PDB Short entry for 3BDN HEADER TRANSCRIPTION/DNA 15-NOV-07 3BDN TITLE CRYSTAL STRUCTURE OF THE LAMBDA REPRESSOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*DAP*DAP*DTP*DAP*DCP*DCP*DAP*DCP*DTP*DGP*DGP*DCP*DGP*DGP*DTP*DGP*DA COMPND 4 P*DTP*DAP*DT)-3'); COMPND 5 CHAIN: C; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'- COMPND 9 D(*DTP*DAP*DTP*DAP*DTP*DCP*DAP*DCP*DCP*DGP*DCP*DCP*DAP*DGP*DTP*DGP*DG COMPND 10 P*DTP*DAP*DT)-3'); COMPND 11 CHAIN: D; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: LAMBDA REPRESSOR; COMPND 15 CHAIN: A, B; COMPND 16 SYNONYM: REPRESSOR PROTEIN CI; COMPND 17 ENGINEERED: YES; COMPND 18 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE LAMBDA; SOURCE 7 ORGANISM_TAXID: 10710; SOURCE 8 STRAIN: BL21 DE3; SOURCE 9 GENE: CI; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 12 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 13 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 14 EXPRESSION_SYSTEM_PLASMID: PET17B KEYWDS LAMBDA, REPRESSOR, ALLOSTERY, COOPERATIVITY, DNA BINDING, KEYWDS 2 TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.E.STAYROOK,P.JARU-AMPORNPAN,A.HOCHSCHILD,M.LEWIS REVDAT 4 30-AUG-23 3BDN 1 REMARK REVDAT 3 20-OCT-21 3BDN 1 SEQADV REVDAT 2 23-DEC-08 3BDN 1 JRNL VERSN REVDAT 1 15-APR-08 3BDN 0 JRNL AUTH S.E.STAYROOK,P.JARU-AMPORNPAN,J.NI,A.HOCHSCHILD,M.LEWIS JRNL TITL CRYSTAL STRUCTURE OF THE LAMBDA REPRESSOR AND A MODEL FOR JRNL TITL 2 PAIRWISE COOPERATIVE OPERATOR BINDING JRNL REF NATURE V. 452 1022 2008 JRNL REFN ISSN 0028-0836 JRNL PMID 18432246 JRNL DOI 10.1038/NATURE06831 REMARK 2 REMARK 2 RESOLUTION. 3.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.61 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 7238 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) : 0.296 REMARK 3 R VALUE (WORKING SET) : 0.292 REMARK 3 FREE R VALUE : 0.374 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 350 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) : 3.91 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 4.01 REMARK 3 REFLECTION IN BIN (WORKING SET) : 502 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.15 REMARK 3 BIN R VALUE (WORKING SET) : 0.4240 REMARK 3 BIN FREE R VALUE SET COUNT : 23 REMARK 3 BIN FREE R VALUE : 0.4640 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3626 REMARK 3 NUCLEIC ACID ATOMS : 779 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 111.0 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 170.2 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.14000 REMARK 3 B22 (A**2) : 0.89000 REMARK 3 B33 (A**2) : -0.75000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 1.163 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 1.320 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 95.243 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.905 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.826 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4576 ; 0.020 ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6342 ; 1.773 ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 464 ; 9.183 ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 158 ;39.503 ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 691 ; 0.114 ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3199 ; 0.005 ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2947 ; 0.304 ; 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): 217 ; 0.259 ; 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): 45 ; 0.306 ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.295 ; 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): 2387 ; 0.701 ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3748 ; 1.135 ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2676 ; 1.166 ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2594 ; 1.523 ; 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 : FLAT MODEL 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: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3BDN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000045390. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 4 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : UNDULATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7238 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.909 REMARK 200 RESOLUTION RANGE LOW (A) : 34.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.20 REMARK 200 R MERGE FOR SHELL (I) : 0.17600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 8.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: 1LMB, 1F39 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG 4000, 0.1 M SODIUM ACETATE PH REMARK 280 4.6, 0.2 M AMMONIUM SULFATE, 0.05 M MAGNESIUM CHLORIDE, 20% REMARK 280 GLYCEROL, 1 MM SPERMINE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y+1/2,-Z REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 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 0.00000 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 SMTRY1 5 1.000000 0.000000 0.000000 37.21550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 80.54950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 37.21550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 80.54950 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 37.21550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 80.54950 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 37.21550 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 80.54950 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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: 8950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.5 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, A, B 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 DA C 1 REMARK 465 DT D 21 REMARK 465 CYS A 215 REMARK 465 ASN A 216 REMARK 465 CYS B 215 REMARK 465 ASN B 216 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 VAL B 91 CG1 CG2 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 LEU A 165 OG SER A 228 1.91 REMARK 500 O SER B 32 OG SER B 35 1.99 REMARK 500 O GLY A 197 O GLN A 200 2.10 REMARK 500 O PRO B 208 N TYR B 210 2.15 REMARK 500 N6 DA C 17 O4 DT D 25 2.15 REMARK 500 O SER A 72 N GLU A 75 2.15 REMARK 500 O VAL A 73 N PHE A 76 2.16 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 DA D 22 P DA D 22 OP2 0.137 REMARK 500 LYS A 25 CE LYS A 25 NZ 0.405 REMARK 500 SER A 92 CB SER A 92 OG 0.079 REMARK 500 GLU A 100 CD GLU A 100 OE1 0.072 REMARK 500 ARG A 119 CZ ARG A 119 NH1 0.134 REMARK 500 ARG A 128 CD ARG A 128 NE 0.109 REMARK 500 ARG A 128 CZ ARG A 128 NH1 0.301 REMARK 500 GLU B 13 CD GLU B 13 OE1 0.070 REMARK 500 LYS B 25 CE LYS B 25 NZ 0.445 REMARK 500 GLU B 100 CD GLU B 100 OE2 0.073 REMARK 500 GLU B 146 CD GLU B 146 OE1 0.070 REMARK 500 GLU B 146 CD GLU B 146 OE2 0.069 REMARK 500 LYS B 157 CE LYS B 157 NZ 0.217 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 DA C 2 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA C 4 O4' - C4' - C3' ANGL. DEV. = -3.6 DEGREES REMARK 500 DC C 5 C1' - O4' - C4' ANGL. DEV. = -6.6 DEGREES REMARK 500 DC C 5 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES REMARK 500 DC C 6 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA C 7 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DT C 9 C3' - C2' - C1' ANGL. DEV. = -6.2 DEGREES REMARK 500 DT C 9 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG C 11 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 DG C 11 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG C 13 C1' - O4' - C4' ANGL. DEV. = -7.0 DEGREES REMARK 500 DG C 13 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 DT C 15 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 DT C 15 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES REMARK 500 DG C 16 C1' - O4' - C4' ANGL. DEV. = -7.6 DEGREES REMARK 500 DT C 18 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DT D 23 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DT D 25 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DC D 26 C1' - O4' - C4' ANGL. DEV. = -6.5 DEGREES REMARK 500 DC D 26 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 DA D 27 O4' - C4' - C3' ANGL. DEV. = -3.7 DEGREES REMARK 500 DC D 28 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DC D 29 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES REMARK 500 DG D 30 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC D 32 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA D 33 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG D 34 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DT D 38 C1' - O4' - C4' ANGL. DEV. = -7.6 DEGREES REMARK 500 DT D 38 C3' - C2' - C1' ANGL. DEV. = -7.7 DEGREES REMARK 500 DT D 38 O4' - C1' - N1 ANGL. DEV. = 7.7 DEGREES REMARK 500 DA D 39 C3' - O3' - P ANGL. DEV. = 7.2 DEGREES REMARK 500 DT D 40 C1' - O4' - C4' ANGL. DEV. = -8.2 DEGREES REMARK 500 DT D 40 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 119 NH1 - CZ - NH2 ANGL. DEV. = 7.2 DEGREES REMARK 500 ARG A 119 NE - CZ - NH1 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG A 119 NE - CZ - NH2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ARG A 128 CD - NE - CZ ANGL. DEV. = -8.9 DEGREES REMARK 500 ARG A 128 NE - CZ - NH1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ARG A 128 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 LEU B 165 CA - CB - CG ANGL. DEV. = -14.4 DEGREES REMARK 500 CYS B 219 CA - CB - SG ANGL. DEV. = 6.9 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 THR A 2 -21.81 -146.71 REMARK 500 LYS A 4 -134.73 -109.66 REMARK 500 GLN A 9 -87.30 -25.02 REMARK 500 GLN A 11 16.61 -56.16 REMARK 500 LEU A 12 -61.77 -134.79 REMARK 500 GLU A 13 7.10 -66.11 REMARK 500 LEU A 18 -74.60 -54.35 REMARK 500 SER A 32 -104.76 -91.55 REMARK 500 GLN A 33 -44.67 -154.93 REMARK 500 LYS A 39 -45.71 67.25 REMARK 500 TYR A 60 -94.57 -71.23 REMARK 500 ASN A 61 -19.59 -48.24 REMARK 500 ALA A 66 -42.91 -160.00 REMARK 500 ILE A 68 -69.66 -102.97 REMARK 500 LEU A 69 30.25 -85.88 REMARK 500 VAL A 71 -129.33 -120.64 REMARK 500 SER A 72 94.73 175.92 REMARK 500 VAL A 73 -73.43 -8.28 REMARK 500 GLU A 74 -29.29 -33.46 REMARK 500 PHE A 76 -24.65 -144.26 REMARK 500 GLU A 86 44.30 -90.89 REMARK 500 MET A 93 -142.22 34.16 REMARK 500 PRO A 95 92.28 -53.08 REMARK 500 SER A 99 154.74 61.96 REMARK 500 TYR A 101 145.06 176.64 REMARK 500 GLU A 102 -158.14 -132.43 REMARK 500 TYR A 103 170.83 -31.33 REMARK 500 HIS A 108 -102.64 53.64 REMARK 500 VAL A 109 -150.08 32.62 REMARK 500 MET A 113 104.52 65.28 REMARK 500 PRO A 116 -89.18 -93.65 REMARK 500 LEU A 118 111.55 72.93 REMARK 500 THR A 120 165.96 18.79 REMARK 500 PHE A 121 99.00 101.14 REMARK 500 LYS A 123 -59.85 -157.79 REMARK 500 ALA A 126 -64.63 -161.81 REMARK 500 GLU A 127 88.89 70.29 REMARK 500 TRP A 129 -146.60 -95.47 REMARK 500 VAL A 130 139.81 64.23 REMARK 500 THR A 132 -167.54 -165.12 REMARK 500 THR A 133 93.10 -63.54 REMARK 500 LYS A 134 119.78 -37.38 REMARK 500 LYS A 135 -144.88 -136.51 REMARK 500 ASP A 138 114.63 -174.71 REMARK 500 SER A 139 -11.58 74.85 REMARK 500 ALA A 140 -179.34 -66.99 REMARK 500 SER A 149 17.33 -62.46 REMARK 500 MET A 150 -37.55 -152.28 REMARK 500 THR A 151 107.10 -22.08 REMARK 500 THR A 154 -81.43 35.17 REMARK 500 REMARK 500 THIS ENTRY HAS 136 RAMACHANDRAN OUTLIERS. 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 LYS A 157 PRO A 158 -146.55 REMARK 500 REMARK 500 REMARK: NULL DBREF 3BDN A 1 236 UNP P03034 RPC1_LAMBD 2 237 DBREF 3BDN B 1 236 UNP P03034 RPC1_LAMBD 2 237 DBREF 3BDN C 1 20 PDB 3BDN 3BDN 1 20 DBREF 3BDN D 21 40 PDB 3BDN 3BDN 21 40 SEQADV 3BDN GLY A 197 UNP P03034 ASP 198 ENGINEERED MUTATION SEQADV 3BDN GLY B 197 UNP P03034 ASP 198 ENGINEERED MUTATION SEQRES 1 C 20 DA DA DT DA DC DC DA DC DT DG DG DC DG SEQRES 2 C 20 DG DT DG DA DT DA DT SEQRES 1 D 20 DT DA DT DA DT DC DA DC DC DG DC DC DA SEQRES 2 D 20 DG DT DG DG DT DA DT SEQRES 1 A 236 SER THR LYS LYS LYS PRO LEU THR GLN GLU GLN LEU GLU SEQRES 2 A 236 ASP ALA ARG ARG LEU LYS ALA ILE TYR GLU LYS LYS LYS SEQRES 3 A 236 ASN GLU LEU GLY LEU SER GLN GLU SER VAL ALA ASP LYS SEQRES 4 A 236 MET GLY MET GLY GLN SER GLY VAL GLY ALA LEU PHE ASN SEQRES 5 A 236 GLY ILE ASN ALA LEU ASN ALA TYR ASN ALA ALA LEU LEU SEQRES 6 A 236 ALA LYS ILE LEU LYS VAL SER VAL GLU GLU PHE SER PRO SEQRES 7 A 236 SER ILE ALA ARG GLU ILE TYR GLU MET TYR GLU ALA VAL SEQRES 8 A 236 SER MET GLN PRO SER LEU ARG SER GLU TYR GLU TYR PRO SEQRES 9 A 236 VAL PHE SER HIS VAL GLN ALA GLY MET PHE SER PRO GLU SEQRES 10 A 236 LEU ARG THR PHE THR LYS GLY ASP ALA GLU ARG TRP VAL SEQRES 11 A 236 SER THR THR LYS LYS ALA SER ASP SER ALA PHE TRP LEU SEQRES 12 A 236 GLU VAL GLU GLY ASN SER MET THR ALA PRO THR GLY SER SEQRES 13 A 236 LYS PRO SER PHE PRO ASP GLY MET LEU ILE LEU VAL ASP SEQRES 14 A 236 PRO GLU GLN ALA VAL GLU PRO GLY ASP PHE CYS ILE ALA SEQRES 15 A 236 ARG LEU GLY GLY ASP GLU PHE THR PHE LYS LYS LEU ILE SEQRES 16 A 236 ARG GLY SER GLY GLN VAL PHE LEU GLN PRO LEU ASN PRO SEQRES 17 A 236 GLN TYR PRO MET ILE PRO CYS ASN GLU SER CYS SER VAL SEQRES 18 A 236 VAL GLY LYS VAL ILE ALA SER GLN TRP PRO GLU GLU THR SEQRES 19 A 236 PHE GLY SEQRES 1 B 236 SER THR LYS LYS LYS PRO LEU THR GLN GLU GLN LEU GLU SEQRES 2 B 236 ASP ALA ARG ARG LEU LYS ALA ILE TYR GLU LYS LYS LYS SEQRES 3 B 236 ASN GLU LEU GLY LEU SER GLN GLU SER VAL ALA ASP LYS SEQRES 4 B 236 MET GLY MET GLY GLN SER GLY VAL GLY ALA LEU PHE ASN SEQRES 5 B 236 GLY ILE ASN ALA LEU ASN ALA TYR ASN ALA ALA LEU LEU SEQRES 6 B 236 ALA LYS ILE LEU LYS VAL SER VAL GLU GLU PHE SER PRO SEQRES 7 B 236 SER ILE ALA ARG GLU ILE TYR GLU MET TYR GLU ALA VAL SEQRES 8 B 236 SER MET GLN PRO SER LEU ARG SER GLU TYR GLU TYR PRO SEQRES 9 B 236 VAL PHE SER HIS VAL GLN ALA GLY MET PHE SER PRO GLU SEQRES 10 B 236 LEU ARG THR PHE THR LYS GLY ASP ALA GLU ARG TRP VAL SEQRES 11 B 236 SER THR THR LYS LYS ALA SER ASP SER ALA PHE TRP LEU SEQRES 12 B 236 GLU VAL GLU GLY ASN SER MET THR ALA PRO THR GLY SER SEQRES 13 B 236 LYS PRO SER PHE PRO ASP GLY MET LEU ILE LEU VAL ASP SEQRES 14 B 236 PRO GLU GLN ALA VAL GLU PRO GLY ASP PHE CYS ILE ALA SEQRES 15 B 236 ARG LEU GLY GLY ASP GLU PHE THR PHE LYS LYS LEU ILE SEQRES 16 B 236 ARG GLY SER GLY GLN VAL PHE LEU GLN PRO LEU ASN PRO SEQRES 17 B 236 GLN TYR PRO MET ILE PRO CYS ASN GLU SER CYS SER VAL SEQRES 18 B 236 VAL GLY LYS VAL ILE ALA SER GLN TRP PRO GLU GLU THR SEQRES 19 B 236 PHE GLY HELIX 1 1 GLN A 9 LYS A 26 1 18 HELIX 2 2 GLN A 33 GLY A 41 1 9 HELIX 3 3 GLY A 43 PHE A 51 1 9 HELIX 4 4 ASN A 58 LEU A 65 1 8 HELIX 5 5 SER A 72 PHE A 76 5 5 HELIX 6 6 SER A 77 MET A 93 1 17 HELIX 7 7 THR B 8 GLY B 30 1 23 HELIX 8 8 SER B 32 LYS B 39 1 8 HELIX 9 9 VAL B 47 GLY B 53 1 7 HELIX 10 10 ASN B 58 LEU B 69 1 12 HELIX 11 11 SER B 77 ALA B 90 1 14 SHEET 1 A 6 PHE A 141 GLU A 144 0 SHEET 2 A 6 LEU A 165 VAL A 168 -1 O VAL A 168 N PHE A 141 SHEET 3 A 6 SER A 220 ALA A 227 -1 O ALA A 227 N LEU A 167 SHEET 4 A 6 PHE A 179 ARG A 183 -1 N PHE A 179 O VAL A 225 SHEET 5 A 6 LYS A 192 ILE A 195 -1 O LYS A 192 N CYS A 180 SHEET 6 A 6 PHE A 202 GLN A 204 -1 O GLN A 204 N LYS A 193 SHEET 1 B 2 TRP B 142 GLU B 144 0 SHEET 2 B 2 LEU B 165 LEU B 167 -1 O ILE B 166 N LEU B 143 SHEET 1 C 4 VAL B 201 GLN B 204 0 SHEET 2 C 4 GLU B 188 ARG B 196 -1 N LYS B 193 O GLN B 204 SHEET 3 C 4 PHE B 179 LEU B 184 -1 N CYS B 180 O LYS B 192 SHEET 4 C 4 SER B 220 GLY B 223 -1 O SER B 220 N ARG B 183 CRYST1 74.431 161.099 135.256 90.00 90.00 90.00 C 2 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 0.013435 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006207 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007393 0.00000