HEADER ISOMERASE 18-OCT-16 5M47 TITLE CRYSTAL STRUCTURE OF DAPF FROM CORYNEBACTERIUM GLUTAMICUM IN COMPLEX TITLE 2 WITH D,L-DIAMINOPIMELATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIAMINOPIMELATE EPIMERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EPIMERASE; COMPND 5 SYNONYM: DAP EPIMERASE; COMPND 6 EC: 5.1.1.7; COMPND 7 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: DAPF, CGL1943, CG2129; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET30A KEYWDS ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.-Y.SAGONG,K.-J.KIM REVDAT 5 17-JAN-24 5M47 1 REMARK REVDAT 4 15-NOV-23 5M47 1 ATOM REVDAT 3 18-NOV-20 5M47 1 TITLE REVDAT 2 19-JUL-17 5M47 1 REVDAT 1 02-NOV-16 5M47 0 JRNL AUTH H.Y.SAGONG,K.J.KIM JRNL TITL STRUCTURAL BASIS FOR REDOX SENSITIVITY IN CORYNEBACTERIUM JRNL TITL 2 GLUTAMICUM DIAMINOPIMELATE EPIMERASE: AN ENZYME INVOLVED IN JRNL TITL 3 L-LYSINE BIOSYNTHESIS. JRNL REF SCI REP V. 7 42318 2017 JRNL REFN ESSN 2045-2322 JRNL PMID 28176858 JRNL DOI 10.1038/SREP42318 REMARK 2 REMARK 2 RESOLUTION. 2.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0155 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) : 2.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 110.09 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 19071 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 976 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) : 2.59 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.66 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1323 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.04 REMARK 3 BIN R VALUE (WORKING SET) : 0.3680 REMARK 3 BIN FREE R VALUE SET COUNT : 65 REMARK 3 BIN FREE R VALUE : 0.4150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2073 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 68 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.231 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.205 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.161 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.502 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2122 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1989 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2887 ; 2.103 ; 1.953 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4565 ; 1.122 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 279 ; 8.478 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 94 ;40.374 ;24.468 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 322 ;17.160 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;17.697 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 335 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2470 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 470 ; 0.002 ; 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): 1119 ; 2.710 ; 3.233 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1118 ; 2.534 ; 3.231 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1397 ; 4.387 ; 4.841 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5M47 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1200001906. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 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, HKL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19071 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.590 REMARK 200 RESOLUTION RANGE LOW (A) : 110.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 12.00 REMARK 200 R MERGE (I) : 0.11500 REMARK 200 R SYM (I) : 0.34400 REMARK 200 FOR THE DATA SET : 21.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.34400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.000 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: 5H2Y REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 76.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CITRATE, CHES, PH 9.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 3 2 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 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 REMARK 290 13555 Y+1/4,X+3/4,-Z+3/4 REMARK 290 14555 -Y+1/4,-X+1/4,-Z+1/4 REMARK 290 15555 Y+3/4,-X+3/4,Z+1/4 REMARK 290 16555 -Y+3/4,X+1/4,Z+3/4 REMARK 290 17555 X+1/4,Z+3/4,-Y+3/4 REMARK 290 18555 -X+3/4,Z+1/4,Y+3/4 REMARK 290 19555 -X+1/4,-Z+1/4,-Y+1/4 REMARK 290 20555 X+3/4,-Z+3/4,Y+1/4 REMARK 290 21555 Z+1/4,Y+3/4,-X+3/4 REMARK 290 22555 Z+3/4,-Y+3/4,X+1/4 REMARK 290 23555 -Z+3/4,Y+1/4,X+3/4 REMARK 290 24555 -Z+1/4,-Y+1/4,-X+1/4 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 77.84750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 77.84750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 77.84750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 77.84750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 77.84750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 77.84750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 77.84750 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 77.84750 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 77.84750 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 77.84750 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 77.84750 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 77.84750 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 77.84750 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 77.84750 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 77.84750 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 77.84750 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 77.84750 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 77.84750 REMARK 290 SMTRY1 13 0.000000 1.000000 0.000000 38.92375 REMARK 290 SMTRY2 13 1.000000 0.000000 0.000000 116.77125 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 116.77125 REMARK 290 SMTRY1 14 0.000000 -1.000000 0.000000 38.92375 REMARK 290 SMTRY2 14 -1.000000 0.000000 0.000000 38.92375 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 38.92375 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 116.77125 REMARK 290 SMTRY2 15 -1.000000 0.000000 0.000000 116.77125 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 38.92375 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 116.77125 REMARK 290 SMTRY2 16 1.000000 0.000000 0.000000 38.92375 REMARK 290 SMTRY3 16 0.000000 0.000000 1.000000 116.77125 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 38.92375 REMARK 290 SMTRY2 17 0.000000 0.000000 1.000000 116.77125 REMARK 290 SMTRY3 17 0.000000 -1.000000 0.000000 116.77125 REMARK 290 SMTRY1 18 -1.000000 0.000000 0.000000 116.77125 REMARK 290 SMTRY2 18 0.000000 0.000000 1.000000 38.92375 REMARK 290 SMTRY3 18 0.000000 1.000000 0.000000 116.77125 REMARK 290 SMTRY1 19 -1.000000 0.000000 0.000000 38.92375 REMARK 290 SMTRY2 19 0.000000 0.000000 -1.000000 38.92375 REMARK 290 SMTRY3 19 0.000000 -1.000000 0.000000 38.92375 REMARK 290 SMTRY1 20 1.000000 0.000000 0.000000 116.77125 REMARK 290 SMTRY2 20 0.000000 0.000000 -1.000000 116.77125 REMARK 290 SMTRY3 20 0.000000 1.000000 0.000000 38.92375 REMARK 290 SMTRY1 21 0.000000 0.000000 1.000000 38.92375 REMARK 290 SMTRY2 21 0.000000 1.000000 0.000000 116.77125 REMARK 290 SMTRY3 21 -1.000000 0.000000 0.000000 116.77125 REMARK 290 SMTRY1 22 0.000000 0.000000 1.000000 116.77125 REMARK 290 SMTRY2 22 0.000000 -1.000000 0.000000 116.77125 REMARK 290 SMTRY3 22 1.000000 0.000000 0.000000 38.92375 REMARK 290 SMTRY1 23 0.000000 0.000000 -1.000000 116.77125 REMARK 290 SMTRY2 23 0.000000 1.000000 0.000000 38.92375 REMARK 290 SMTRY3 23 1.000000 0.000000 0.000000 116.77125 REMARK 290 SMTRY1 24 0.000000 0.000000 -1.000000 38.92375 REMARK 290 SMTRY2 24 0.000000 -1.000000 0.000000 38.92375 REMARK 290 SMTRY3 24 -1.000000 0.000000 0.000000 38.92375 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 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 0.000000 -1.000000 0.000000 38.92375 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 38.92375 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -116.77125 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 HIS A 281 REMARK 465 HIS A 282 REMARK 465 HIS A 283 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 ARG A 40 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 110 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ASP A 131 CB - CG - OD1 ANGL. DEV. = -6.1 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 ASP A 22 57.67 -155.65 REMARK 500 SER A 78 127.78 -35.05 REMARK 500 ASP A 101 46.70 -142.83 REMARK 500 ASN A 146 66.90 64.79 REMARK 500 VAL A 215 -52.29 -139.10 REMARK 500 HIS A 279 129.58 -39.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 HIS A 278 HIS A 279 142.34 REMARK 500 HIS A 279 HIS A 280 135.33 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 API A 301 DBREF 5M47 A 1 277 UNP Q8NP73 DAPF_CORGL 1 277 SEQADV 5M47 HIS A 278 UNP Q8NP73 EXPRESSION TAG SEQADV 5M47 HIS A 279 UNP Q8NP73 EXPRESSION TAG SEQADV 5M47 HIS A 280 UNP Q8NP73 EXPRESSION TAG SEQADV 5M47 HIS A 281 UNP Q8NP73 EXPRESSION TAG SEQADV 5M47 HIS A 282 UNP Q8NP73 EXPRESSION TAG SEQADV 5M47 HIS A 283 UNP Q8NP73 EXPRESSION TAG SEQRES 1 A 283 MET ASN LEU THR ILE PRO PHE ALA LYS GLY HIS ALA THR SEQRES 2 A 283 GLU ASN ASP PHE ILE ILE ILE PRO ASP GLU ASP ALA ARG SEQRES 3 A 283 LEU ASP LEU THR PRO GLU MET VAL VAL THR LEU CYS ASP SEQRES 4 A 283 ARG ARG ALA GLY ILE GLY ALA ASP GLY ILE LEU ARG VAL SEQRES 5 A 283 VAL LYS ALA ALA ASP VAL GLU GLY SER THR VAL ASP PRO SEQRES 6 A 283 SER LEU TRP PHE MET ASP TYR ARG ASN ALA ASP GLY SER SEQRES 7 A 283 LEU ALA GLU MET CYS GLY ASN GLY VAL ARG LEU PHE ALA SEQRES 8 A 283 HIS TRP LEU TYR SER ARG GLY LEU VAL ASP ASN THR SER SEQRES 9 A 283 PHE ASP ILE GLY THR ARG ALA GLY VAL ARG HIS VAL ASP SEQRES 10 A 283 ILE LEU GLN ALA ASP GLN HIS SER ALA GLN VAL ARG VAL SEQRES 11 A 283 ASP MET GLY ILE PRO ASP VAL THR GLY LEU SER THR CYS SEQRES 12 A 283 ASP ILE ASN GLY GLN VAL PHE ALA GLY LEU GLY VAL ASP SEQRES 13 A 283 MET GLY ASN PRO HIS LEU ALA CYS VAL VAL PRO GLY LEU SEQRES 14 A 283 SER ALA SER ALA LEU ALA ASP MET GLU LEU ARG ALA PRO SEQRES 15 A 283 THR PHE ASP GLN GLU PHE PHE PRO HIS GLY VAL ASN VAL SEQRES 16 A 283 GLU ILE VAL THR GLU LEU GLU ASP ASP ALA VAL SER MET SEQRES 17 A 283 ARG VAL TRP GLU ARG GLY VAL GLY GLU THR ARG SER CYS SEQRES 18 A 283 GLY THR GLY THR VAL ALA ALA ALA CYS ALA ALA LEU ALA SEQRES 19 A 283 ASP ALA GLY LEU GLY GLU GLY THR VAL LYS VAL CYS VAL SEQRES 20 A 283 PRO GLY GLY GLU VAL GLU VAL GLN ILE PHE ASP ASP GLY SEQRES 21 A 283 SER THR LEU THR GLY PRO SER ALA ILE ILE ALA LEU GLY SEQRES 22 A 283 GLU VAL GLN ILE HIS HIS HIS HIS HIS HIS HET API A 301 13 HETNAM API 2,6-DIAMINOPIMELIC ACID FORMUL 2 API C7 H14 N2 O4 FORMUL 3 HOH *68(H2 O) HELIX 1 AA1 THR A 30 ASP A 39 1 10 HELIX 2 AA2 ALA A 56 VAL A 58 5 3 HELIX 3 AA3 CYS A 83 ARG A 97 1 15 HELIX 4 AA4 SER A 170 MET A 177 1 8 HELIX 5 AA5 CYS A 221 ALA A 236 1 16 SHEET 1 AA110 THR A 183 PHE A 184 0 SHEET 2 AA110 ASP A 136 ASP A 144 -1 N ASP A 144 O THR A 183 SHEET 3 AA110 VAL A 149 ASP A 156 -1 O ASP A 156 N ASP A 136 SHEET 4 AA110 PRO A 160 VAL A 166 -1 O ALA A 163 N LEU A 153 SHEET 5 AA110 ASN A 194 THR A 199 1 O VAL A 198 N VAL A 166 SHEET 6 AA110 ALA A 205 GLU A 212 -1 O TRP A 211 N VAL A 195 SHEET 7 AA110 GLY A 241 VAL A 247 1 O CYS A 246 N MET A 208 SHEET 8 AA110 GLY A 250 ILE A 256 -1 O ILE A 256 N GLY A 241 SHEET 9 AA110 SER A 261 HIS A 278 -1 O THR A 264 N GLU A 253 SHEET 10 AA110 GLY A 216 GLU A 217 0 SHEET 1 AA215 THR A 183 PHE A 184 0 SHEET 2 AA215 ASP A 136 ASP A 144 -1 N ASP A 144 O THR A 183 SHEET 3 AA215 VAL A 149 ASP A 156 -1 O ASP A 156 N ASP A 136 SHEET 4 AA215 PRO A 160 VAL A 166 -1 O ALA A 163 N LEU A 153 SHEET 5 AA215 ASN A 194 THR A 199 1 O VAL A 198 N VAL A 166 SHEET 6 AA215 ALA A 205 GLU A 212 -1 O TRP A 211 N VAL A 195 SHEET 7 AA215 SER A 125 ASP A 131 0 SHEET 8 AA215 GLY A 112 ALA A 121 -1 N ASP A 117 O ARG A 129 SHEET 9 AA215 SER A 104 THR A 109 -1 N PHE A 105 O VAL A 116 SHEET 10 AA215 TRP A 68 ASN A 74 1 N TRP A 68 O GLY A 108 SHEET 11 AA215 GLY A 48 LYS A 54 -1 N VAL A 53 O PHE A 69 SHEET 12 AA215 ASN A 15 PRO A 21 1 N ILE A 20 O VAL A 52 SHEET 13 AA215 ASN A 2 ALA A 12 -1 N ALA A 8 O ILE A 19 SHEET 14 AA215 SER A 261 HIS A 278 -1 O GLY A 273 N PHE A 7 SHEET 15 AA215 GLY A 216 GLU A 217 0 SITE 1 AC1 13 ASN A 15 ASN A 74 ALA A 80 CYS A 83 SITE 2 AC1 13 GLY A 84 ASN A 85 ASN A 159 ASN A 194 SITE 3 AC1 13 GLU A 212 ARG A 213 CYS A 221 GLY A 222 SITE 4 AC1 13 THR A 223 CRYST1 155.695 155.695 155.695 90.00 90.00 90.00 P 43 3 2 24 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 0.006423 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006423 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006423 0.00000