PDB Short entry for 3HDV HEADER TRANSCRIPTION REGULATOR 07-MAY-09 3HDV TITLE CRYSTAL STRUCTURE OF RESPONSE REGULATOR RECEIVER PROTEIN FROM TITLE 2 PSEUDOMONAS PUTIDA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RESPONSE REGULATOR; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: RESPONSE REGULATOR; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PUTIDA; SOURCE 3 ORGANISM_TAXID: 160488; SOURCE 4 STRAIN: KT2440; SOURCE 5 GENE: PP_0355, PP0355; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PSGX3(BC) KEYWDS RESPONSE REGULATOR, PSI-II, 11224L, STRUCTURAL GENOMICS, PROTEIN KEYWDS 2 STRUCTURE INITIATIVE, NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL KEYWDS 3 GENOMICS, NYSGXRC, TRANSCRIPTION REGULATOR EXPDTA X-RAY DIFFRACTION AUTHOR A.BAGARIA,S.K.BURLEY,S.SWAMINATHAN,NEW YORK SGX RESEARCH CENTER FOR AUTHOR 2 STRUCTURAL GENOMICS (NYSGXRC) REVDAT 3 10-FEB-21 3HDV 1 AUTHOR JRNL LINK REVDAT 2 13-JUL-11 3HDV 1 VERSN REVDAT 1 26-MAY-09 3HDV 0 JRNL AUTH A.BAGARIA,S.K.BURLEY,S.SWAMINATHAN JRNL TITL CRYSTAL STRUCTURE OF RESPONSE REGULATOR RECEIVER PROTEIN JRNL TITL 2 FROM PSEUDOMONAS PUTIDA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 43315 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2304 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) : 2.09 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.14 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2958 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.33 REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE SET COUNT : 187 REMARK 3 BIN FREE R VALUE : 0.3000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3735 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 243 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.168 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.159 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.113 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.178 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3767 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5095 ; 1.875 ; 2.008 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 480 ; 6.498 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 159 ;29.945 ;24.088 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 712 ;16.856 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;26.637 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 634 ; 0.126 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2711 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1722 ; 0.224 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2570 ; 0.307 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 281 ; 0.225 ; 0.200 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 ; 0.206 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 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): 2517 ; 1.372 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3858 ; 2.035 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1423 ; 3.449 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1237 ; 4.999 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3HDV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1000053012. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9790 REMARK 200 MONOCHROMATOR : SI(111)CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45411 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.090 REMARK 200 RESOLUTION RANGE LOW (A) : 44.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 14.20 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.3000 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) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 13.10 REMARK 200 R MERGE FOR SHELL (I) : 0.52000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXD, SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH7.5, 0.8M POTASSIUM REMARK 280 SODIUM TARTARATE TETRAHYDRATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+1/2,Y+1/2,-Z REMARK 290 4555 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 55.38450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 70.21800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 55.38450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 70.21800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 300 REMARK: TETRAMER 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: 2950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 MSE A 62 REMARK 465 SER A 63 REMARK 465 LEU A 64 REMARK 465 VAL A 65 REMARK 465 ALA A 66 REMARK 465 ALA A 67 REMARK 465 ILE A 188 REMARK 465 GLY A 189 REMARK 465 GLU A 190 REMARK 465 GLY A 191 REMARK 465 HIS A 192 REMARK 465 HIS A 193 REMARK 465 HIS A 194 REMARK 465 HIS A 195 REMARK 465 HIS A 196 REMARK 465 HIS A 197 REMARK 465 MSE B 62 REMARK 465 GLY B 189 REMARK 465 GLU B 190 REMARK 465 GLY B 191 REMARK 465 HIS B 192 REMARK 465 HIS B 193 REMARK 465 HIS B 194 REMARK 465 HIS B 195 REMARK 465 HIS B 196 REMARK 465 HIS B 197 REMARK 465 MSE C 62 REMARK 465 SER C 63 REMARK 465 LEU C 64 REMARK 465 LEU C 186 REMARK 465 LYS C 187 REMARK 465 ILE C 188 REMARK 465 GLY C 189 REMARK 465 GLU C 190 REMARK 465 GLY C 191 REMARK 465 HIS C 192 REMARK 465 HIS C 193 REMARK 465 HIS C 194 REMARK 465 HIS C 195 REMARK 465 HIS C 196 REMARK 465 HIS C 197 REMARK 465 MSE D 62 REMARK 465 SER D 63 REMARK 465 LEU D 64 REMARK 465 VAL D 65 REMARK 465 ALA D 66 REMARK 465 ALA D 67 REMARK 465 ARG D 68 REMARK 465 LEU D 186 REMARK 465 LYS D 187 REMARK 465 ILE D 188 REMARK 465 GLY D 189 REMARK 465 GLU D 190 REMARK 465 GLY D 191 REMARK 465 HIS D 192 REMARK 465 HIS D 193 REMARK 465 HIS D 194 REMARK 465 HIS D 195 REMARK 465 HIS D 196 REMARK 465 HIS D 197 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 MSE D 123 C GLN D 124 N 0.221 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 122 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG C 122 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG C 122 NE - CZ - NH2 ANGL. DEV. = -6.0 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 ASP A 151 88.18 -160.73 REMARK 500 ARG C 113 -37.20 100.61 REMARK 500 ILE C 114 106.75 -53.51 REMARK 500 ARG D 91 -162.86 -101.49 REMARK 500 GLN D 124 -95.83 -51.61 REMARK 500 VAL D 173 -139.14 -50.93 REMARK 500 ASP D 174 -95.50 -179.95 REMARK 500 LEU D 175 -18.93 147.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGXRC-11224L RELATED DB: TARGETDB DBREF 3HDV A 65 189 UNP Q88QX9 Q88QX9_PSEPK 65 189 DBREF 3HDV B 65 189 UNP Q88QX9 Q88QX9_PSEPK 65 189 DBREF 3HDV C 65 189 UNP Q88QX9 Q88QX9_PSEPK 65 189 DBREF 3HDV D 65 189 UNP Q88QX9 Q88QX9_PSEPK 65 189 SEQADV 3HDV MSE A 62 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV SER A 63 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV LEU A 64 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV GLU A 190 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV GLY A 191 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV HIS A 192 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV HIS A 193 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV HIS A 194 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV HIS A 195 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV HIS A 196 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV HIS A 197 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV MSE B 62 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV SER B 63 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV LEU B 64 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV GLU B 190 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV GLY B 191 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV HIS B 192 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV HIS B 193 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV HIS B 194 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV HIS B 195 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV HIS B 196 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV HIS B 197 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV MSE C 62 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV SER C 63 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV LEU C 64 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV GLU C 190 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV GLY C 191 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV HIS C 192 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV HIS C 193 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV HIS C 194 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV HIS C 195 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV HIS C 196 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV HIS C 197 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV MSE D 62 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV SER D 63 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV LEU D 64 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV GLU D 190 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV GLY D 191 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV HIS D 192 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV HIS D 193 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV HIS D 194 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV HIS D 195 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV HIS D 196 UNP Q88QX9 EXPRESSION TAG SEQADV 3HDV HIS D 197 UNP Q88QX9 EXPRESSION TAG SEQRES 1 A 136 MSE SER LEU VAL ALA ALA ARG PRO LEU VAL LEU VAL VAL SEQRES 2 A 136 ASP ASP ASN ALA VAL ASN ARG GLU ALA LEU ILE LEU TYR SEQRES 3 A 136 LEU LYS SER ARG GLY ILE ASP ALA VAL GLY ALA ASP GLY SEQRES 4 A 136 ALA GLU GLU ALA ARG LEU TYR LEU HIS TYR GLN LYS ARG SEQRES 5 A 136 ILE GLY LEU MSE ILE THR ASP LEU ARG MSE GLN PRO GLU SEQRES 6 A 136 SER GLY LEU ASP LEU ILE ARG THR ILE ARG ALA SER GLU SEQRES 7 A 136 ARG ALA ALA LEU SER ILE ILE VAL VAL SER GLY ASP THR SEQRES 8 A 136 ASP VAL GLU GLU ALA VAL ASP VAL MSE HIS LEU GLY VAL SEQRES 9 A 136 VAL ASP PHE LEU LEU LYS PRO VAL ASP LEU GLY LYS LEU SEQRES 10 A 136 LEU GLU LEU VAL ASN LYS GLU LEU LYS ILE GLY GLU GLY SEQRES 11 A 136 HIS HIS HIS HIS HIS HIS SEQRES 1 B 136 MSE SER LEU VAL ALA ALA ARG PRO LEU VAL LEU VAL VAL SEQRES 2 B 136 ASP ASP ASN ALA VAL ASN ARG GLU ALA LEU ILE LEU TYR SEQRES 3 B 136 LEU LYS SER ARG GLY ILE ASP ALA VAL GLY ALA ASP GLY SEQRES 4 B 136 ALA GLU GLU ALA ARG LEU TYR LEU HIS TYR GLN LYS ARG SEQRES 5 B 136 ILE GLY LEU MSE ILE THR ASP LEU ARG MSE GLN PRO GLU SEQRES 6 B 136 SER GLY LEU ASP LEU ILE ARG THR ILE ARG ALA SER GLU SEQRES 7 B 136 ARG ALA ALA LEU SER ILE ILE VAL VAL SER GLY ASP THR SEQRES 8 B 136 ASP VAL GLU GLU ALA VAL ASP VAL MSE HIS LEU GLY VAL SEQRES 9 B 136 VAL ASP PHE LEU LEU LYS PRO VAL ASP LEU GLY LYS LEU SEQRES 10 B 136 LEU GLU LEU VAL ASN LYS GLU LEU LYS ILE GLY GLU GLY SEQRES 11 B 136 HIS HIS HIS HIS HIS HIS SEQRES 1 C 136 MSE SER LEU VAL ALA ALA ARG PRO LEU VAL LEU VAL VAL SEQRES 2 C 136 ASP ASP ASN ALA VAL ASN ARG GLU ALA LEU ILE LEU TYR SEQRES 3 C 136 LEU LYS SER ARG GLY ILE ASP ALA VAL GLY ALA ASP GLY SEQRES 4 C 136 ALA GLU GLU ALA ARG LEU TYR LEU HIS TYR GLN LYS ARG SEQRES 5 C 136 ILE GLY LEU MSE ILE THR ASP LEU ARG MSE GLN PRO GLU SEQRES 6 C 136 SER GLY LEU ASP LEU ILE ARG THR ILE ARG ALA SER GLU SEQRES 7 C 136 ARG ALA ALA LEU SER ILE ILE VAL VAL SER GLY ASP THR SEQRES 8 C 136 ASP VAL GLU GLU ALA VAL ASP VAL MSE HIS LEU GLY VAL SEQRES 9 C 136 VAL ASP PHE LEU LEU LYS PRO VAL ASP LEU GLY LYS LEU SEQRES 10 C 136 LEU GLU LEU VAL ASN LYS GLU LEU LYS ILE GLY GLU GLY SEQRES 11 C 136 HIS HIS HIS HIS HIS HIS SEQRES 1 D 136 MSE SER LEU VAL ALA ALA ARG PRO LEU VAL LEU VAL VAL SEQRES 2 D 136 ASP ASP ASN ALA VAL ASN ARG GLU ALA LEU ILE LEU TYR SEQRES 3 D 136 LEU LYS SER ARG GLY ILE ASP ALA VAL GLY ALA ASP GLY SEQRES 4 D 136 ALA GLU GLU ALA ARG LEU TYR LEU HIS TYR GLN LYS ARG SEQRES 5 D 136 ILE GLY LEU MSE ILE THR ASP LEU ARG MSE GLN PRO GLU SEQRES 6 D 136 SER GLY LEU ASP LEU ILE ARG THR ILE ARG ALA SER GLU SEQRES 7 D 136 ARG ALA ALA LEU SER ILE ILE VAL VAL SER GLY ASP THR SEQRES 8 D 136 ASP VAL GLU GLU ALA VAL ASP VAL MSE HIS LEU GLY VAL SEQRES 9 D 136 VAL ASP PHE LEU LEU LYS PRO VAL ASP LEU GLY LYS LEU SEQRES 10 D 136 LEU GLU LEU VAL ASN LYS GLU LEU LYS ILE GLY GLU GLY SEQRES 11 D 136 HIS HIS HIS HIS HIS HIS MODRES 3HDV MSE A 117 MET SELENOMETHIONINE MODRES 3HDV MSE A 123 MET SELENOMETHIONINE MODRES 3HDV MSE A 161 MET SELENOMETHIONINE MODRES 3HDV MSE B 117 MET SELENOMETHIONINE MODRES 3HDV MSE B 123 MET SELENOMETHIONINE MODRES 3HDV MSE B 161 MET SELENOMETHIONINE MODRES 3HDV MSE C 117 MET SELENOMETHIONINE MODRES 3HDV MSE C 123 MET SELENOMETHIONINE MODRES 3HDV MSE C 161 MET SELENOMETHIONINE MODRES 3HDV MSE D 117 MET SELENOMETHIONINE MODRES 3HDV MSE D 123 MET SELENOMETHIONINE MODRES 3HDV MSE D 161 MET SELENOMETHIONINE HET MSE A 117 8 HET MSE A 123 8 HET MSE A 161 8 HET MSE B 117 8 HET MSE B 123 8 HET MSE B 161 8 HET MSE C 117 8 HET MSE C 123 8 HET MSE C 161 8 HET MSE D 117 8 HET MSE D 123 8 HET MSE D 161 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 12(C5 H11 N O2 SE) FORMUL 5 HOH *243(H2 O) HELIX 1 1 ASN A 77 ARG A 91 1 15 HELIX 2 2 GLY A 100 GLN A 111 1 12 HELIX 3 3 SER A 127 ALA A 137 1 11 HELIX 4 4 ASP A 153 LEU A 163 1 11 HELIX 5 5 ASP A 174 LYS A 187 1 14 HELIX 6 6 ASN B 77 ARG B 91 1 15 HELIX 7 7 GLY B 100 GLN B 111 1 12 HELIX 8 8 SER B 127 ALA B 137 1 11 HELIX 9 9 ASP B 153 LEU B 163 1 11 HELIX 10 10 ASP B 174 LEU B 186 1 13 HELIX 11 11 ASN C 77 SER C 90 1 14 HELIX 12 12 GLY C 100 GLN C 111 1 12 HELIX 13 13 SER C 127 ALA C 137 1 11 HELIX 14 14 ASP C 153 LEU C 163 1 11 HELIX 15 15 ASP C 174 GLU C 185 1 12 HELIX 16 16 ASN D 77 SER D 90 1 14 HELIX 17 17 GLY D 100 GLN D 111 1 12 HELIX 18 18 SER D 127 ALA D 137 1 11 HELIX 19 19 ASP D 153 LEU D 163 1 11 HELIX 20 20 LEU D 175 GLU D 185 1 11 SHEET 1 A 5 ALA A 95 ALA A 98 0 SHEET 2 A 5 LEU A 70 VAL A 74 1 N VAL A 73 O VAL A 96 SHEET 3 A 5 ILE A 114 THR A 119 1 O ILE A 118 N LEU A 72 SHEET 4 A 5 SER A 144 SER A 149 1 O ILE A 146 N MSE A 117 SHEET 5 A 5 ASP A 167 LEU A 170 1 O LEU A 169 N VAL A 147 SHEET 1 B 5 ASP B 94 ALA B 98 0 SHEET 2 B 5 LEU B 70 VAL B 74 1 N VAL B 73 O VAL B 96 SHEET 3 B 5 ILE B 114 THR B 119 1 O ILE B 118 N VAL B 74 SHEET 4 B 5 SER B 144 SER B 149 1 O VAL B 148 N THR B 119 SHEET 5 B 5 ASP B 167 LEU B 170 1 O LEU B 169 N VAL B 147 SHEET 1 C 5 ASP C 94 ALA C 98 0 SHEET 2 C 5 LEU C 70 VAL C 74 1 N VAL C 73 O VAL C 96 SHEET 3 C 5 ILE C 114 THR C 119 1 O ILE C 118 N VAL C 74 SHEET 4 C 5 SER C 144 SER C 149 1 O ILE C 146 N MSE C 117 SHEET 5 C 5 ASP C 167 LEU C 170 1 O LEU C 169 N VAL C 147 SHEET 1 D 5 ALA D 95 ALA D 98 0 SHEET 2 D 5 LEU D 70 VAL D 74 1 N VAL D 73 O VAL D 96 SHEET 3 D 5 ILE D 114 THR D 119 1 O ILE D 118 N VAL D 74 SHEET 4 D 5 SER D 144 SER D 149 1 O VAL D 148 N THR D 119 SHEET 5 D 5 ASP D 167 LEU D 170 1 O ASP D 167 N VAL D 147 LINK C LEU A 116 N MSE A 117 1555 1555 1.33 LINK C MSE A 117 N ILE A 118 1555 1555 1.33 LINK C ARG A 122 N MSE A 123 1555 1555 1.32 LINK C MSE A 123 N GLN A 124 1555 1555 1.33 LINK C VAL A 160 N MSE A 161 1555 1555 1.33 LINK C MSE A 161 N HIS A 162 1555 1555 1.31 LINK C LEU B 116 N MSE B 117 1555 1555 1.33 LINK C MSE B 117 N ILE B 118 1555 1555 1.32 LINK C ARG B 122 N MSE B 123 1555 1555 1.32 LINK C MSE B 123 N GLN B 124 1555 1555 1.34 LINK C VAL B 160 N MSE B 161 1555 1555 1.33 LINK C MSE B 161 N HIS B 162 1555 1555 1.33 LINK C LEU C 116 N MSE C 117 1555 1555 1.33 LINK C MSE C 117 N ILE C 118 1555 1555 1.33 LINK C ARG C 122 N MSE C 123 1555 1555 1.32 LINK C MSE C 123 N GLN C 124 1555 1555 1.32 LINK C VAL C 160 N MSE C 161 1555 1555 1.33 LINK C MSE C 161 N HIS C 162 1555 1555 1.33 LINK C LEU D 116 N MSE D 117 1555 1555 1.34 LINK C MSE D 117 N ILE D 118 1555 1555 1.33 LINK C ARG D 122 N MSE D 123 1555 1555 1.22 LINK C MSE D 123 N GLN D 124 1555 1555 1.56 LINK C VAL D 160 N MSE D 161 1555 1555 1.34 LINK C MSE D 161 N HIS D 162 1555 1555 1.34 CISPEP 1 GLN A 124 PRO A 125 0 5.54 CISPEP 2 LYS A 171 PRO A 172 0 -2.33 CISPEP 3 GLN B 124 PRO B 125 0 3.90 CISPEP 4 LYS B 171 PRO B 172 0 -7.77 CISPEP 5 GLN C 124 PRO C 125 0 1.29 CISPEP 6 LYS C 171 PRO C 172 0 3.20 CISPEP 7 LYS D 171 PRO D 172 0 8.71 CRYST1 110.769 140.436 48.571 90.00 90.00 90.00 P 21 21 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 0.009028 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007121 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020588 0.00000