HEADER OXIDOREDUCTASE 23-OCT-15 5EES TITLE CRYSTAL STRUCTURE OF DAPB IN COMPLEX WITH NADP+ FROM CORYNEBACTERIUM TITLE 2 GLUTAMICUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: 4-HYDROXY-TETRAHYDRODIPICOLINATE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HTPA REDUCTASE; COMPND 5 EC: 1.17.1.8; COMPND 6 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: DAPB, CGL1973, CG2163; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE)-T1R; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET30A KEYWDS OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR H.-Y.SAGONG,K.-J.KIM REVDAT 4 08-NOV-23 5EES 1 REMARK REVDAT 3 09-SEP-20 5EES 1 TITLE REVDAT 2 19-JUL-17 5EES 1 JRNL REMARK REVDAT 1 11-NOV-15 5EES 0 JRNL AUTH H.Y.SAGONG,K.J.KIM JRNL TITL STRUCTURAL INSIGHT INTO DIHYDRODIPICOLINATE REDUCTASE FROM JRNL TITL 2 CORYBEBACTERIUM GLUTAMICUM FOR LYSINE BIOSYNTHESIS. JRNL REF J. MICROBIOL. BIOTECHNOL. V. 26 226 2016 JRNL REFN ESSN 1738-8872 JRNL PMID 26502738 JRNL DOI 10.4014/JMB.1508.08086 REMARK 2 REMARK 2 RESOLUTION. 2.15 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 25394 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) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1364 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) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.20 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1687 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.54 REMARK 3 BIN R VALUE (WORKING SET) : 0.4040 REMARK 3 BIN FREE R VALUE SET COUNT : 101 REMARK 3 BIN FREE R VALUE : 0.3920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1820 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.84000 REMARK 3 B22 (A**2) : 0.84000 REMARK 3 B33 (A**2) : -1.68000 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): 0.135 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.132 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.118 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.142 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1912 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1808 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2606 ; 2.203 ; 1.986 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4144 ; 1.093 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 246 ; 7.841 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 82 ;43.398 ;25.488 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 292 ;15.359 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;19.538 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 307 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2189 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 419 ; 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): 987 ; 4.292 ; 4.916 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 986 ; 4.257 ; 4.913 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1232 ; 6.089 ; 7.358 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 5EES COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214657. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUL-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.75 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 : 25394 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.140 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 (%) : 95.1 REMARK 200 DATA REDUNDANCY : 8.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.14 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 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: 5EER REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 74.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, SODIUM ACETATE REMARK 280 TRIHYDRATE, PH 4.75, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 53.98450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 53.98450 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 86.02450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 53.98450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 43.01225 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 53.98450 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 129.03675 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 53.98450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 129.03675 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 53.98450 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 43.01225 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 53.98450 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 53.98450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 86.02450 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 53.98450 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 53.98450 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 86.02450 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 53.98450 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 129.03675 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 53.98450 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 43.01225 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 53.98450 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 43.01225 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 53.98450 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 129.03675 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 53.98450 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 53.98450 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 86.02450 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 18980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -203.0 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 0.000000 -1.000000 0.000000 107.96900 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 107.96900 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 107.96900 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 107.96900 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 483 O HOH A 483 10665 1.20 REMARK 500 O HOH A 434 O HOH A 495 15555 2.06 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 ARG A 85 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 177 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 177 NE - CZ - NH2 ANGL. DEV. = -3.6 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 LEU A 42 -38.60 -39.67 REMARK 500 THR A 55 -115.69 -125.75 REMARK 500 ASP A 82 -178.27 -68.89 REMARK 500 ASP A 167 114.80 -174.03 REMARK 500 VAL A 195 -99.00 -106.36 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 GLY A 2 ILE A 3 139.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 518 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH A 519 DISTANCE = 6.99 ANGSTROMS REMARK 525 HOH A 520 DISTANCE = 10.50 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAP A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5EER RELATED DB: PDB DBREF 5EES A 2 248 UNP P40110 DAPB_CORGL 2 248 SEQRES 1 A 247 GLY ILE LYS VAL GLY VAL LEU GLY ALA LYS GLY ARG VAL SEQRES 2 A 247 GLY GLN THR ILE VAL ALA ALA VAL ASN GLU SER ASP ASP SEQRES 3 A 247 LEU GLU LEU VAL ALA GLU ILE GLY VAL ASP ASP ASP LEU SEQRES 4 A 247 SER LEU LEU VAL ASP ASN GLY ALA GLU VAL VAL VAL ASP SEQRES 5 A 247 PHE THR THR PRO ASN ALA VAL MET GLY ASN LEU GLU PHE SEQRES 6 A 247 CYS ILE ASN ASN GLY ILE SER ALA VAL VAL GLY THR THR SEQRES 7 A 247 GLY PHE ASP ASP ALA ARG LEU GLU GLN VAL ARG ASP TRP SEQRES 8 A 247 LEU GLU GLY LYS ASP ASN VAL GLY VAL LEU ILE ALA PRO SEQRES 9 A 247 ASN PHE ALA ILE SER ALA VAL LEU THR MET VAL PHE SER SEQRES 10 A 247 LYS GLN ALA ALA ARG PHE PHE GLU SER ALA GLU VAL ILE SEQRES 11 A 247 GLU LEU HIS HIS PRO ASN LYS LEU ASP ALA PRO SER GLY SEQRES 12 A 247 THR ALA ILE HIS THR ALA GLN GLY ILE ALA ALA ALA ARG SEQRES 13 A 247 LYS GLU ALA GLY MET ASP ALA GLN PRO ASP ALA THR GLU SEQRES 14 A 247 GLN ALA LEU GLU GLY SER ARG GLY ALA SER VAL ASP GLY SEQRES 15 A 247 ILE PRO VAL HIS ALA VAL ARG MET SER GLY MET VAL ALA SEQRES 16 A 247 HIS GLU GLN VAL ILE PHE GLY THR GLN GLY GLN THR LEU SEQRES 17 A 247 THR ILE LYS GLN ASP SER TYR ASP ARG ASN SER PHE ALA SEQRES 18 A 247 PRO GLY VAL LEU VAL GLY VAL ARG ASN ILE ALA GLN HIS SEQRES 19 A 247 PRO GLY LEU VAL VAL GLY LEU GLU HIS TYR LEU GLY LEU HET GOL A 301 6 HET NAP A 302 48 HET SO4 A 303 5 HET SO4 A 304 5 HETNAM GOL GLYCEROL HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 2 GOL C3 H8 O3 FORMUL 3 NAP C21 H28 N7 O17 P3 FORMUL 4 SO4 2(O4 S 2-) FORMUL 6 HOH *120(H2 O) HELIX 1 AA1 GLY A 12 SER A 25 1 14 HELIX 2 AA2 LEU A 40 ASN A 46 1 7 HELIX 3 AA3 THR A 56 ASN A 70 1 15 HELIX 4 AA4 ASP A 82 GLU A 94 1 13 HELIX 5 AA5 ALA A 108 ALA A 122 1 15 HELIX 6 AA6 ARG A 123 PHE A 125 5 3 HELIX 7 AA7 SER A 143 ALA A 160 1 18 HELIX 8 AA8 PHE A 221 ILE A 232 1 12 HELIX 9 AA9 ALA A 233 HIS A 235 5 3 HELIX 10 AB1 LEU A 242 LEU A 246 5 5 SHEET 1 AA1 6 GLU A 29 ILE A 34 0 SHEET 2 AA1 6 LYS A 4 LEU A 8 1 N VAL A 5 O GLU A 29 SHEET 3 AA1 6 VAL A 50 ASP A 53 1 O VAL A 52 N LEU A 8 SHEET 4 AA1 6 SER A 73 VAL A 76 1 O SER A 73 N VAL A 51 SHEET 5 AA1 6 GLY A 100 ILE A 103 1 O LEU A 102 N VAL A 76 SHEET 6 AA1 6 GLY A 237 VAL A 240 1 O GLY A 237 N VAL A 101 SHEET 1 AA2 5 ALA A 179 VAL A 181 0 SHEET 2 AA2 5 ILE A 184 ARG A 190 -1 O VAL A 186 N ALA A 179 SHEET 3 AA2 5 SER A 127 HIS A 134 1 N GLU A 132 O VAL A 189 SHEET 4 AA2 5 ALA A 196 THR A 204 -1 O GLN A 199 N ILE A 131 SHEET 5 AA2 5 GLN A 207 SER A 215 -1 O LEU A 209 N PHE A 202 CISPEP 1 ALA A 141 PRO A 142 0 -13.21 SITE 1 AC1 9 ASN A 58 ARG A 85 GLN A 88 PRO A 142 SITE 2 AC1 9 GLN A 171 HOH A 416 HOH A 431 HOH A 449 SITE 3 AC1 9 HOH A 484 SITE 1 AC2 24 GLY A 9 LYS A 11 GLY A 12 ARG A 13 SITE 2 AC2 24 VAL A 14 ILE A 34 GLY A 35 VAL A 36 SITE 3 AC2 24 PHE A 54 THR A 55 ALA A 59 GLY A 77 SITE 4 AC2 24 THR A 79 ALA A 104 PRO A 105 ASN A 106 SITE 5 AC2 24 PHE A 107 PHE A 221 HOH A 401 HOH A 407 SITE 6 AC2 24 HOH A 413 HOH A 414 HOH A 465 HOH A 470 SITE 1 AC3 5 LYS A 138 ASP A 140 SER A 143 GLY A 144 SITE 2 AC3 5 THR A 145 SITE 1 AC4 2 HIS A 135 LYS A 138 CRYST1 107.969 107.969 172.049 90.00 90.00 90.00 I 41 2 2 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 0.009262 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009262 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005812 0.00000