HEADER TRANSFERASE 03-OCT-15 5E3Q TITLE CRYSTAL STRUCTURE OF DAPD IN COMPLEX WITH SUCCINYL-COA FROM TITLE 2 CORYNEBACTERIUM GLUTAMICUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2,3,4,5-TETRAHYDROPYRIDINE-2,6-DICARBOXYLATE N- COMPND 3 SUCCINYLTRANSFERASE; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE,THP COMPND 6 SUCCINYLTRANSFERASE,TETRAHYDROPICOLINATE SUCCINYLASE; COMPND 7 EC: 2.3.1.117; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CORYNEBACTERIUM GLUTAMICUM (STRAIN ATCC 13032 / SOURCE 3 DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025); SOURCE 4 ORGANISM_TAXID: 196627; SOURCE 5 STRAIN: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025; SOURCE 6 GENE: DAPD, CGL1106, CG1256; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET30A KEYWDS TRANSFERASE, CORYNEBACTERIUM GLUTAMICUM, L-LYSINE EXPDTA X-RAY DIFFRACTION AUTHOR H.-Y.SAGONG,K.-J.KIM REVDAT 4 08-NOV-23 5E3Q 1 REMARK REVDAT 3 09-SEP-20 5E3Q 1 TITLE REMARK REVDAT 2 30-DEC-15 5E3Q 1 JRNL REVDAT 1 04-NOV-15 5E3Q 0 JRNL AUTH H.Y.SAGONG,K.J.KIM JRNL TITL CRYSTAL STRUCTURE AND BIOCHEMICAL CHARACTERIZATION OF JRNL TITL 2 TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE FROM JRNL TITL 3 CORYNEBACTERIUM GLUTAMICUM. JRNL REF J.AGRIC.FOOD CHEM. V. 63 10641 2015 JRNL REFN ESSN 1520-5118 JRNL PMID 26602189 JRNL DOI 10.1021/ACS.JAFC.5B04785 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0131 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 94.11 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 41214 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) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2093 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3023 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.31 REMARK 3 BIN R VALUE (WORKING SET) : 0.1610 REMARK 3 BIN FREE R VALUE SET COUNT : 155 REMARK 3 BIN FREE R VALUE : 0.1830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2052 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.22000 REMARK 3 B22 (A**2) : 0.22000 REMARK 3 B33 (A**2) : -0.71000 REMARK 3 B12 (A**2) : 0.11000 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): 0.078 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.082 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.047 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.455 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2142 ; 0.026 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2029 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2923 ; 2.424 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4642 ; 1.137 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 276 ; 6.524 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 82 ;28.128 ;23.049 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 320 ;11.935 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;20.274 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 348 ; 0.148 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2426 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 478 ; 0.003 ; 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): 1110 ; 2.416 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1109 ; 2.414 ; 1.995 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1384 ; 3.288 ; 2.977 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5E3Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214297. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAY-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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) : 0.97934 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR 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 : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41214 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 94.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 10.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 61.6800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 3FSX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 200, LI2SO4, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 0.00000 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 0.00000 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 0.00000 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 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 46.22850 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 26.69004 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 94.11367 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 46.22850 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 26.69004 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 94.11367 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 46.22850 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 26.69004 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 94.11367 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 46.22850 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 26.69004 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 94.11367 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 46.22850 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 26.69004 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 94.11367 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 46.22850 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 26.69004 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 94.11367 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 53.38007 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 188.22733 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 53.38007 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 188.22733 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 53.38007 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 188.22733 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 53.38007 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 188.22733 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 53.38007 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 188.22733 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 53.38007 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 188.22733 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 13040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 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 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 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 506 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 512 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 546 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 572 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 THR A 205 REMARK 465 LEU A 206 REMARK 465 SER A 207 REMARK 465 GLY A 208 REMARK 465 GLY A 209 REMARK 465 GLY A 210 REMARK 465 GLN A 211 REMARK 465 HIS A 212 REMARK 465 VAL A 288 REMARK 465 GLU A 289 REMARK 465 LEU A 290 REMARK 465 ASN A 291 REMARK 465 THR A 292 REMARK 465 ALA A 293 REMARK 465 LEU A 294 REMARK 465 HIS A 295 REMARK 465 SER A 296 REMARK 465 ASN A 297 REMARK 465 HIS A 298 REMARK 465 HIS A 299 REMARK 465 HIS A 300 REMARK 465 HIS A 301 REMARK 465 HIS A 302 REMARK 465 HIS A 303 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 SER A 28 OG REMARK 470 ILE A 57 CD1 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 601 O HOH A 699 2.06 REMARK 500 O HOH A 517 O HOH A 636 2.08 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 ARG A 80 CZ ARG A 80 NH1 0.081 REMARK 500 TYR A 136 CE1 TYR A 136 CZ -0.087 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 20 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG A 44 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP A 63 CB - CG - OD1 ANGL. DEV. = 8.6 DEGREES REMARK 500 ARG A 80 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 80 NE - CZ - NH2 ANGL. DEV. = -5.1 DEGREES REMARK 500 ASP A 87 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG A 118 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 143 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 ARG A 143 NE - CZ - NH2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ASP A 148 CB - CG - OD1 ANGL. DEV. = 7.1 DEGREES REMARK 500 ASP A 192 CB - CG - OD1 ANGL. DEV. = 8.3 DEGREES REMARK 500 ARG A 272 NE - CZ - NH2 ANGL. DEV. = -3.1 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 ASN A 225 19.81 58.28 REMARK 500 LYS A 286 78.60 30.82 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 SCA A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5E3P RELATED DB: PDB REMARK 900 RELATED ID: 5E3R RELATED DB: PDB DBREF 5E3Q A 2 297 UNP Q8NRE3 DAPD_CORGL 2 297 SEQADV 5E3Q ILE A 57 UNP Q8NRE3 THR 57 CONFLICT SEQADV 5E3Q HIS A 298 UNP Q8NRE3 EXPRESSION TAG SEQADV 5E3Q HIS A 299 UNP Q8NRE3 EXPRESSION TAG SEQADV 5E3Q HIS A 300 UNP Q8NRE3 EXPRESSION TAG SEQADV 5E3Q HIS A 301 UNP Q8NRE3 EXPRESSION TAG SEQADV 5E3Q HIS A 302 UNP Q8NRE3 EXPRESSION TAG SEQADV 5E3Q HIS A 303 UNP Q8NRE3 EXPRESSION TAG SEQRES 1 A 302 THR THR ALA SER ALA THR GLY ILE ALA THR LEU THR SER SEQRES 2 A 302 THR GLY ASP VAL LEU ASP VAL TRP TYR PRO GLU ILE GLY SEQRES 3 A 302 SER THR ASP GLN SER ALA LEU THR PRO LEU GLU GLY VAL SEQRES 4 A 302 ASP GLU ASP ARG ASN VAL THR ARG LYS ILE VAL THR THR SEQRES 5 A 302 THR ILE ASP ILE ASP ALA ALA PRO THR ASP THR TYR ASP SEQRES 6 A 302 ALA TRP LEU ARG LEU HIS LEU LEU SER HIS ARG VAL PHE SEQRES 7 A 302 ARG PRO HIS THR ILE ASN LEU ASP GLY ILE PHE GLY LEU SEQRES 8 A 302 LEU ASN ASN VAL VAL TRP THR ASN PHE GLY PRO CYS ALA SEQRES 9 A 302 VAL ASP GLY PHE ALA LEU THR ARG ALA ARG LEU SER ARG SEQRES 10 A 302 ARG GLY GLN VAL THR VAL TYR SER VAL ASP LYS PHE PRO SEQRES 11 A 302 ARG MET VAL ASP TYR VAL VAL PRO SER GLY VAL ARG ILE SEQRES 12 A 302 GLY ASP ALA ASP ARG VAL ARG LEU GLY ALA TYR LEU ALA SEQRES 13 A 302 ASP GLY THR THR VAL MET HIS GLU GLY PHE VAL ASN PHE SEQRES 14 A 302 ASN ALA GLY THR LEU GLY ALA SER MET VAL GLU GLY ARG SEQRES 15 A 302 ILE SER ALA GLY VAL THR VAL ASP ASP GLY THR ASP VAL SEQRES 16 A 302 GLY GLY GLY ALA SER ILE MET GLY THR LEU SER GLY GLY SEQRES 17 A 302 GLY GLN HIS VAL ILE SER LEU GLY LYS ARG CYS LEU LEU SEQRES 18 A 302 GLY ALA ASN SER GLY CYS GLY ILE PRO LEU GLY ASP ASP SEQRES 19 A 302 CYS ILE ILE GLU ALA GLY LEU TYR ILE THR ALA GLY THR SEQRES 20 A 302 LYS VAL LEU PHE ASP GLY SER LEU HIS LYS ALA SER THR SEQRES 21 A 302 LEU ALA GLY SER ASN GLY LEU ILE PHE ARG ARG ASP SER SEQRES 22 A 302 VAL SER GLY GLN VAL VAL ALA VAL PRO ASN THR LYS VAL SEQRES 23 A 302 VAL GLU LEU ASN THR ALA LEU HIS SER ASN HIS HIS HIS SEQRES 24 A 302 HIS HIS HIS HET SCA A 401 55 HETNAM SCA SUCCINYL-COENZYME A FORMUL 2 SCA C25 H40 N7 O19 P3 S FORMUL 3 HOH *230(H2 O) HELIX 1 AA1 LEU A 34 GLU A 38 5 5 HELIX 2 AA2 ASP A 63 HIS A 76 1 14 HELIX 3 AA3 GLY A 88 LEU A 93 1 6 HELIX 4 AA4 GLY A 108 SER A 117 1 10 HELIX 5 AA5 ARG A 132 TYR A 136 5 5 HELIX 6 AA6 ASP A 146 VAL A 150 5 5 HELIX 7 AA7 SER A 260 ALA A 263 5 4 SHEET 1 AA1 4 VAL A 18 TRP A 22 0 SHEET 2 AA1 4 THR A 3 THR A 13 -1 N THR A 11 O LEU A 19 SHEET 3 AA1 4 VAL A 46 ASP A 56 -1 O ILE A 55 N ALA A 4 SHEET 4 AA1 4 GLY A 39 ASP A 41 -1 N GLY A 39 O ARG A 48 SHEET 1 AA2 3 GLY A 102 ALA A 105 0 SHEET 2 AA2 3 VAL A 96 THR A 99 -1 N VAL A 97 O CYS A 104 SHEET 3 AA2 3 VAL A 124 ASP A 128 -1 O TYR A 125 N TRP A 98 SHEET 1 AA3 3 ARG A 143 ILE A 144 0 SHEET 2 AA3 3 THR A 161 VAL A 162 1 O VAL A 162 N ARG A 143 SHEET 3 AA3 3 MET A 179 VAL A 180 1 O VAL A 180 N THR A 161 SHEET 1 AA4 4 ALA A 154 LEU A 156 0 SHEET 2 AA4 4 ALA A 172 THR A 174 1 O ALA A 172 N TYR A 155 SHEET 3 AA4 4 THR A 189 VAL A 190 1 O VAL A 190 N GLY A 173 SHEET 4 AA4 4 SER A 215 LEU A 216 1 O LEU A 216 N THR A 189 SHEET 1 AA5 5 PHE A 167 VAL A 168 0 SHEET 2 AA5 5 ARG A 183 ILE A 184 1 O ILE A 184 N PHE A 167 SHEET 3 AA5 5 SER A 201 ILE A 202 1 O ILE A 202 N ARG A 183 SHEET 4 AA5 5 GLY A 227 CYS A 228 1 O CYS A 228 N SER A 201 SHEET 5 AA5 5 TYR A 243 ILE A 244 1 O ILE A 244 N GLY A 227 SHEET 1 AA6 5 ASP A 195 VAL A 196 0 SHEET 2 AA6 5 LEU A 221 LEU A 222 1 O LEU A 222 N ASP A 195 SHEET 3 AA6 5 ILE A 237 ILE A 238 1 O ILE A 238 N LEU A 221 SHEET 4 AA6 5 LEU A 268 ARG A 272 1 O PHE A 270 N ILE A 237 SHEET 5 AA6 5 VAL A 279 PRO A 283 -1 O VAL A 282 N ILE A 269 SHEET 1 AA7 2 LYS A 249 PHE A 252 0 SHEET 2 AA7 2 SER A 255 LYS A 258 -1 O HIS A 257 N VAL A 250 CISPEP 1 LYS A 286 VAL A 287 0 16.14 SITE 1 AC1 22 GLU A 181 ARG A 183 SER A 185 GLY A 198 SITE 2 AC1 22 SER A 201 MET A 203 GLY A 223 ALA A 224 SITE 3 AC1 22 GLU A 239 ALA A 240 GLY A 247 LYS A 249 SITE 4 AC1 22 LYS A 258 ARG A 271 ARG A 272 ASP A 273 SITE 5 AC1 22 SER A 274 HOH A 513 HOH A 537 HOH A 580 SITE 6 AC1 22 HOH A 614 HOH A 620 CRYST1 92.457 92.457 282.341 90.00 90.00 120.00 H 3 2 18 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 0.010816 0.006245 0.000000 0.00000 SCALE2 0.000000 0.012489 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003542 0.00000