 HOH A 550 SITE 1 AC4 1 HIS A 319 SITE 1 AC5 2 ARG A 239 GLU A 242 SITE 1 AC6 3 VAL A 46 TRP A 181 ASP A 273 SITE 1 AC7 5 LYS A 338 GLY A 340 GLU A 341 HOH A 544 SITE 2 AC7 5 HOH A 557 SITE 1 AC8 2 ASP A 255 SER A 256 SITE 1 AC9 3 ARG A 80 THR A 89 LYS A 338 SITE 1 BC1 5 HIS A 27 HIS A 246 ALA A 247 TYR A 248 SITE 2 BC1 5 HOH A 542 CRYST1 61.645 98.352 121.072 90.00 90.00 90.00 C 2 2 21 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 0.016222 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010168 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008260 0.00000