HEADER TRANSFERASE 12-AUG-08 3E4Q TITLE CRYSTAL STRUCTURE OF APO DCTB CAVEAT 3E4Q CHIRALITY ERROR AT CA CENTER OF LYS B 174 COMPND MOL_ID: 1; COMPND 2 MOLECULE: C4-DICARBOXYLATE TRANSPORT SENSOR PROTEIN DCTB; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: PERIPLASMIC SENSOR DOMAIN; COMPND 5 EC: 2.7.13.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SINORHIZOBIUM MELILOTI; SOURCE 3 ORGANISM_TAXID: 382; SOURCE 4 GENE: DCTB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS PAS DOMAIN, N-TERM HELICAL DIMERIZATION DOMAIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.F.ZHOU,J.NAN,B.Y.NAN,Y.H.LIANG,S.PANJIKAR,X.D.SU REVDAT 5 01-NOV-23 3E4Q 1 REMARK SEQADV REVDAT 4 25-OCT-17 3E4Q 1 REMARK REVDAT 3 13-JUL-11 3E4Q 1 VERSN REVDAT 2 24-FEB-09 3E4Q 1 VERSN REVDAT 1 21-OCT-08 3E4Q 0 JRNL AUTH Y.F.ZHOU,B.Y.NAN,J.NAN,Q.J.MA,S.PANJIKAR,Y.H.LIANG,Y.P.WANG, JRNL AUTH 2 X.D.SU JRNL TITL C4-DICARBOXYLATES SENSING MECHANISM REVEALED BY THE CRYSTAL JRNL TITL 2 STRUCTURES OF DCTB SENSOR DOMAIN. JRNL REF J.MOL.BIOL. V. 383 49 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18725229 JRNL DOI 10.1016/J.JMB.2008.08.010 REMARK 2 REMARK 2 RESOLUTION. 2.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 11984 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 663 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) : 2.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.82 REMARK 3 REFLECTION IN BIN (WORKING SET) : 884 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.89 REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE SET COUNT : 42 REMARK 3 BIN FREE R VALUE : 0.4090 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3890 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 10 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.16000 REMARK 3 B22 (A**2) : 2.08000 REMARK 3 B33 (A**2) : -2.90000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.18000 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): 0.443 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.341 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 37.097 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.906 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3956 ; 0.022 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5380 ; 2.290 ; 1.986 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 506 ;10.102 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 164 ;38.084 ;22.073 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 640 ;23.398 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 46 ;20.675 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 612 ; 0.209 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3016 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1942 ; 0.269 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2702 ; 0.333 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 189 ; 0.183 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.309 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 41 ; 0.231 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.176 ; 0.200 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): 2577 ; 0.778 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4066 ; 1.333 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1535 ; 2.182 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1314 ; 3.541 ; 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 : 2 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 56 A 305 REMARK 3 ORIGIN FOR THE GROUP (A): 23.6561 0.1167 41.2877 REMARK 3 T TENSOR REMARK 3 T11: -0.1958 T22: -0.2066 REMARK 3 T33: -0.1861 T12: -0.0335 REMARK 3 T13: 0.0057 T23: 0.0436 REMARK 3 L TENSOR REMARK 3 L11: 3.4297 L22: 2.0039 REMARK 3 L33: 4.7546 L12: -1.1137 REMARK 3 L13: -0.8515 L23: 0.9455 REMARK 3 S TENSOR REMARK 3 S11: -0.0294 S12: -0.1324 S13: 0.0365 REMARK 3 S21: 0.1501 S22: -0.0087 S23: 0.0012 REMARK 3 S31: -0.0117 S32: 0.2242 S33: 0.0381 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 56 B 305 REMARK 3 ORIGIN FOR THE GROUP (A): 13.6017 3.2501 13.9865 REMARK 3 T TENSOR REMARK 3 T11: -0.0980 T22: -0.2158 REMARK 3 T33: -0.1082 T12: 0.0126 REMARK 3 T13: 0.0228 T23: 0.0184 REMARK 3 L TENSOR REMARK 3 L11: 3.7252 L22: 3.2397 REMARK 3 L33: 3.6974 L12: -2.1896 REMARK 3 L13: -0.6613 L23: 1.0520 REMARK 3 S TENSOR REMARK 3 S11: 0.1142 S12: 0.2881 S13: 0.1222 REMARK 3 S21: -0.2464 S22: -0.1601 S23: 0.3951 REMARK 3 S31: -0.3025 S32: -0.4253 S33: 0.0459 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 3E4Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-AUG-08. REMARK 100 THE DEPOSITION ID IS D_1000048872. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-07 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BSRF REMARK 200 BEAMLINE : 3W1A 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000, DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12743 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.36900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB 3E4O REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 7.5, 15-20% PEG 3350, REMARK 280 0.04M CALCIUM CHLORIDE, VAPOR DIFFUSION, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 19.36750 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A 8 REMARK 465 GLY A 9 REMARK 465 SER A 10 REMARK 465 SER A 11 REMARK 465 HIS A 12 REMARK 465 HIS A 13 REMARK 465 HIS A 14 REMARK 465 HIS A 15 REMARK 465 HIS A 16 REMARK 465 HIS A 17 REMARK 465 SER A 18 REMARK 465 SER A 19 REMARK 465 GLY A 20 REMARK 465 LEU A 21 REMARK 465 VAL A 22 REMARK 465 PRO A 23 REMARK 465 ARG A 24 REMARK 465 GLY A 25 REMARK 465 SER A 26 REMARK 465 HIS A 27 REMARK 465 MET A 28 REMARK 465 ALA A 29 REMARK 465 SER A 30 REMARK 465 MET A 31 REMARK 465 THR A 32 REMARK 465 GLY A 33 REMARK 465 GLY A 34 REMARK 465 GLU A 35 REMARK 465 GLU A 36 REMARK 465 MET A 37 REMARK 465 GLY A 38 REMARK 465 ARG A 39 REMARK 465 GLY A 40 REMARK 465 SER A 41 REMARK 465 LEU A 42 REMARK 465 LEU A 43 REMARK 465 LEU A 44 REMARK 465 ALA A 45 REMARK 465 ARG A 46 REMARK 465 ASP A 47 REMARK 465 TYR A 48 REMARK 465 GLY A 49 REMARK 465 ARG A 50 REMARK 465 SER A 51 REMARK 465 GLN A 52 REMARK 465 ALA A 53 REMARK 465 LEU A 54 REMARK 465 ASN A 309 REMARK 465 ALA A 310 REMARK 465 PRO A 311 REMARK 465 LEU A 312 REMARK 465 MET B 8 REMARK 465 GLY B 9 REMARK 465 SER B 10 REMARK 465 SER B 11 REMARK 465 HIS B 12 REMARK 465 HIS B 13 REMARK 465 HIS B 14 REMARK 465 HIS B 15 REMARK 465 HIS B 16 REMARK 465 HIS B 17 REMARK 465 SER B 18 REMARK 465 SER B 19 REMARK 465 GLY B 20 REMARK 465 LEU B 21 REMARK 465 VAL B 22 REMARK 465 PRO B 23 REMARK 465 ARG B 24 REMARK 465 GLY B 25 REMARK 465 SER B 26 REMARK 465 HIS B 27 REMARK 465 MET B 28 REMARK 465 ALA B 29 REMARK 465 SER B 30 REMARK 465 MET B 31 REMARK 465 THR B 32 REMARK 465 GLY B 33 REMARK 465 GLY B 34 REMARK 465 GLU B 35 REMARK 465 GLU B 36 REMARK 465 MET B 37 REMARK 465 GLY B 38 REMARK 465 ARG B 39 REMARK 465 GLY B 40 REMARK 465 SER B 41 REMARK 465 LEU B 42 REMARK 465 LEU B 43 REMARK 465 LEU B 44 REMARK 465 ALA B 45 REMARK 465 ARG B 46 REMARK 465 ASP B 47 REMARK 465 TYR B 48 REMARK 465 GLY B 49 REMARK 465 ARG B 50 REMARK 465 SER B 51 REMARK 465 GLN B 52 REMARK 465 ALA B 53 REMARK 465 LEU B 54 REMARK 465 ASN B 309 REMARK 465 ALA B 310 REMARK 465 PRO B 311 REMARK 465 LEU B 312 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 LYS B 265 CE LYS B 265 NZ 0.338 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 156 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 PRO A 307 C - N - CA ANGL. DEV. = 14.1 DEGREES REMARK 500 LEU B 82 CA - CB - CG ANGL. DEV. = -21.6 DEGREES REMARK 500 LEU B 114 CB - CG - CD2 ANGL. DEV. = -10.3 DEGREES REMARK 500 PRO B 176 C - N - CA ANGL. DEV. = 10.1 DEGREES REMARK 500 ARG B 232 NE - CZ - NH2 ANGL. DEV. = -3.2 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 PRO A 99 18.03 -50.91 REMARK 500 ASP A 100 159.72 -12.37 REMARK 500 THR A 142 30.92 -90.54 REMARK 500 ALA A 164 139.36 -176.81 REMARK 500 ASP A 218 -157.20 -72.14 REMARK 500 GLU A 241 -74.02 -21.31 REMARK 500 ALA A 245 -72.27 -36.45 REMARK 500 PHE A 253 75.41 -158.10 REMARK 500 LEU A 261 142.54 -33.39 REMARK 500 PRO A 281 111.76 -39.93 REMARK 500 ASP A 283 -170.45 129.76 REMARK 500 SER A 284 -177.06 -63.78 REMARK 500 PRO A 307 -176.20 -44.49 REMARK 500 PHE B 144 7.66 -69.87 REMARK 500 PHE B 155 -76.99 -83.99 REMARK 500 PRO B 229 -62.61 -27.29 REMARK 500 MET B 234 -158.58 -96.04 REMARK 500 PRO B 238 126.93 -31.44 REMARK 500 GLU B 241 -72.49 -19.96 REMARK 500 GLU B 249 -77.17 -28.01 REMARK 500 PHE B 253 55.25 -144.39 REMARK 500 ALA B 256 142.19 -22.20 REMARK 500 PRO B 262 74.33 -58.55 REMARK 500 LYS B 265 27.38 88.73 REMARK 500 PRO B 270 -34.13 -35.84 REMARK 500 PRO B 281 -58.60 -18.42 REMARK 500 ASP B 283 47.34 -179.25 REMARK 500 SER B 284 -63.90 -11.99 REMARK 500 ALA B 286 119.11 -166.09 REMARK 500 SER B 297 11.02 82.59 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 ASP A 283 SER A 284 -45.51 REMARK 500 GLY B 211 LYS B 212 149.93 REMARK 500 ASP B 271 GLY B 272 -144.77 REMARK 500 GLY B 282 ASP B 283 -33.06 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 CA A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 601 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3E4O RELATED DB: PDB REMARK 900 RELATED ID: 3E4P RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE FEATURE OF UNIPROT (DCTB_RHIME P13633) SHOWS CONFLICT AT THE REMARK 999 POSITION 174: N -> K (IN REF. 5). REFERENCE FOR THE POSITION 309 (K REMARK 999 -> N) IS FEMS MICROBIOLOGY LETTERS 14 (1982) 95-99, DEREPRESSION OF REMARK 999 RIBULOSE BISPHOSPHATE CARBOXYLASE ACTIVITY IN RHIZOBIUM MELILOTI REMARK 999 SUNDARAM S. MANIAN AND FERGAL O'GARA DBREF 3E4Q A 42 312 UNP P13633 DCTB_RHIME 42 312 DBREF 3E4Q B 42 312 UNP P13633 DCTB_RHIME 42 312 SEQADV 3E4Q MET A 8 UNP P13633 EXPRESSION TAG SEQADV 3E4Q GLY A 9 UNP P13633 EXPRESSION TAG SEQADV 3E4Q SER A 10 UNP P13633 EXPRESSION TAG SEQADV 3E4Q SER A 11 UNP P13633 EXPRESSION TAG SEQADV 3E4Q HIS A 12 UNP P13633 EXPRESSION TAG SEQADV 3E4Q HIS A 13 UNP P13633 EXPRESSION TAG SEQADV 3E4Q HIS A 14 UNP P13633 EXPRESSION TAG SEQADV 3E4Q HIS A 15 UNP P13633 EXPRESSION TAG SEQADV 3E4Q HIS A 16 UNP P13633 EXPRESSION TAG SEQADV 3E4Q HIS A 17 UNP P13633 EXPRESSION TAG SEQADV 3E4Q SER A 18 UNP P13633 EXPRESSION TAG SEQADV 3E4Q SER A 19 UNP P13633 EXPRESSION TAG SEQADV 3E4Q GLY A 20 UNP P13633 EXPRESSION TAG SEQADV 3E4Q LEU A 21 UNP P13633 EXPRESSION TAG SEQADV 3E4Q VAL A 22 UNP P13633 EXPRESSION TAG SEQADV 3E4Q PRO A 23 UNP P13633 EXPRESSION TAG SEQADV 3E4Q ARG A 24 UNP P13633 EXPRESSION TAG SEQADV 3E4Q GLY A 25 UNP P13633 EXPRESSION TAG SEQADV 3E4Q SER A 26 UNP P13633 EXPRESSION TAG SEQADV 3E4Q HIS A 27 UNP P13633 EXPRESSION TAG SEQADV 3E4Q MET A 28 UNP P13633 EXPRESSION TAG SEQADV 3E4Q ALA A 29 UNP P13633 EXPRESSION TAG SEQADV 3E4Q SER A 30 UNP P13633 EXPRESSION TAG SEQADV 3E4Q MET A 31 UNP P13633 EXPRESSION TAG SEQADV 3E4Q THR A 32 UNP P13633 EXPRESSION TAG SEQADV 3E4Q GLY A 33 UNP P13633 EXPRESSION TAG SEQADV 3E4Q GLY A 34 UNP P13633 EXPRESSION TAG SEQADV 3E4Q GLU A 35 UNP P13633 EXPRESSION TAG SEQADV 3E4Q GLU A 36 UNP P13633 EXPRESSION TAG SEQADV 3E4Q MET A 37 UNP P13633 EXPRESSION TAG SEQADV 3E4Q GLY A 38 UNP P13633 EXPRESSION TAG SEQADV 3E4Q ARG A 39 UNP P13633 EXPRESSION TAG SEQADV 3E4Q GLY A 40 UNP P13633 EXPRESSION TAG SEQADV 3E4Q SER A 41 UNP P13633 EXPRESSION TAG SEQADV 3E4Q LYS A 174 UNP P13633 ASN 174 SEE REMARK 999 SEQADV 3E4Q ASN A 309 UNP P13633 LYS 309 SEE REMARK 999 SEQADV 3E4Q MET B 8 UNP P13633 EXPRESSION TAG SEQADV 3E4Q GLY B 9 UNP P13633 EXPRESSION TAG SEQADV 3E4Q SER B 10 UNP P13633 EXPRESSION TAG SEQADV 3E4Q SER B 11 UNP P13633 EXPRESSION TAG SEQADV 3E4Q HIS B 12 UNP P13633 EXPRESSION TAG SEQADV 3E4Q HIS B 13 UNP P13633 EXPRESSION TAG SEQADV 3E4Q HIS B 14 UNP P13633 EXPRESSION TAG SEQADV 3E4Q HIS B 15 UNP P13633 EXPRESSION TAG SEQADV 3E4Q HIS B 16 UNP P13633 EXPRESSION TAG SEQADV 3E4Q HIS B 17 UNP P13633 EXPRESSION TAG SEQADV 3E4Q SER B 18 UNP P13633 EXPRESSION TAG SEQADV 3E4Q SER B 19 UNP P13633 EXPRESSION TAG SEQADV 3E4Q GLY B 20 UNP P13633 EXPRESSION TAG SEQADV 3E4Q LEU B 21 UNP P13633 EXPRESSION TAG SEQADV 3E4Q VAL B 22 UNP P13633 EXPRESSION TAG SEQADV 3E4Q PRO B 23 UNP P13633 EXPRESSION TAG SEQADV 3E4Q ARG B 24 UNP P13633 EXPRESSION TAG SEQADV 3E4Q GLY B 25 UNP P13633 EXPRESSION TAG SEQADV 3E4Q SER B 26 UNP P13633 EXPRESSION TAG SEQADV 3E4Q HIS B 27 UNP P13633 EXPRESSION TAG SEQADV 3E4Q MET B 28 UNP P13633 EXPRESSION TAG SEQADV 3E4Q ALA B 29 UNP P13633 EXPRESSION TAG SEQADV 3E4Q SER B 30 UNP P13633 EXPRESSION TAG SEQADV 3E4Q MET B 31 UNP P13633 EXPRESSION TAG SEQADV 3E4Q THR B 32 UNP P13633 EXPRESSION TAG SEQADV 3E4Q GLY B 33 UNP P13633 EXPRESSION TAG SEQADV 3E4Q GLY B 34 UNP P13633 EXPRESSION TAG SEQADV 3E4Q GLU B 35 UNP P13633 EXPRESSION TAG SEQADV 3E4Q GLU B 36 UNP P13633 EXPRESSION TAG SEQADV 3E4Q MET B 37 UNP P13633 EXPRESSION TAG SEQADV 3E4Q GLY B 38 UNP P13633 EXPRESSION TAG SEQADV 3E4Q ARG B 39 UNP P13633 EXPRESSION TAG SEQADV 3E4Q GLY B 40 UNP P13633 EXPRESSION TAG SEQADV 3E4Q SER B 41 UNP P13633 EXPRESSION TAG SEQADV 3E4Q LYS B 174 UNP P13633 ASN 174 SEE REMARK 999 SEQADV 3E4Q ASN B 309 UNP P13633 LYS 309 SEE REMARK 999 SEQRES 1 A 305 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 305 LEU VAL PRO ARG GLY SER HIS MET ALA SER MET THR GLY SEQRES 3 A 305 GLY GLU GLU MET GLY ARG GLY SER LEU LEU LEU ALA ARG SEQRES 4 A 305 ASP TYR GLY ARG SER GLN ALA LEU ALA GLY LEU ALA GLY SEQRES 5 A 305 GLN SER ARG ILE ASP ALA SER LEU LYS ALA SER LEU LEU SEQRES 6 A 305 ARG ALA VAL VAL GLU ARG GLN ARG ALA LEU PRO LEU VAL SEQRES 7 A 305 LEU ALA ASP ASP ALA ALA ILE ARG GLY ALA LEU LEU SER SEQRES 8 A 305 PRO ASP ARG PRO SER LEU ASP ARG ILE ASN ARG LYS LEU SEQRES 9 A 305 GLU ALA LEU ALA THR SER ALA GLU ALA ALA VAL ILE TYR SEQRES 10 A 305 LEU ILE ASP ARG SER GLY VAL ALA VAL ALA ALA SER ASN SEQRES 11 A 305 TRP GLN GLU PRO THR SER PHE VAL GLY ASN ASP TYR ALA SEQRES 12 A 305 PHE ARG ASP TYR PHE ARG LEU ALA VAL ARG ASP GLY MET SEQRES 13 A 305 ALA GLU HIS PHE ALA MET GLY THR VAL SER LYS ARG PRO SEQRES 14 A 305 GLY LEU TYR ILE SER ARG ARG VAL ASP GLY PRO GLY GLY SEQRES 15 A 305 PRO LEU GLY VAL ILE VAL ALA LYS LEU GLU PHE ASP GLY SEQRES 16 A 305 VAL GLU ALA ASP TRP GLN ALA SER GLY LYS PRO ALA TYR SEQRES 17 A 305 VAL THR ASP ARG ARG GLY ILE VAL LEU ILE THR SER LEU SEQRES 18 A 305 PRO SER TRP ARG PHE MET THR THR LYS PRO ILE ALA GLU SEQRES 19 A 305 ASP ARG LEU ALA PRO ILE ARG GLU SER LEU GLN PHE GLY SEQRES 20 A 305 ASP ALA PRO LEU LEU PRO LEU PRO PHE ARG LYS ILE GLU SEQRES 21 A 305 ALA ARG PRO ASP GLY SER SER THR LEU ASP ALA LEU LEU SEQRES 22 A 305 PRO GLY ASP SER THR ALA ALA PHE LEU ARG VAL GLU THR SEQRES 23 A 305 MET VAL PRO SER THR ASN TRP ARG LEU GLU GLN LEU SER SEQRES 24 A 305 PRO LEU ASN ALA PRO LEU SEQRES 1 B 305 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 305 LEU VAL PRO ARG GLY SER HIS MET ALA SER MET THR GLY SEQRES 3 B 305 GLY GLU GLU MET GLY ARG GLY SER LEU LEU LEU ALA ARG SEQRES 4 B 305 ASP TYR GLY ARG SER GLN ALA LEU ALA GLY LEU ALA GLY SEQRES 5 B 305 GLN SER ARG ILE ASP ALA SER LEU LYS ALA SER LEU LEU SEQRES 6 B 305 ARG ALA VAL VAL GLU ARG GLN ARG ALA LEU PRO LEU VAL SEQRES 7 B 305 LEU ALA ASP ASP ALA ALA ILE ARG GLY ALA LEU LEU SER SEQRES 8 B 305 PRO ASP ARG PRO SER LEU ASP ARG ILE ASN ARG LYS LEU SEQRES 9 B 305 GLU ALA LEU ALA THR SER ALA GLU ALA ALA VAL ILE TYR SEQRES 10 B 305 LEU ILE ASP ARG SER GLY VAL ALA VAL ALA ALA SER ASN SEQRES 11 B 305 TRP GLN GLU PRO THR SER PHE VAL GLY ASN ASP TYR ALA SEQRES 12 B 305 PHE ARG ASP TYR PHE ARG LEU ALA VAL ARG ASP GLY MET SEQRES 13 B 305 ALA GLU HIS PHE ALA MET GLY THR VAL SER LYS ARG PRO SEQRES 14 B 305 GLY LEU TYR ILE SER ARG ARG VAL ASP GLY PRO GLY GLY SEQRES 15 B 305 PRO LEU GLY VAL ILE VAL ALA LYS LEU GLU PHE ASP GLY SEQRES 16 B 305 VAL GLU ALA ASP TRP GLN ALA SER GLY LYS PRO ALA TYR SEQRES 17 B 305 VAL THR ASP ARG ARG GLY ILE VAL LEU ILE THR SER LEU SEQRES 18 B 305 PRO SER TRP ARG PHE MET THR THR LYS PRO ILE ALA GLU SEQRES 19 B 305 ASP ARG LEU ALA PRO ILE ARG GLU SER LEU GLN PHE GLY SEQRES 20 B 305 ASP ALA PRO LEU LEU PRO LEU PRO PHE ARG LYS ILE GLU SEQRES 21 B 305 ALA ARG PRO ASP GLY SER SER THR LEU ASP ALA LEU LEU SEQRES 22 B 305 PRO GLY ASP SER THR ALA ALA PHE LEU ARG VAL GLU THR SEQRES 23 B 305 MET VAL PRO SER THR ASN TRP ARG LEU GLU GLN LEU SER SEQRES 24 B 305 PRO LEU ASN ALA PRO LEU HET CA A 501 1 HET CA B 601 1 HETNAM CA CALCIUM ION FORMUL 3 CA 2(CA 2+) FORMUL 5 HOH *10(H2 O) HELIX 1 1 ALA A 55 ALA A 87 1 33 HELIX 2 2 ASP A 89 SER A 98 1 10 HELIX 3 3 ASP A 100 GLU A 119 1 20 HELIX 4 4 ARG A 152 GLY A 162 1 11 HELIX 5 5 PHE A 200 GLY A 211 1 12 HELIX 6 6 LEU A 228 ARG A 232 5 5 HELIX 7 7 ALA A 240 ASP A 242 5 3 HELIX 8 8 ARG A 243 GLN A 252 1 10 HELIX 9 9 GLY B 56 ASP B 89 1 34 HELIX 10 10 ASP B 89 SER B 98 1 10 HELIX 11 11 ASP B 100 GLU B 119 1 20 HELIX 12 12 ARG B 152 GLY B 162 1 11 HELIX 13 13 PHE B 200 ALA B 209 1 10 HELIX 14 14 LEU B 228 ARG B 232 5 5 HELIX 15 15 ALA B 240 ASP B 242 5 3 HELIX 16 16 ARG B 243 GLN B 252 1 10 SHEET 1 A 5 ALA A 132 ALA A 135 0 SHEET 2 A 5 VAL A 122 ASP A 127 -1 N LEU A 125 O VAL A 133 SHEET 3 A 5 PRO A 190 LEU A 198 -1 O LYS A 197 N VAL A 122 SHEET 4 A 5 PRO A 176 ASP A 185 -1 N VAL A 184 O LEU A 191 SHEET 5 A 5 MET A 163 MET A 169 -1 N ALA A 164 O SER A 181 SHEET 1 B 6 VAL A 223 THR A 226 0 SHEET 2 B 6 ALA A 214 THR A 217 -1 N VAL A 216 O ILE A 225 SHEET 3 B 6 ARG A 301 SER A 306 -1 O GLU A 303 N TYR A 215 SHEET 4 B 6 THR A 285 MET A 294 -1 N LEU A 289 O SER A 306 SHEET 5 B 6 SER A 274 LEU A 279 -1 N LEU A 276 O PHE A 288 SHEET 6 B 6 PHE A 263 ALA A 268 -1 N ARG A 264 O ASP A 277 SHEET 1 C 5 ALA B 132 ALA B 135 0 SHEET 2 C 5 VAL B 122 ASP B 127 -1 N LEU B 125 O ALA B 134 SHEET 3 C 5 PRO B 190 LEU B 198 -1 O VAL B 193 N ILE B 126 SHEET 4 C 5 PRO B 176 ASP B 185 -1 N ILE B 180 O ALA B 196 SHEET 5 C 5 MET B 163 MET B 169 -1 N ALA B 164 O SER B 181 SHEET 1 D 6 VAL B 223 THR B 226 0 SHEET 2 D 6 ALA B 214 THR B 217 -1 N VAL B 216 O ILE B 225 SHEET 3 D 6 ARG B 301 SER B 306 -1 O ARG B 301 N THR B 217 SHEET 4 D 6 ALA B 286 MET B 294 -1 N THR B 293 O LEU B 302 SHEET 5 D 6 SER B 273 ALA B 278 -1 N SER B 274 O ARG B 290 SHEET 6 D 6 PHE B 263 ARG B 269 -1 N ARG B 264 O ASP B 277 LINK ND2 ASN A 299 CA CA A 501 1555 1555 2.15 SITE 1 AC1 3 THR A 298 ASN A 299 TRP A 300 SITE 1 AC2 2 ASN B 299 TRP B 300 CRYST1 57.988 38.735 111.172 90.00 94.47 90.00 P 1 21 1 4 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 0.017245 0.000000 0.001348 0.00000 SCALE2 0.000000 0.025816 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009023 0.00000