HEADER TRANSCRIPTION/DNA 25-APR-13 4KDP TITLE TCAR-SSDNA COMPLEX CRYSTAL STRUCTURE REVEALS THE NOVEL SSDNA BINDING TITLE 2 MECHANISM OF THE MARR FAMILY PROTEINS COMPND MOL_ID: 1; COMPND 2 MOLECULE: TCAR TRANSCRIPTION REGULATOR; COMPND 3 CHAIN: A, B, C, D, E, F, G; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'- COMPND 7 D(*CP*GP*CP*AP*GP*CP*GP*CP*GP*CP*AP*GP*CP*CP*CP*TP*A)-3'); COMPND 8 CHAIN: H, J; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS EPIDERMIDIS; SOURCE 3 ORGANISM_TAXID: 176280; SOURCE 4 STRAIN: ATCC 12228; SOURCE 5 GENE: SE_1937; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET32 XA/LIC; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES KEYWDS MULTIPLE DRUG RESISTANCE, SSDNA BINDING, ANTIBIOTICS, STAPHYLOCOCCI, KEYWDS 2 TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.M.CHANG,C.K.-M.CHEN,A.H.-J.WANG REVDAT 3 20-SEP-23 4KDP 1 REMARK REVDAT 2 14-MAY-14 4KDP 1 JRNL REVDAT 1 19-MAR-14 4KDP 0 JRNL AUTH Y.M.CHANG,C.H.HO,C.K.CHEN,M.MAESTRE-REYNA,M.W.CHANG-CHIEN, JRNL AUTH 2 A.H.WANG JRNL TITL TCAR-SSDNA COMPLEX CRYSTAL STRUCTURE REVEALS NEW DNA BINDING JRNL TITL 2 MECHANISM OF THE MARR FAMILY PROTEINS. JRNL REF NUCLEIC ACIDS RES. V. 42 5314 2014 JRNL REFN ISSN 0305-1048 JRNL PMID 24531929 JRNL DOI 10.1093/NAR/GKU128 REMARK 2 REMARK 2 RESOLUTION. 3.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 14084 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 SET) : 0.274 REMARK 3 FREE R VALUE : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 706 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.73 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.12 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3730 REMARK 3 BIN FREE R VALUE : 0.4380 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 57 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8509 REMARK 3 NUCLEIC ACID ATOMS : 420 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 91 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 112.2 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.020 REMARK 3 BOND ANGLES (DEGREES) : 1.985 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4KDP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000079208. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JAN-12 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 : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER DIP-6040 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15179 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.52600 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: CNS REMARK 200 STARTING MODEL: 3KP7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40 % ETHYLENE GLYCOL, 0.1 M TRIS , PH REMARK 280 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-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 174.35600 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 87.17800 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 87.17800 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 174.35600 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 APPLY THE FOLLOWING TO CHAINS: A, B, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, J 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: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: G 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 -137.84850 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 79.58687 REMARK 350 BIOMT3 2 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 LEU E 151 REMARK 465 DG H 12 REMARK 465 DC H 13 REMARK 465 DC H 14 REMARK 465 DC H 15 REMARK 465 DT H 16 REMARK 465 DA H 17 REMARK 465 DC J -4 REMARK 465 DG J -3 REMARK 465 DC J -2 REMARK 465 DA J -1 REMARK 465 DG J 0 REMARK 465 DT J 11 REMARK 465 DA J 12 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 DC J 1 P OP1 OP2 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 SER A 146 OG SER A 149 2.01 REMARK 500 O ASP E 120 OG SER E 123 2.11 REMARK 500 O LEU E 80 OG SER E 100 2.11 REMARK 500 O ASP B 120 N THR B 122 2.16 REMARK 500 O GLU C 6 OG SER C 10 2.18 REMARK 500 O ILE B 144 OG1 THR B 148 2.18 REMARK 500 O ASN C 17 OG1 THR C 21 2.19 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 GLU A 138 CD GLU A 138 OE1 0.082 REMARK 500 GLU C 131 CG GLU C 131 CD 0.093 REMARK 500 GLU C 138 CG GLU C 138 CD 0.096 REMARK 500 GLU D 129 CG GLU D 129 CD 0.098 REMARK 500 GLU E 138 CG GLU E 138 CD 0.131 REMARK 500 GLU E 138 CD GLU E 138 OE2 0.068 REMARK 500 GLU G 109 CG GLU G 109 CD 0.096 REMARK 500 DC H 1 N1 DC H 1 C2 0.126 REMARK 500 DC H 3 N1 DC H 3 C2 0.086 REMARK 500 DC H 8 C3' DC H 8 C2' 0.099 REMARK 500 DC H 8 N1 DC H 8 C2 0.090 REMARK 500 DC H 8 C2 DC H 8 N3 0.049 REMARK 500 DC H 8 C5 DC H 8 C6 0.056 REMARK 500 DC H 10 O3' DC H 10 C3' -0.047 REMARK 500 DC H 10 N1 DC H 10 C2 0.081 REMARK 500 DC H 10 C4 DC H 10 C5 0.064 REMARK 500 DC J 10 O3' DC J 10 C3' -0.041 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 93 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ASP A 124 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG B 143 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 PRO E 86 C - N - CA ANGL. DEV. = 9.9 DEGREES REMARK 500 DC H 1 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC H 6 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG H 7 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 DC H 8 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DC H 10 O4' - C4' - C3' ANGL. DEV. = -2.4 DEGREES REMARK 500 DA H 11 O4' - C1' - C2' ANGL. DEV. = 3.3 DEGREES REMARK 500 DC J 9 C1' - O4' - C4' ANGL. DEV. = 4.2 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 ARG A 4 -37.07 -31.76 REMARK 500 LYS A 25 9.26 -64.64 REMARK 500 ASP A 29 -95.72 -64.64 REMARK 500 GLU A 33 1.78 -65.19 REMARK 500 SER A 41 -51.10 -28.84 REMARK 500 GLN A 61 -122.74 -135.38 REMARK 500 VAL A 63 30.49 -55.95 REMARK 500 LEU A 76 -66.60 -109.40 REMARK 500 GLU A 79 175.71 -55.03 REMARK 500 LEU A 80 178.07 63.49 REMARK 500 VAL A 81 107.87 55.12 REMARK 500 LYS A 82 -155.52 -72.74 REMARK 500 LEU A 83 -30.63 -140.91 REMARK 500 GLU A 84 115.20 80.41 REMARK 500 LYS A 85 91.78 57.58 REMARK 500 PRO A 86 -13.10 -37.91 REMARK 500 THR A 90 -12.62 -162.49 REMARK 500 LYS A 98 -141.91 -102.57 REMARK 500 ARG A 110 -38.38 -38.89 REMARK 500 MET A 114 6.30 -63.99 REMARK 500 SER A 123 6.24 -156.02 REMARK 500 TYR A 147 -5.93 -53.51 REMARK 500 THR A 148 64.91 -103.21 REMARK 500 SER A 149 -56.94 -145.24 REMARK 500 LEU B 22 -76.02 -54.76 REMARK 500 THR B 23 -61.75 -29.53 REMARK 500 LYS B 28 -36.59 -39.49 REMARK 500 ILE B 36 -132.25 -99.08 REMARK 500 GLU B 39 10.30 -57.01 REMARK 500 GLU B 50 153.22 172.41 REMARK 500 GLN B 61 -94.40 -113.90 REMARK 500 VAL B 63 45.15 -73.20 REMARK 500 GLU B 79 -32.33 66.53 REMARK 500 LYS B 85 111.43 60.63 REMARK 500 PRO B 86 0.83 -66.51 REMARK 500 ASN B 89 -154.87 -156.22 REMARK 500 LEU B 94 -76.98 -64.60 REMARK 500 LYS B 111 29.32 -74.50 REMARK 500 SER B 115 45.46 -79.59 REMARK 500 HIS B 116 -72.32 -145.04 REMARK 500 ASP B 120 -75.73 -68.13 REMARK 500 MET B 121 -18.39 -27.79 REMARK 500 LYS B 128 41.40 -69.90 REMARK 500 GLU B 129 -16.51 -173.14 REMARK 500 LYS B 132 -7.16 -57.16 REMARK 500 GLN B 135 -71.52 -56.23 REMARK 500 LYS B 150 -143.17 -63.27 REMARK 500 GLU C 6 -17.42 -48.50 REMARK 500 ASP C 29 -90.44 -24.43 REMARK 500 GLU C 33 5.81 -66.89 REMARK 500 REMARK 500 THIS ENTRY HAS 156 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG D 70 0.11 SIDE CHAIN REMARK 500 TYR G 147 0.11 SIDE CHAIN REMARK 500 DC H 1 0.06 SIDE CHAIN REMARK 500 DG H 2 0.07 SIDE CHAIN REMARK 500 DG J 2 0.07 SIDE CHAIN 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 EDO B 2002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS B 2003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO E 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS F 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO H 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS H 103 DBREF 4KDP A 1 151 UNP Q8CN94 Q8CN94_STAES 1 151 DBREF 4KDP B 1 151 UNP Q8CN94 Q8CN94_STAES 1 151 DBREF 4KDP C 1 151 UNP Q8CN94 Q8CN94_STAES 1 151 DBREF 4KDP D 1 151 UNP Q8CN94 Q8CN94_STAES 1 151 DBREF 4KDP E 1 151 UNP Q8CN94 Q8CN94_STAES 1 151 DBREF 4KDP F 1 151 UNP Q8CN94 Q8CN94_STAES 1 151 DBREF 4KDP G 1 151 UNP Q8CN94 Q8CN94_STAES 1 151 DBREF 4KDP H 1 17 PDB 4KDP 4KDP 1 17 DBREF 4KDP J -4 12 PDB 4KDP 4KDP -4 12 SEQRES 1 A 151 MET VAL ARG ARG ILE GLU ASP HIS ILE SER PHE LEU GLU SEQRES 2 A 151 LYS PHE ILE ASN ASP VAL ASN THR LEU THR ALA LYS LEU SEQRES 3 A 151 LEU LYS ASP LEU GLN THR GLU TYR GLY ILE SER ALA GLU SEQRES 4 A 151 GLN SER HIS VAL LEU ASN MET LEU SER ILE GLU ALA LEU SEQRES 5 A 151 THR VAL GLY GLN ILE THR GLU LYS GLN GLY VAL ASN LYS SEQRES 6 A 151 ALA ALA VAL SER ARG ARG VAL LYS LYS LEU LEU ASN ALA SEQRES 7 A 151 GLU LEU VAL LYS LEU GLU LYS PRO ASP SER ASN THR ASP SEQRES 8 A 151 GLN ARG LEU LYS ILE ILE LYS LEU SER ASN LYS GLY LYS SEQRES 9 A 151 LYS TYR ILE LYS GLU ARG LYS ALA ILE MET SER HIS ILE SEQRES 10 A 151 ALA SER ASP MET THR SER ASP PHE ASP SER LYS GLU ILE SEQRES 11 A 151 GLU LYS VAL ARG GLN VAL LEU GLU ILE ILE ASP TYR ARG SEQRES 12 A 151 ILE GLN SER TYR THR SER LYS LEU SEQRES 1 B 151 MET VAL ARG ARG ILE GLU ASP HIS ILE SER PHE LEU GLU SEQRES 2 B 151 LYS PHE ILE ASN ASP VAL ASN THR LEU THR ALA LYS LEU SEQRES 3 B 151 LEU LYS ASP LEU GLN THR GLU TYR GLY ILE SER ALA GLU SEQRES 4 B 151 GLN SER HIS VAL LEU ASN MET LEU SER ILE GLU ALA LEU SEQRES 5 B 151 THR VAL GLY GLN ILE THR GLU LYS GLN GLY VAL ASN LYS SEQRES 6 B 151 ALA ALA VAL SER ARG ARG VAL LYS LYS LEU LEU ASN ALA SEQRES 7 B 151 GLU LEU VAL LYS LEU GLU LYS PRO ASP SER ASN THR ASP SEQRES 8 B 151 GLN ARG LEU LYS ILE ILE LYS LEU SER ASN LYS GLY LYS SEQRES 9 B 151 LYS TYR ILE LYS GLU ARG LYS ALA ILE MET SER HIS ILE SEQRES 10 B 151 ALA SER ASP MET THR SER ASP PHE ASP SER LYS GLU ILE SEQRES 11 B 151 GLU LYS VAL ARG GLN VAL LEU GLU ILE ILE ASP TYR ARG SEQRES 12 B 151 ILE GLN SER TYR THR SER LYS LEU SEQRES 1 C 151 MET VAL ARG ARG ILE GLU ASP HIS ILE SER PHE LEU GLU SEQRES 2 C 151 LYS PHE ILE ASN ASP VAL ASN THR LEU THR ALA LYS LEU SEQRES 3 C 151 LEU LYS ASP LEU GLN THR GLU TYR GLY ILE SER ALA GLU SEQRES 4 C 151 GLN SER HIS VAL LEU ASN MET LEU SER ILE GLU ALA LEU SEQRES 5 C 151 THR VAL GLY GLN ILE THR GLU LYS GLN GLY VAL ASN LYS SEQRES 6 C 151 ALA ALA VAL SER ARG ARG VAL LYS LYS LEU LEU ASN ALA SEQRES 7 C 151 GLU LEU VAL LYS LEU GLU LYS PRO ASP SER ASN THR ASP SEQRES 8 C 151 GLN ARG LEU LYS ILE ILE LYS LEU SER ASN LYS GLY LYS SEQRES 9 C 151 LYS TYR ILE LYS GLU ARG LYS ALA ILE MET SER HIS ILE SEQRES 10 C 151 ALA SER ASP MET THR SER ASP PHE ASP SER LYS GLU ILE SEQRES 11 C 151 GLU LYS VAL ARG GLN VAL LEU GLU ILE ILE ASP TYR ARG SEQRES 12 C 151 ILE GLN SER TYR THR SER LYS LEU SEQRES 1 D 151 MET VAL ARG ARG ILE GLU ASP HIS ILE SER PHE LEU GLU SEQRES 2 D 151 LYS PHE ILE ASN ASP VAL ASN THR LEU THR ALA LYS LEU SEQRES 3 D 151 LEU LYS ASP LEU GLN THR GLU TYR GLY ILE SER ALA GLU SEQRES 4 D 151 GLN SER HIS VAL LEU ASN MET LEU SER ILE GLU ALA LEU SEQRES 5 D 151 THR VAL GLY GLN ILE THR GLU LYS GLN GLY VAL ASN LYS SEQRES 6 D 151 ALA ALA VAL SER ARG ARG VAL LYS LYS LEU LEU ASN ALA SEQRES 7 D 151 GLU LEU VAL LYS LEU GLU LYS PRO ASP SER ASN THR ASP SEQRES 8 D 151 GLN ARG LEU LYS ILE ILE LYS LEU SER ASN LYS GLY LYS SEQRES 9 D 151 LYS TYR ILE LYS GLU ARG LYS ALA ILE MET SER HIS ILE SEQRES 10 D 151 ALA SER ASP MET THR SER ASP PHE ASP SER LYS GLU ILE SEQRES 11 D 151 GLU LYS VAL ARG GLN VAL LEU GLU ILE ILE ASP TYR ARG SEQRES 12 D 151 ILE GLN SER TYR THR SER LYS LEU SEQRES 1 E 151 MET VAL ARG ARG ILE GLU ASP HIS ILE SER PHE LEU GLU SEQRES 2 E 151 LYS PHE ILE ASN ASP VAL ASN THR LEU THR ALA LYS LEU SEQRES 3 E 151 LEU LYS ASP LEU GLN THR GLU TYR GLY ILE SER ALA GLU SEQRES 4 E 151 GLN SER HIS VAL LEU ASN MET LEU SER ILE GLU ALA LEU SEQRES 5 E 151 THR VAL GLY GLN ILE THR GLU LYS GLN GLY VAL ASN LYS SEQRES 6 E 151 ALA ALA VAL SER ARG ARG VAL LYS LYS LEU LEU ASN ALA SEQRES 7 E 151 GLU LEU VAL LYS LEU GLU LYS PRO ASP SER ASN THR ASP SEQRES 8 E 151 GLN ARG LEU LYS ILE ILE LYS LEU SER ASN LYS GLY LYS SEQRES 9 E 151 LYS TYR ILE LYS GLU ARG LYS ALA ILE MET SER HIS ILE SEQRES 10 E 151 ALA SER ASP MET THR SER ASP PHE ASP SER LYS GLU ILE SEQRES 11 E 151 GLU LYS VAL ARG GLN VAL LEU GLU ILE ILE ASP TYR ARG SEQRES 12 E 151 ILE GLN SER TYR THR SER LYS LEU SEQRES 1 F 151 MET VAL ARG ARG ILE GLU ASP HIS ILE SER PHE LEU GLU SEQRES 2 F 151 LYS PHE ILE ASN ASP VAL ASN THR LEU THR ALA LYS LEU SEQRES 3 F 151 LEU LYS ASP LEU GLN THR GLU TYR GLY ILE SER ALA GLU SEQRES 4 F 151 GLN SER HIS VAL LEU ASN MET LEU SER ILE GLU ALA LEU SEQRES 5 F 151 THR VAL GLY GLN ILE THR GLU LYS GLN GLY VAL ASN LYS SEQRES 6 F 151 ALA ALA VAL SER ARG ARG VAL LYS LYS LEU LEU ASN ALA SEQRES 7 F 151 GLU LEU VAL LYS LEU GLU LYS PRO ASP SER ASN THR ASP SEQRES 8 F 151 GLN ARG LEU LYS ILE ILE LYS LEU SER ASN LYS GLY LYS SEQRES 9 F 151 LYS TYR ILE LYS GLU ARG LYS ALA ILE MET SER HIS ILE SEQRES 10 F 151 ALA SER ASP MET THR SER ASP PHE ASP SER LYS GLU ILE SEQRES 11 F 151 GLU LYS VAL ARG GLN VAL LEU GLU ILE ILE ASP TYR ARG SEQRES 12 F 151 ILE GLN SER TYR THR SER LYS LEU SEQRES 1 G 151 MET VAL ARG ARG ILE GLU ASP HIS ILE SER PHE LEU GLU SEQRES 2 G 151 LYS PHE ILE ASN ASP VAL ASN THR LEU THR ALA LYS LEU SEQRES 3 G 151 LEU LYS ASP LEU GLN THR GLU TYR GLY ILE SER ALA GLU SEQRES 4 G 151 GLN SER HIS VAL LEU ASN MET LEU SER ILE GLU ALA LEU SEQRES 5 G 151 THR VAL GLY GLN ILE THR GLU LYS GLN GLY VAL ASN LYS SEQRES 6 G 151 ALA ALA VAL SER ARG ARG VAL LYS LYS LEU LEU ASN ALA SEQRES 7 G 151 GLU LEU VAL LYS LEU GLU LYS PRO ASP SER ASN THR ASP SEQRES 8 G 151 GLN ARG LEU LYS ILE ILE LYS LEU SER ASN LYS GLY LYS SEQRES 9 G 151 LYS TYR ILE LYS GLU ARG LYS ALA ILE MET SER HIS ILE SEQRES 10 G 151 ALA SER ASP MET THR SER ASP PHE ASP SER LYS GLU ILE SEQRES 11 G 151 GLU LYS VAL ARG GLN VAL LEU GLU ILE ILE ASP TYR ARG SEQRES 12 G 151 ILE GLN SER TYR THR SER LYS LEU SEQRES 1 H 17 DC DG DC DA DG DC DG DC DG DC DA DG DC SEQRES 2 H 17 DC DC DT DA SEQRES 1 J 17 DC DG DC DA DG DC DG DC DG DC DA DG DC SEQRES 2 J 17 DC DC DT DA HET EDO B2001 4 HET EDO B2002 4 HET TRS B2003 8 HET EDO E 201 4 HET EDO F 201 4 HET TRS F 202 8 HET EDO H 101 4 HET EDO H 102 4 HET TRS H 103 8 HET TRS J 101 8 HET TRS J 102 8 HETNAM EDO 1,2-ETHANEDIOL HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN EDO ETHYLENE GLYCOL HETSYN TRS TRIS BUFFER FORMUL 10 EDO 6(C2 H6 O2) FORMUL 12 TRS 5(C4 H12 N O3 1+) FORMUL 21 HOH *91(H2 O) HELIX 1 1 ARG A 4 GLU A 33 1 30 HELIX 2 2 SER A 37 SER A 48 1 12 HELIX 3 3 THR A 53 LYS A 60 1 8 HELIX 4 4 VAL A 68 LYS A 74 1 7 HELIX 5 5 SER A 100 THR A 122 1 23 HELIX 6 6 ASP A 126 THR A 148 1 23 HELIX 7 7 VAL B 2 LYS B 28 1 27 HELIX 8 8 ASP B 29 THR B 32 5 4 HELIX 9 9 SER B 37 SER B 48 1 12 HELIX 10 10 THR B 53 GLU B 59 1 7 HELIX 11 11 VAL B 72 ALA B 78 1 7 HELIX 12 12 SER B 100 THR B 122 1 23 HELIX 13 13 ILE B 130 SER B 146 1 17 HELIX 14 14 ARG C 4 LEU C 26 1 23 HELIX 15 15 LEU C 27 GLU C 33 1 7 HELIX 16 16 GLN C 40 GLU C 50 1 11 HELIX 17 17 THR C 53 GLN C 61 1 9 HELIX 18 18 SER C 69 ASN C 77 1 9 HELIX 19 19 SER C 100 SER C 123 1 24 HELIX 20 20 ASP C 126 GLN C 135 1 10 HELIX 21 21 GLN C 135 LYS C 150 1 16 HELIX 22 22 ARG D 4 TYR D 34 1 31 HELIX 23 23 THR D 53 THR D 58 1 6 HELIX 24 24 LYS D 65 ALA D 78 1 14 HELIX 25 25 SER D 100 SER D 123 1 24 HELIX 26 26 ASP D 126 LEU D 151 1 26 HELIX 27 27 ARG E 4 ALA E 24 1 21 HELIX 28 28 ASP E 29 TYR E 34 1 6 HELIX 29 29 GLU E 39 SER E 48 1 10 HELIX 30 30 THR E 53 THR E 58 1 6 HELIX 31 31 ASN E 64 LEU E 75 1 12 HELIX 32 32 SER E 100 LYS E 111 1 12 HELIX 33 33 ILE E 113 MET E 121 1 9 HELIX 34 34 ASP E 126 THR E 148 1 23 HELIX 35 35 ARG F 4 LYS F 28 1 25 HELIX 36 36 ASP F 29 TYR F 34 1 6 HELIX 37 37 SER F 37 GLU F 50 1 14 HELIX 38 38 VAL F 54 THR F 58 1 5 HELIX 39 39 ASN F 64 SER F 69 1 6 HELIX 40 40 ARG F 70 ALA F 78 1 9 HELIX 41 41 ASN F 101 SER F 123 1 23 HELIX 42 42 ASP F 126 SER F 149 1 24 HELIX 43 43 ILE G 5 LEU G 27 1 23 HELIX 44 44 LEU G 27 TYR G 34 1 8 HELIX 45 45 GLU G 39 SER G 48 1 10 HELIX 46 46 THR G 53 LYS G 60 1 8 HELIX 47 47 ALA G 66 ALA G 78 1 13 HELIX 48 48 ASN G 101 ASP G 120 1 20 HELIX 49 49 MET G 121 PHE G 125 5 5 HELIX 50 50 ASP G 126 SER G 149 1 24 SHEET 1 A 2 VAL B 81 LYS B 82 0 SHEET 2 A 2 LYS B 98 LEU B 99 -1 O LYS B 98 N LYS B 82 SHEET 1 B 2 VAL D 81 LEU D 83 0 SHEET 2 B 2 ILE D 97 LEU D 99 -1 O LYS D 98 N LYS D 82 SHEET 1 C 2 LEU F 52 THR F 53 0 SHEET 2 C 2 ILE F 96 ILE F 97 -1 O ILE F 97 N LEU F 52 SHEET 1 D 2 VAL G 81 LYS G 82 0 SHEET 2 D 2 LYS G 98 LEU G 99 -1 O LYS G 98 N LYS G 82 SITE 1 AC1 2 LYS F 128 TRS F 202 SITE 1 AC2 1 ARG B 3 SITE 1 AC3 1 LYS E 85 SITE 1 AC4 1 EDO B2002 SITE 1 AC5 1 DG H 7 SITE 1 AC6 2 DG H 5 HOH H 207 CRYST1 91.899 91.899 261.534 90.00 90.00 120.00 P 32 2 1 42 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 0.010882 0.006282 0.000000 0.00000 SCALE2 0.000000 0.012565 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003824 0.00000