PDB Short entry for 3S8Q HEADER PROTEIN BINDING/DNA 30-MAY-11 3S8Q TITLE CRYSTAL STRUCTURE OF THE R-M CONTROLLER PROTEIN C.ESP1396I OL OPERATOR TITLE 2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: R-M CONTROLLER PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'- COMPND 7 D(*AP*TP*GP*TP*GP*AP*CP*TP*TP*AP*TP*AP*GP*TP*CP*CP*GP*TP*G)-3'); COMPND 8 CHAIN: C; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: C.ESP1396I; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'- COMPND 13 D(*TP*CP*AP*CP*GP*GP*AP*CP*TP*AP*TP*AP*AP*GP*TP*CP*AP*CP*A)-3'); COMPND 14 CHAIN: D; COMPND 15 ENGINEERED: YES; COMPND 16 OTHER_DETAILS: DNA SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTER SP. RFL1396; SOURCE 3 ORGANISM_TAXID: 211595; SOURCE 4 GENE: ESP1396IC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)GOLD; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET23; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES KEYWDS PROTEIN-DNA COMPLEX, HELIX-TURN-HELIX, TRANSCRIPTIONAL REGULATOR, KEYWDS 2 DNA-BINDING PROTEIN, PROTEIN BINDING-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.E.MCGEEHAN,N.J.BALL,S.D.STREETER,S.-J.THRESH,G.G.KNEALE REVDAT 3 28-FEB-24 3S8Q 1 SEQADV REVDAT 2 25-JUL-12 3S8Q 1 JRNL REVDAT 1 18-JAN-12 3S8Q 0 JRNL AUTH J.E.MCGEEHAN,N.J.BALL,S.D.STREETER,S.J.THRESH,G.G.KNEALE JRNL TITL RECOGNITION OF DUAL SYMMETRY BY THE CONTROLLER PROTEIN JRNL TITL 2 C.ESP1396I BASED ON THE STRUCTURE OF THE TRANSCRIPTIONAL JRNL TITL 3 ACTIVATION COMPLEX. JRNL REF NUCLEIC ACIDS RES. V. 40 4158 2012 JRNL REFN ISSN 0305-1048 JRNL PMID 22210861 JRNL DOI 10.1093/NAR/GKR1250 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 17823 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) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 913 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1262 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.29 REMARK 3 BIN R VALUE (WORKING SET) : 0.2020 REMARK 3 BIN FREE R VALUE SET COUNT : 68 REMARK 3 BIN FREE R VALUE : 0.2950 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1243 REMARK 3 NUCLEIC ACID ATOMS : 773 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 296 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.24 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.16000 REMARK 3 B22 (A**2) : 2.46000 REMARK 3 B33 (A**2) : -1.30000 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): 0.178 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.116 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.058 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2168 ; 0.022 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3082 ; 2.282 ; 2.433 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 165 ; 5.286 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 52 ;35.414 ;24.423 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 288 ;15.266 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;17.531 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 361 ; 0.124 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1305 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 790 ; 1.003 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1294 ; 1.735 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1378 ; 2.603 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1785 ; 3.538 ; 4.500 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 77 REMARK 3 ORIGIN FOR THE GROUP (A): -13.8540 10.8605 -12.0763 REMARK 3 T TENSOR REMARK 3 T11: 0.1004 T22: 0.0273 REMARK 3 T33: 0.0845 T12: -0.0105 REMARK 3 T13: 0.0593 T23: 0.0127 REMARK 3 L TENSOR REMARK 3 L11: 2.3823 L22: 1.6616 REMARK 3 L33: 4.7103 L12: 0.4486 REMARK 3 L13: 0.8484 L23: -0.2291 REMARK 3 S TENSOR REMARK 3 S11: 0.0233 S12: -0.2965 S13: -0.0640 REMARK 3 S21: 0.2991 S22: -0.0606 S23: 0.1801 REMARK 3 S31: 0.2318 S32: -0.1802 S33: 0.0373 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 3 B 79 REMARK 3 ORIGIN FOR THE GROUP (A): -12.0307 10.8678 -33.0558 REMARK 3 T TENSOR REMARK 3 T11: 0.0573 T22: 0.0459 REMARK 3 T33: 0.1380 T12: -0.0029 REMARK 3 T13: -0.0120 T23: -0.0165 REMARK 3 L TENSOR REMARK 3 L11: 2.5383 L22: 1.2752 REMARK 3 L33: 2.3361 L12: 0.3429 REMARK 3 L13: -0.7772 L23: 0.1049 REMARK 3 S TENSOR REMARK 3 S11: -0.0233 S12: 0.3152 S13: -0.1596 REMARK 3 S21: -0.1292 S22: -0.0396 S23: 0.1075 REMARK 3 S31: 0.0608 S32: -0.1670 S33: 0.0629 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 19 REMARK 3 ORIGIN FOR THE GROUP (A): 3.7408 16.3602 -20.3907 REMARK 3 T TENSOR REMARK 3 T11: 0.0448 T22: 0.0978 REMARK 3 T33: 0.0820 T12: -0.0118 REMARK 3 T13: -0.0021 T23: 0.0293 REMARK 3 L TENSOR REMARK 3 L11: 1.5891 L22: 0.7339 REMARK 3 L33: 5.1371 L12: 0.0198 REMARK 3 L13: -1.4070 L23: 0.7099 REMARK 3 S TENSOR REMARK 3 S11: 0.0370 S12: -0.1808 S13: -0.0484 REMARK 3 S21: -0.0033 S22: 0.0568 S23: -0.0201 REMARK 3 S31: -0.1445 S32: 0.6331 S33: -0.0938 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1 D 19 REMARK 3 ORIGIN FOR THE GROUP (A): 4.6467 14.5007 -22.8198 REMARK 3 T TENSOR REMARK 3 T11: 0.0193 T22: 0.0968 REMARK 3 T33: 0.0514 T12: 0.0253 REMARK 3 T13: -0.0115 T23: 0.0196 REMARK 3 L TENSOR REMARK 3 L11: 1.5210 L22: 0.9501 REMARK 3 L33: 4.9393 L12: -0.1087 REMARK 3 L13: -1.4014 L23: 1.0523 REMARK 3 S TENSOR REMARK 3 S11: 0.0227 S12: -0.1784 S13: -0.0621 REMARK 3 S21: 0.0615 S22: 0.0514 S23: -0.0414 REMARK 3 S31: 0.1319 S32: 0.5211 S33: -0.0741 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 3S8Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-MAY-11. REMARK 100 THE DEPOSITION ID IS D_1000065902. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9334 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17823 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.6600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.47800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.110 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 1.3.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM ACETATE, 0.1 M BIS-TRIS REMARK 280 -PROPANE, 20% W/V PEG 3350, PH 6.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+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 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 30.77300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.84350 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.77300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 56.84350 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: 6800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 HIS A 78 REMARK 465 ASP A 79 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 GLU B 2 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 77 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 HOH B 179 O HOH B 215 1.94 REMARK 500 O HOH D 181 O HOH D 238 1.97 REMARK 500 O HOH A 106 O HOH A 286 1.98 REMARK 500 O HOH C 135 O HOH C 159 2.02 REMARK 500 O HOH B 260 O HOH D 226 2.05 REMARK 500 O HOH D 33 O HOH D 184 2.12 REMARK 500 O HOH A 90 O HOH A 155 2.14 REMARK 500 REMARK 500 REMARK: NULL 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 B 189 O HOH D 273 3544 2.17 REMARK 500 O HOH A 254 O HOH D 288 3554 2.18 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 DT C 4 O3' DT C 4 C3' -0.041 REMARK 500 DA C 10 N9 DA C 10 C4 0.045 REMARK 500 DA C 12 C6 DA C 12 N6 0.050 REMARK 500 DG D 5 C6 DG D 5 N1 0.042 REMARK 500 DA D 7 N9 DA D 7 C4 0.037 REMARK 500 DA D 10 C5 DA D 10 N7 0.039 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 LEU A 18 CB - CG - CD1 ANGL. DEV. = -10.4 DEGREES REMARK 500 ARG B 35 NE - CZ - NH2 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG B 43 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ASP B 79 CB - CG - OD1 ANGL. DEV. = -6.9 DEGREES REMARK 500 DA C 1 O4' - C1' - C2' ANGL. DEV. = 5.6 DEGREES REMARK 500 DT C 2 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG C 3 O5' - C5' - C4' ANGL. DEV. = -5.6 DEGREES REMARK 500 DG C 3 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 DG C 3 C4' - C3' - C2' ANGL. DEV. = 7.4 DEGREES REMARK 500 DG C 5 O4' - C1' - C2' ANGL. DEV. = 3.0 DEGREES REMARK 500 DA C 6 O5' - C5' - C4' ANGL. DEV. = -8.4 DEGREES REMARK 500 DC C 7 O4' - C1' - C2' ANGL. DEV. = 3.3 DEGREES REMARK 500 DC C 7 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT C 8 C2 - N3 - C4 ANGL. DEV. = -3.7 DEGREES REMARK 500 DT C 9 O5' - P - OP2 ANGL. DEV. = -5.8 DEGREES REMARK 500 DA C 10 N1 - C6 - N6 ANGL. DEV. = -3.6 DEGREES REMARK 500 DT C 11 C3' - C2' - C1' ANGL. DEV. = -9.3 DEGREES REMARK 500 DT C 11 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 DT C 11 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 DA C 12 O4' - C1' - N9 ANGL. DEV. = -5.1 DEGREES REMARK 500 DA C 12 N1 - C2 - N3 ANGL. DEV. = -4.6 DEGREES REMARK 500 DG C 13 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG C 13 C3' - O3' - P ANGL. DEV. = 8.5 DEGREES REMARK 500 DT C 14 O4' - C1' - C2' ANGL. DEV. = 3.8 DEGREES REMARK 500 DT C 14 O4' - C1' - N1 ANGL. DEV. = -4.7 DEGREES REMARK 500 DT C 14 N3 - C4 - C5 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT C 14 C5 - C4 - O4 ANGL. DEV. = -4.3 DEGREES REMARK 500 DC C 16 O5' - C5' - C4' ANGL. DEV. = -6.0 DEGREES REMARK 500 DG C 19 O4' - C4' - C3' ANGL. DEV. = -3.4 DEGREES REMARK 500 DG C 19 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG C 19 C4 - C5 - N7 ANGL. DEV. = -3.2 DEGREES REMARK 500 DT D 1 O4' - C1' - N1 ANGL. DEV. = -4.7 DEGREES REMARK 500 DT D 1 N1 - C2 - O2 ANGL. DEV. = 5.6 DEGREES REMARK 500 DC D 2 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 DC D 4 O4' - C4' - C3' ANGL. DEV. = -3.6 DEGREES REMARK 500 DC D 4 C1' - O4' - C4' ANGL. DEV. = -7.1 DEGREES REMARK 500 DG D 5 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG D 6 O4' - C1' - N9 ANGL. DEV. = -5.0 DEGREES REMARK 500 DA D 7 C3' - O3' - P ANGL. DEV. = 12.3 DEGREES REMARK 500 DC D 8 C1' - O4' - C4' ANGL. DEV. = -7.6 DEGREES REMARK 500 DT D 9 O4' - C1' - N1 ANGL. DEV. = -4.8 DEGREES REMARK 500 DA D 10 O3' - P - OP2 ANGL. DEV. = 7.0 DEGREES REMARK 500 DA D 10 O4' - C1' - C2' ANGL. DEV. = 3.8 DEGREES REMARK 500 DA D 10 O4' - C1' - N9 ANGL. DEV. = -4.6 DEGREES REMARK 500 DA D 10 C8 - N9 - C4 ANGL. DEV. = 3.3 DEGREES REMARK 500 DA D 10 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES REMARK 500 DT D 11 C3' - C2' - C1' ANGL. DEV. = -6.8 DEGREES REMARK 500 DA D 13 O4' - C1' - N9 ANGL. DEV. = -7.2 DEGREES REMARK 500 DT D 15 C4 - C5 - C7 ANGL. DEV. = 4.5 DEGREES REMARK 500 DT D 15 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 53 ANGLE DEVIATIONS. 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 SER B 45 56.90 39.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3CLC RELATED DB: PDB REMARK 900 C.ESP1396I TETRAMER COMPLEX REMARK 900 RELATED ID: 3G5G RELATED DB: PDB REMARK 900 C.ESP1396I, FREE PROTEIN REMARK 900 RELATED ID: 3FYA RELATED DB: PDB REMARK 900 C.ESP1396I, FREE PROTEIN, R35A MUTANT DBREF 3S8Q A 1 79 UNP Q8GGH0 Q8GGH0_9ENTR 1 79 DBREF 3S8Q B 1 79 UNP Q8GGH0 Q8GGH0_9ENTR 1 79 DBREF 3S8Q C 1 19 PDB 3S8Q 3S8Q 1 19 DBREF 3S8Q D 1 19 PDB 3S8Q 3S8Q 1 19 SEQADV 3S8Q GLY A -2 UNP Q8GGH0 EXPRESSION TAG SEQADV 3S8Q SER A -1 UNP Q8GGH0 EXPRESSION TAG SEQADV 3S8Q HIS A 0 UNP Q8GGH0 EXPRESSION TAG SEQADV 3S8Q GLY B -2 UNP Q8GGH0 EXPRESSION TAG SEQADV 3S8Q SER B -1 UNP Q8GGH0 EXPRESSION TAG SEQADV 3S8Q HIS B 0 UNP Q8GGH0 EXPRESSION TAG SEQRES 1 A 82 GLY SER HIS MET GLU SER PHE LEU LEU SER LYS VAL SER SEQRES 2 A 82 PHE VAL ILE LYS LYS ILE ARG LEU GLU LYS GLY MET THR SEQRES 3 A 82 GLN GLU ASP LEU ALA TYR LYS SER ASN LEU ASP ARG THR SEQRES 4 A 82 TYR ILE SER GLY ILE GLU ARG ASN SER ARG ASN LEU THR SEQRES 5 A 82 ILE LYS SER LEU GLU LEU ILE MET LYS GLY LEU GLU VAL SEQRES 6 A 82 SER ASP VAL VAL PHE PHE GLU MET LEU ILE LYS GLU ILE SEQRES 7 A 82 LEU LYS HIS ASP SEQRES 1 B 82 GLY SER HIS MET GLU SER PHE LEU LEU SER LYS VAL SER SEQRES 2 B 82 PHE VAL ILE LYS LYS ILE ARG LEU GLU LYS GLY MET THR SEQRES 3 B 82 GLN GLU ASP LEU ALA TYR LYS SER ASN LEU ASP ARG THR SEQRES 4 B 82 TYR ILE SER GLY ILE GLU ARG ASN SER ARG ASN LEU THR SEQRES 5 B 82 ILE LYS SER LEU GLU LEU ILE MET LYS GLY LEU GLU VAL SEQRES 6 B 82 SER ASP VAL VAL PHE PHE GLU MET LEU ILE LYS GLU ILE SEQRES 7 B 82 LEU LYS HIS ASP SEQRES 1 C 19 DA DT DG DT DG DA DC DT DT DA DT DA DG SEQRES 2 C 19 DT DC DC DG DT DG SEQRES 1 D 19 DT DC DA DC DG DG DA DC DT DA DT DA DA SEQRES 2 D 19 DG DT DC DA DC DA FORMUL 5 HOH *296(H2 O) HELIX 1 1 SER A 3 LYS A 20 1 18 HELIX 2 2 THR A 23 ASN A 32 1 10 HELIX 3 3 ASP A 34 ARG A 43 1 10 HELIX 4 4 THR A 49 LEU A 60 1 12 HELIX 5 5 SER A 63 LYS A 77 1 15 HELIX 6 6 SER B 3 LYS B 20 1 18 HELIX 7 7 THR B 23 ASN B 32 1 10 HELIX 8 8 ASP B 34 SER B 45 1 12 HELIX 9 9 THR B 49 LEU B 60 1 12 HELIX 10 10 SER B 63 LYS B 77 1 15 CRYST1 44.316 61.546 113.687 90.00 90.00 90.00 P 2 21 21 8 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 0.022565 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016248 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008796 0.00000