HEADER DNA BINDING PROTEIN 24-SEP-15 5DY0 TITLE CRYSTAL OF AMTR FROM CORYNEBACTERIUM GLUTAMICUM IN COMPLEX WITH DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: TETR FAMILY TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA; COMPND 7 CHAIN: E, F, G, H; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CORYNEBACTERIUM GLUTAMICUM; SOURCE 3 ORGANISM_TAXID: 1718; SOURCE 4 STRAIN: ATCC 13969; SOURCE 5 GENE: KIQ_008455; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-26; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: CORYNEBACTERIUM GLUTAMICUM; SOURCE 13 ORGANISM_TAXID: 1718 KEYWDS TETR FAMILY REGULATOR, DNA BINDING PROTEIN, NITROGEN MASTER KEYWDS 2 REGULATOR, PII, GLNK, GLNB, TFR EXPDTA X-RAY DIFFRACTION AUTHOR C.PALANCA,V.RUBIO REVDAT 4 10-JAN-24 5DY0 1 REMARK REVDAT 3 30-MAR-16 5DY0 1 JRNL REVDAT 2 20-JAN-16 5DY0 1 JRNL REVDAT 1 13-JAN-16 5DY0 0 JRNL AUTH C.PALANCA,V.RUBIO JRNL TITL STRUCTURE OF AMTR, THE GLOBAL NITROGEN REGULATOR OF JRNL TITL 2 CORYNEBACTERIUM GLUTAMICUM, IN FREE AND DNA-BOUND FORMS. JRNL REF FEBS J. V. 283 1039 2016 JRNL REFN ISSN 1742-464X JRNL PMID 26744254 JRNL DOI 10.1111/FEBS.13643 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0124 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 137.42 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 62963 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) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3348 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) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4142 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.16 REMARK 3 BIN R VALUE (WORKING SET) : 0.3260 REMARK 3 BIN FREE R VALUE SET COUNT : 214 REMARK 3 BIN FREE R VALUE : 0.3900 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6589 REMARK 3 NUCLEIC ACID ATOMS : 2120 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 91.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 7.98000 REMARK 3 B22 (A**2) : -1.92000 REMARK 3 B33 (A**2) : -6.06000 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): 0.353 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.257 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.221 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.778 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.925 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 9093 ; 0.010 ; 0.017 REMARK 3 BOND LENGTHS OTHERS (A): 7627 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 12821 ; 1.385 ; 1.750 REMARK 3 BOND ANGLES OTHERS (DEGREES): 17577 ; 1.223 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 871 ; 5.420 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 269 ;32.744 ;22.900 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1062 ;18.104 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 60 ;19.058 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1406 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8809 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1923 ; 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): 3496 ; 6.744 ; 9.090 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3495 ; 6.743 ; 9.090 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4363 ; 9.738 ;13.651 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4364 ; 9.737 ;13.652 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 5597 ; 8.468 ; 9.582 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 5596 ; 8.464 ; 9.583 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 8458 ;12.957 ;14.265 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 38888 ;16.561 ;87.640 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 38889 ;16.561 ;87.640 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 5DY0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000212781. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-SEP-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.1.29 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 67304 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 119.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.68300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5DY1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 80.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 6.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2 M TRISODIUM CITRATE, 0.1 M NAHEPES REMARK 280 PH 6.8, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 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 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 119.93700 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 119.93700 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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 7390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, E, F 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 REMARK 350 BIOMOLECULE: 2 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: 8220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, G, H 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 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 LEU A 223 REMARK 465 GLU A 224 REMARK 465 HIS A 225 REMARK 465 HIS A 226 REMARK 465 HIS A 227 REMARK 465 HIS A 228 REMARK 465 HIS A 229 REMARK 465 HIS A 230 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 GLY B 3 REMARK 465 LYS B 222 REMARK 465 LEU B 223 REMARK 465 GLU B 224 REMARK 465 HIS B 225 REMARK 465 HIS B 226 REMARK 465 HIS B 227 REMARK 465 HIS B 228 REMARK 465 HIS B 229 REMARK 465 HIS B 230 REMARK 465 MET C 1 REMARK 465 ALA C 2 REMARK 465 GLY C 3 REMARK 465 ALA C 4 REMARK 465 LEU C 223 REMARK 465 GLU C 224 REMARK 465 HIS C 225 REMARK 465 HIS C 226 REMARK 465 HIS C 227 REMARK 465 HIS C 228 REMARK 465 HIS C 229 REMARK 465 HIS C 230 REMARK 465 MET D 1 REMARK 465 ALA D 2 REMARK 465 GLY D 3 REMARK 465 LEU D 223 REMARK 465 GLU D 224 REMARK 465 HIS D 225 REMARK 465 HIS D 226 REMARK 465 HIS D 227 REMARK 465 HIS D 228 REMARK 465 HIS D 229 REMARK 465 HIS D 230 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 LYS A 18 CG CD CE NZ REMARK 470 ASP A 84 CG OD1 OD2 REMARK 470 ILE A 122 CG1 CG2 CD1 REMARK 470 SER A 125 OG REMARK 470 GLU A 126 CG CD OE1 OE2 REMARK 470 GLU A 130 CG CD OE1 OE2 REMARK 470 GLU A 210 CG CD OE1 OE2 REMARK 470 GLU A 214 CG CD OE1 OE2 REMARK 470 LYS A 217 CG CD CE NZ REMARK 470 ASP A 220 CG OD1 OD2 REMARK 470 LYS A 222 CG CD CE NZ REMARK 470 ARG B 10 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 14 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 18 CG CD CE NZ REMARK 470 LYS B 72 CG CD CE NZ REMARK 470 GLU B 76 CG CD OE1 OE2 REMARK 470 ILE B 122 CG1 CG2 CD1 REMARK 470 GLU B 126 CG CD OE1 OE2 REMARK 470 GLU B 127 CG CD OE1 OE2 REMARK 470 GLU B 130 CG CD OE1 OE2 REMARK 470 LYS B 175 CG CD CE NZ REMARK 470 GLU B 187 CG CD OE1 OE2 REMARK 470 VAL C 5 CG1 CG2 REMARK 470 ARG C 10 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 18 CG CD CE NZ REMARK 470 LYS C 72 CG CD CE NZ REMARK 470 GLU C 76 CG CD OE1 OE2 REMARK 470 LYS C 111 CG CD CE NZ REMARK 470 ILE C 122 CG1 CG2 CD1 REMARK 470 SER C 125 OG REMARK 470 GLU C 126 CG CD OE1 OE2 REMARK 470 GLU C 127 CG CD OE1 OE2 REMARK 470 GLU C 130 CG CD OE1 OE2 REMARK 470 LYS C 175 CG CD CE NZ REMARK 470 GLU C 187 CG CD OE1 OE2 REMARK 470 LYS C 217 CG CD CE NZ REMARK 470 LYS C 222 CG CD CE NZ REMARK 470 ARG D 10 CG CD NE CZ NH1 NH2 REMARK 470 SER D 11 OG REMARK 470 LYS D 18 CG CD CE NZ REMARK 470 GLU D 76 CG CD OE1 OE2 REMARK 470 LEU D 88 CG CD1 CD2 REMARK 470 ASP D 89 CG OD1 OD2 REMARK 470 GLU D 126 CG CD OE1 OE2 REMARK 470 GLU D 127 CG CD OE1 OE2 REMARK 470 GLU D 130 CG CD OE1 OE2 REMARK 470 TYR D 131 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU D 136 CG CD OE1 OE2 REMARK 470 LYS D 217 CG CD CE NZ REMARK 470 LYS D 222 CG CD CE NZ 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 VAL D 80 OD1 ASP D 84 1.22 REMARK 500 OG SER B 125 CD2 PHE B 128 1.78 REMARK 500 O ALA D 90 NH1 ARG D 95 1.96 REMARK 500 O ILE D 162 OG SER D 165 2.07 REMARK 500 O VAL C 80 OD1 ASP C 84 2.09 REMARK 500 O THR C 110 NH2 ARG C 170 2.13 REMARK 500 NH1 ARG C 15 OD1 ASP C 26 2.13 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 DT E 5 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 DA E 23 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 DA F 23 O4' - C4' - C3' ANGL. DEV. = -3.8 DEGREES REMARK 500 DA G 23 O4' - C4' - C3' ANGL. DEV. = -3.7 DEGREES REMARK 500 DA H 23 O4' - C4' - C3' ANGL. DEV. = -2.6 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 ILE A 122 -35.10 -38.36 REMARK 500 PHE A 128 53.20 -102.16 REMARK 500 ASN A 172 67.32 -150.49 REMARK 500 ASP A 207 54.11 39.85 REMARK 500 ALA B 12 159.27 -47.62 REMARK 500 PHE B 128 -8.11 -59.75 REMARK 500 ASN B 172 52.36 -156.83 REMARK 500 ILE C 149 -63.06 -91.34 REMARK 500 ASN C 172 63.46 -150.79 REMARK 500 GLN D 119 56.98 -91.58 REMARK 500 SER D 125 152.22 -48.70 REMARK 500 REMARK 500 REMARK: NULL DBREF1 5DY0 A 1 222 UNP A0A072Z681_CORGT DBREF2 5DY0 A A0A072Z681 1 222 DBREF1 5DY0 B 1 222 UNP A0A072Z681_CORGT DBREF2 5DY0 B A0A072Z681 1 222 DBREF1 5DY0 C 1 222 UNP A0A072Z681_CORGT DBREF2 5DY0 C A0A072Z681 1 222 DBREF1 5DY0 D 1 222 UNP A0A072Z681_CORGT DBREF2 5DY0 D A0A072Z681 1 222 DBREF 5DY0 E 1 26 PDB 5DY0 5DY0 1 26 DBREF 5DY0 F 1 26 PDB 5DY0 5DY0 1 26 DBREF 5DY0 G 1 26 PDB 5DY0 5DY0 1 26 DBREF 5DY0 H 1 26 PDB 5DY0 5DY0 1 26 SEQADV 5DY0 ILE A 141 UNP A0A072Z68 VAL 141 CONFLICT SEQADV 5DY0 LEU A 223 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 GLU A 224 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 HIS A 225 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 HIS A 226 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 HIS A 227 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 HIS A 228 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 HIS A 229 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 HIS A 230 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 ILE B 141 UNP A0A072Z68 VAL 141 CONFLICT SEQADV 5DY0 LEU B 223 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 GLU B 224 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 HIS B 225 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 HIS B 226 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 HIS B 227 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 HIS B 228 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 HIS B 229 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 HIS B 230 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 ILE C 141 UNP A0A072Z68 VAL 141 CONFLICT SEQADV 5DY0 LEU C 223 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 GLU C 224 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 HIS C 225 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 HIS C 226 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 HIS C 227 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 HIS C 228 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 HIS C 229 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 HIS C 230 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 ILE D 141 UNP A0A072Z68 VAL 141 CONFLICT SEQADV 5DY0 LEU D 223 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 GLU D 224 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 HIS D 225 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 HIS D 226 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 HIS D 227 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 HIS D 228 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 HIS D 229 UNP A0A072Z68 EXPRESSION TAG SEQADV 5DY0 HIS D 230 UNP A0A072Z68 EXPRESSION TAG SEQRES 1 A 230 MET ALA GLY ALA VAL GLY ARG PRO ARG ARG SER ALA PRO SEQRES 2 A 230 ARG ARG ALA GLY LYS ASN PRO ARG GLU GLU ILE LEU ASP SEQRES 3 A 230 ALA SER ALA GLU LEU PHE THR HIS GLN GLY PHE ALA THR SEQRES 4 A 230 THR SER THR HIS GLN ILE ALA ASP ALA VAL GLY ILE ARG SEQRES 5 A 230 GLN ALA SER LEU TYR TYR HIS PHE PRO SER LYS THR GLU SEQRES 6 A 230 ILE PHE LEU THR LEU LEU LYS SER THR VAL GLU PRO SER SEQRES 7 A 230 THR VAL LEU ALA GLU ASP LEU SER ILE LEU ASP ALA GLY SEQRES 8 A 230 PRO GLU MET ARG LEU TRP ALA ILE VAL ALA SER GLU VAL SEQRES 9 A 230 ARG LEU LEU LEU SER THR LYS TRP ASN VAL GLY ARG LEU SEQRES 10 A 230 TYR GLN LEU PRO ILE VAL GLY SER GLU GLU PHE ALA GLU SEQRES 11 A 230 TYR HIS SER GLN ARG GLU ALA LEU THR ASN ILE PHE ARG SEQRES 12 A 230 ASP LEU ALA THR GLU ILE VAL GLY ASP ASP PRO ARG ALA SEQRES 13 A 230 GLU LEU PRO PHE HIS ILE THR MET SER VAL ILE GLU MET SEQRES 14 A 230 ARG ARG ASN ASP GLY LYS ILE PRO SER PRO LEU SER ALA SEQRES 15 A 230 ASP SER LEU PRO GLU THR ALA ILE MET LEU ALA ASP ALA SEQRES 16 A 230 SER LEU ALA VAL LEU GLY ALA SER LEU PRO ALA ASP ARG SEQRES 17 A 230 VAL GLU LYS THR LEU GLU LEU ILE LYS GLN ALA ASP ALA SEQRES 18 A 230 LYS LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 230 MET ALA GLY ALA VAL GLY ARG PRO ARG ARG SER ALA PRO SEQRES 2 B 230 ARG ARG ALA GLY LYS ASN PRO ARG GLU GLU ILE LEU ASP SEQRES 3 B 230 ALA SER ALA GLU LEU PHE THR HIS GLN GLY PHE ALA THR SEQRES 4 B 230 THR SER THR HIS GLN ILE ALA ASP ALA VAL GLY ILE ARG SEQRES 5 B 230 GLN ALA SER LEU TYR TYR HIS PHE PRO SER LYS THR GLU SEQRES 6 B 230 ILE PHE LEU THR LEU LEU LYS SER THR VAL GLU PRO SER SEQRES 7 B 230 THR VAL LEU ALA GLU ASP LEU SER ILE LEU ASP ALA GLY SEQRES 8 B 230 PRO GLU MET ARG LEU TRP ALA ILE VAL ALA SER GLU VAL SEQRES 9 B 230 ARG LEU LEU LEU SER THR LYS TRP ASN VAL GLY ARG LEU SEQRES 10 B 230 TYR GLN LEU PRO ILE VAL GLY SER GLU GLU PHE ALA GLU SEQRES 11 B 230 TYR HIS SER GLN ARG GLU ALA LEU THR ASN ILE PHE ARG SEQRES 12 B 230 ASP LEU ALA THR GLU ILE VAL GLY ASP ASP PRO ARG ALA SEQRES 13 B 230 GLU LEU PRO PHE HIS ILE THR MET SER VAL ILE GLU MET SEQRES 14 B 230 ARG ARG ASN ASP GLY LYS ILE PRO SER PRO LEU SER ALA SEQRES 15 B 230 ASP SER LEU PRO GLU THR ALA ILE MET LEU ALA ASP ALA SEQRES 16 B 230 SER LEU ALA VAL LEU GLY ALA SER LEU PRO ALA ASP ARG SEQRES 17 B 230 VAL GLU LYS THR LEU GLU LEU ILE LYS GLN ALA ASP ALA SEQRES 18 B 230 LYS LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 C 230 MET ALA GLY ALA VAL GLY ARG PRO ARG ARG SER ALA PRO SEQRES 2 C 230 ARG ARG ALA GLY LYS ASN PRO ARG GLU GLU ILE LEU ASP SEQRES 3 C 230 ALA SER ALA GLU LEU PHE THR HIS GLN GLY PHE ALA THR SEQRES 4 C 230 THR SER THR HIS GLN ILE ALA ASP ALA VAL GLY ILE ARG SEQRES 5 C 230 GLN ALA SER LEU TYR TYR HIS PHE PRO SER LYS THR GLU SEQRES 6 C 230 ILE PHE LEU THR LEU LEU LYS SER THR VAL GLU PRO SER SEQRES 7 C 230 THR VAL LEU ALA GLU ASP LEU SER ILE LEU ASP ALA GLY SEQRES 8 C 230 PRO GLU MET ARG LEU TRP ALA ILE VAL ALA SER GLU VAL SEQRES 9 C 230 ARG LEU LEU LEU SER THR LYS TRP ASN VAL GLY ARG LEU SEQRES 10 C 230 TYR GLN LEU PRO ILE VAL GLY SER GLU GLU PHE ALA GLU SEQRES 11 C 230 TYR HIS SER GLN ARG GLU ALA LEU THR ASN ILE PHE ARG SEQRES 12 C 230 ASP LEU ALA THR GLU ILE VAL GLY ASP ASP PRO ARG ALA SEQRES 13 C 230 GLU LEU PRO PHE HIS ILE THR MET SER VAL ILE GLU MET SEQRES 14 C 230 ARG ARG ASN ASP GLY LYS ILE PRO SER PRO LEU SER ALA SEQRES 15 C 230 ASP SER LEU PRO GLU THR ALA ILE MET LEU ALA ASP ALA SEQRES 16 C 230 SER LEU ALA VAL LEU GLY ALA SER LEU PRO ALA ASP ARG SEQRES 17 C 230 VAL GLU LYS THR LEU GLU LEU ILE LYS GLN ALA ASP ALA SEQRES 18 C 230 LYS LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 D 230 MET ALA GLY ALA VAL GLY ARG PRO ARG ARG SER ALA PRO SEQRES 2 D 230 ARG ARG ALA GLY LYS ASN PRO ARG GLU GLU ILE LEU ASP SEQRES 3 D 230 ALA SER ALA GLU LEU PHE THR HIS GLN GLY PHE ALA THR SEQRES 4 D 230 THR SER THR HIS GLN ILE ALA ASP ALA VAL GLY ILE ARG SEQRES 5 D 230 GLN ALA SER LEU TYR TYR HIS PHE PRO SER LYS THR GLU SEQRES 6 D 230 ILE PHE LEU THR LEU LEU LYS SER THR VAL GLU PRO SER SEQRES 7 D 230 THR VAL LEU ALA GLU ASP LEU SER ILE LEU ASP ALA GLY SEQRES 8 D 230 PRO GLU MET ARG LEU TRP ALA ILE VAL ALA SER GLU VAL SEQRES 9 D 230 ARG LEU LEU LEU SER THR LYS TRP ASN VAL GLY ARG LEU SEQRES 10 D 230 TYR GLN LEU PRO ILE VAL GLY SER GLU GLU PHE ALA GLU SEQRES 11 D 230 TYR HIS SER GLN ARG GLU ALA LEU THR ASN ILE PHE ARG SEQRES 12 D 230 ASP LEU ALA THR GLU ILE VAL GLY ASP ASP PRO ARG ALA SEQRES 13 D 230 GLU LEU PRO PHE HIS ILE THR MET SER VAL ILE GLU MET SEQRES 14 D 230 ARG ARG ASN ASP GLY LYS ILE PRO SER PRO LEU SER ALA SEQRES 15 D 230 ASP SER LEU PRO GLU THR ALA ILE MET LEU ALA ASP ALA SEQRES 16 D 230 SER LEU ALA VAL LEU GLY ALA SER LEU PRO ALA ASP ARG SEQRES 17 D 230 VAL GLU LYS THR LEU GLU LEU ILE LYS GLN ALA ASP ALA SEQRES 18 D 230 LYS LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 E 26 DA DT DT DA DT DC DT DA DT DA DG DA DT SEQRES 2 E 26 DC DT DA DT DA DG DA DT DA DA DT DG DC SEQRES 1 F 26 DA DT DT DA DT DC DT DA DT DA DG DA DT SEQRES 2 F 26 DC DT DA DT DA DG DA DT DA DA DT DG DC SEQRES 1 G 26 DA DT DT DA DT DC DT DA DT DA DG DA DT SEQRES 2 G 26 DC DT DA DT DA DG DA DT DA DA DT DG DC SEQRES 1 H 26 DA DT DT DA DT DC DT DA DT DA DG DA DT SEQRES 2 H 26 DC DT DA DT DA DG DA DT DA DA DT DG DC HELIX 1 AA1 ASN A 19 GLY A 36 1 18 HELIX 2 AA2 SER A 41 GLY A 50 1 10 HELIX 3 AA3 GLN A 53 HIS A 59 5 7 HELIX 4 AA4 SER A 62 ILE A 87 1 26 HELIX 5 AA5 GLY A 91 LEU A 108 1 18 HELIX 6 AA6 VAL A 114 GLN A 119 1 6 HELIX 7 AA7 LEU A 120 GLU A 127 5 8 HELIX 8 AA8 PHE A 128 GLY A 151 1 24 HELIX 9 AA9 ASP A 153 ALA A 156 5 4 HELIX 10 AB1 GLU A 157 SER A 165 1 9 HELIX 11 AB2 VAL A 166 ARG A 170 5 5 HELIX 12 AB3 PRO A 186 LEU A 200 1 15 HELIX 13 AB4 ASP A 207 LYS A 222 1 16 HELIX 14 AB5 ASN B 19 THR B 33 1 15 HELIX 15 AB6 SER B 41 GLY B 50 1 10 HELIX 16 AB7 ARG B 52 ALA B 54 5 3 HELIX 17 AB8 SER B 55 PHE B 60 1 6 HELIX 18 AB9 SER B 62 LEU B 88 1 27 HELIX 19 AC1 GLY B 91 LEU B 108 1 18 HELIX 20 AC2 GLY B 115 LEU B 120 1 6 HELIX 21 AC3 PHE B 128 GLY B 151 1 24 HELIX 22 AC4 ASP B 153 ALA B 156 5 4 HELIX 23 AC5 GLU B 157 SER B 165 1 9 HELIX 24 AC6 VAL B 166 MET B 169 5 4 HELIX 25 AC7 PRO B 186 LEU B 200 1 15 HELIX 26 AC8 ASP B 207 ALA B 221 1 15 HELIX 27 AC9 ASN C 19 THR C 33 1 15 HELIX 28 AD1 SER C 41 GLY C 50 1 10 HELIX 29 AD2 ARG C 52 ALA C 54 5 3 HELIX 30 AD3 SER C 55 PHE C 60 1 6 HELIX 31 AD4 SER C 62 SER C 86 1 25 HELIX 32 AD5 GLY C 91 LEU C 108 1 18 HELIX 33 AD6 VAL C 114 LEU C 120 1 7 HELIX 34 AD7 PRO C 121 GLU C 127 5 7 HELIX 35 AD8 PHE C 128 GLY C 151 1 24 HELIX 36 AD9 ASP C 153 ALA C 156 5 4 HELIX 37 AE1 GLU C 157 SER C 165 1 9 HELIX 38 AE2 VAL C 166 MET C 169 5 4 HELIX 39 AE3 PRO C 186 LEU C 200 1 15 HELIX 40 AE4 ASP C 207 LYS C 222 1 16 HELIX 41 AE5 ASN D 19 GLN D 35 1 17 HELIX 42 AE6 SER D 41 GLY D 50 1 10 HELIX 43 AE7 ARG D 52 ALA D 54 5 3 HELIX 44 AE8 SER D 55 PHE D 60 1 6 HELIX 45 AE9 SER D 62 LEU D 88 1 27 HELIX 46 AF1 GLY D 91 SER D 109 1 19 HELIX 47 AF2 VAL D 114 GLN D 119 1 6 HELIX 48 AF3 LEU D 120 GLU D 127 5 8 HELIX 49 AF4 PHE D 128 GLY D 151 1 24 HELIX 50 AF5 ASP D 153 ALA D 156 5 4 HELIX 51 AF6 GLU D 157 MET D 164 1 8 HELIX 52 AF7 SER D 165 ARG D 170 1 6 HELIX 53 AF8 PRO D 186 LEU D 200 1 15 HELIX 54 AF9 ASP D 207 LYS D 222 1 16 CRYST1 101.731 137.423 239.874 90.00 90.00 90.00 P 2 2 21 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 0.009830 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007277 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004169 0.00000