HEADER TRANSCRIPTION REGULATOR 07-FEB-05 1YS6 TITLE CRYSTAL STRUCTURE OF THE RESPONSE REGULATORY PROTEIN PRRA FROM TITLE 2 MYCOBACTERIUM TUBERCULOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATORY PROTEIN PRRA; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: RESPONSE REGULATOR PRRA; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3)PLYSS; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PETM11 KEYWDS RESPONSE REGULATOR PROTEIN, DNA BINDING DOMAIN, MYCOBACTERIUM KEYWDS 2 TUBERCULOSIS STRUCTURAL PROTEOMICS PROJECT, XMTB, STRUCTURAL KEYWDS 3 GENOMICS, TRANSCRIPTION REGULATOR EXPDTA X-RAY DIFFRACTION AUTHOR E.NOWAK,S.PANJIKAR,P.TUCKER,MYCOBACTERIUM TUBERCULOSIS STRUCTURAL AUTHOR 2 PROTEOMICS PROJECT (XMTB) REVDAT 4 13-MAR-24 1YS6 1 REMARK LINK REVDAT 3 13-JUL-11 1YS6 1 VERSN REVDAT 2 24-FEB-09 1YS6 1 VERSN REVDAT 1 07-FEB-06 1YS6 0 JRNL AUTH E.NOWAK,S.PANJIKAR,P.TUCKER JRNL TITL CRYSTAL STRUCTURE OF THE RESPONSE REGULATORY PROTEIN PRRA JRNL TITL 2 FROM MYCOBACTERIUM TUBERCULOSIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.77 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) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.63 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 3 NUMBER OF REFLECTIONS : 36253 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1898 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) : 1.77 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.82 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1994 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 70.22 REMARK 3 BIN R VALUE (WORKING SET) : 0.2970 REMARK 3 BIN FREE R VALUE SET COUNT : 105 REMARK 3 BIN FREE R VALUE : 0.3080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3408 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.73 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) : 0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.02000 REMARK 3 B23 (A**2) : 0.01000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.146 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.147 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.124 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.839 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): 3442 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4681 ; 1.913 ; 1.989 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 449 ; 7.171 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 146 ;33.796 ;22.740 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 572 ;15.485 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 41 ;24.941 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 577 ; 0.144 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2569 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1845 ; 0.225 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2400 ; 0.314 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 355 ; 0.195 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 10 ; 0.154 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 91 ; 0.256 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 29 ; 0.160 ; 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): 2285 ; 1.201 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3596 ; 1.877 ; 2.500 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1257 ; 4.308 ; 5.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1084 ; 6.585 ;10.000 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 : 2 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 7 A 125 4 REMARK 3 1 B 7 B 125 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 850 ; 0.85 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 850 ; 1.44 ; 2.50 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 136 A 233 4 REMARK 3 1 B 136 B 233 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 2 A (A): 766 ; 0.37 ; 0.50 REMARK 3 MEDIUM THERMAL 2 A (A**2): 766 ; 1.69 ; 2.50 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1YS6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-FEB-05. REMARK 100 THE DEPOSITION ID IS D_1000031870. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-DEC-04 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 : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.81 REMARK 200 MONOCHROMATOR : TRIANGULAR MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39823 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 19.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.57400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG800, SODIUM CACODYLATE, CALCIUM REMARK 280 ACETATE, GLYCEROL, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 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 1 REMARK 465 ASP A 2 REMARK 465 THR A 3 REMARK 465 GLY A 4 REMARK 465 VAL A 5 REMARK 465 THR A 6 REMARK 465 SER A 89 REMARK 465 SER A 90 REMARK 465 MET B 1 REMARK 465 ASP B 2 REMARK 465 THR B 3 REMARK 465 GLY B 4 REMARK 465 VAL B 5 REMARK 465 THR B 6 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 ARG A 88 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 126 CG CD NE CZ NH1 NH2 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 ALA A 87 REMARK 475 ARG A 88 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG B 88 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O SER A 86 N ALA A 87 1.56 REMARK 500 O ARG A 88 N VAL A 91 1.97 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 SER A 86 C ALA A 87 N -0.169 REMARK 500 ALA A 87 N ALA A 87 CA -0.203 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 28 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 VAL A 84 CG1 - CB - CG2 ANGL. DEV. = 11.8 DEGREES REMARK 500 SER A 86 CA - C - N ANGL. DEV. = 16.8 DEGREES REMARK 500 SER A 86 O - C - N ANGL. DEV. = -42.1 DEGREES REMARK 500 ALA A 87 C - N - CA ANGL. DEV. = 32.7 DEGREES REMARK 500 ALA A 87 N - CA - C ANGL. DEV. = 21.6 DEGREES REMARK 500 ARG A 218 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 218 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 163 NE - CZ - NH1 ANGL. DEV. = 4.0 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 ARG A 51 79.86 36.63 REMARK 500 VAL A 63 -64.12 72.51 REMARK 500 ALA A 87 -35.16 -18.10 REMARK 500 ASP A 92 -25.98 85.74 REMARK 500 GLU A 135 -106.46 -105.55 REMARK 500 HIS A 174 47.93 -104.90 REMARK 500 THR A 176 -2.57 65.54 REMARK 500 ALA A 194 -71.83 -49.45 REMARK 500 ALA A 195 116.03 56.02 REMARK 500 ASP A 196 77.08 -102.79 REMARK 500 VAL A 226 -55.55 -135.54 REMARK 500 ARG B 51 83.05 53.20 REMARK 500 VAL B 63 -62.53 72.48 REMARK 500 ASP B 93 -61.33 160.96 REMARK 500 SER B 128 -95.12 -110.13 REMARK 500 THR B 129 144.07 -39.37 REMARK 500 HIS B 174 43.24 -108.71 REMARK 500 THR B 176 -6.22 71.25 REMARK 500 VAL B 226 -56.24 -124.90 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 SER A 86 ALA A 87 149.29 REMARK 500 ASP B 92 ASP B 93 -144.87 REMARK 500 GLY B 127 SER B 128 -142.39 REMARK 500 SER B 128 THR B 129 -133.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 SER A 86 47.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1001 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 15 OD1 REMARK 620 2 ASP A 58 OD2 90.9 REMARK 620 3 ASN A 60 O 86.9 86.9 REMARK 620 4 HOH A1058 O 74.7 159.6 78.2 REMARK 620 5 HOH A1074 O 172.8 82.6 89.8 110.9 REMARK 620 6 HOH A1075 O 91.3 84.7 171.4 109.4 91.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B1002 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 15 OD1 REMARK 620 2 ASP B 58 OD2 85.0 REMARK 620 3 ASN B 60 O 88.1 91.2 REMARK 620 4 HOH B2011 O 76.5 158.2 76.9 REMARK 620 5 HOH B2064 O 86.9 83.3 172.9 106.8 REMARK 620 6 HOH B2067 O 173.7 95.9 98.1 103.8 87.0 REMARK 620 N 1 2 3 4 5 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 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 2001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YS3 RELATED DB: PDB REMARK 900 ATP BINDING DOMAIN OF PRRB REMARK 900 RELATED ID: 1YS7 RELATED DB: PDB REMARK 900 RESPONSE REGULATOR PROTEIN PRRA COMLEXED WITH MG2 REMARK 900 RELATED ID: RV0903C RELATED DB: TARGETDB DBREF 1YS6 A 1 233 UNP Q10531 PRRA_MYCTU 1 233 DBREF 1YS6 B 1 233 UNP Q10531 PRRA_MYCTU 1 233 SEQRES 1 A 233 MET ASP THR GLY VAL THR SER PRO ARG VAL LEU VAL VAL SEQRES 2 A 233 ASP ASP ASP SER ASP VAL LEU ALA SER LEU GLU ARG GLY SEQRES 3 A 233 LEU ARG LEU SER GLY PHE GLU VAL ALA THR ALA VAL ASP SEQRES 4 A 233 GLY ALA GLU ALA LEU ARG SER ALA THR GLU ASN ARG PRO SEQRES 5 A 233 ASP ALA ILE VAL LEU ASP ILE ASN MET PRO VAL LEU ASP SEQRES 6 A 233 GLY VAL SER VAL VAL THR ALA LEU ARG ALA MET ASP ASN SEQRES 7 A 233 ASP VAL PRO VAL CYS VAL LEU SER ALA ARG SER SER VAL SEQRES 8 A 233 ASP ASP ARG VAL ALA GLY LEU GLU ALA GLY ALA ASP ASP SEQRES 9 A 233 TYR LEU VAL LYS PRO PHE VAL LEU ALA GLU LEU VAL ALA SEQRES 10 A 233 ARG VAL LYS ALA LEU LEU ARG ARG ARG GLY SER THR ALA SEQRES 11 A 233 THR SER SER SER GLU THR ILE THR VAL GLY PRO LEU GLU SEQRES 12 A 233 VAL ASP ILE PRO GLY ARG ARG ALA ARG VAL ASN GLY VAL SEQRES 13 A 233 ASP VAL ASP LEU THR LYS ARG GLU PHE ASP LEU LEU ALA SEQRES 14 A 233 VAL LEU ALA GLU HIS LYS THR ALA VAL LEU SER ARG ALA SEQRES 15 A 233 GLN LEU LEU GLU LEU VAL TRP GLY TYR ASP PHE ALA ALA SEQRES 16 A 233 ASP THR ASN VAL VAL ASP VAL PHE ILE GLY TYR LEU ARG SEQRES 17 A 233 ARG LYS LEU GLU ALA GLY GLY GLY PRO ARG LEU LEU HIS SEQRES 18 A 233 THR VAL ARG GLY VAL GLY PHE VAL LEU ARG MET GLN SEQRES 1 B 233 MET ASP THR GLY VAL THR SER PRO ARG VAL LEU VAL VAL SEQRES 2 B 233 ASP ASP ASP SER ASP VAL LEU ALA SER LEU GLU ARG GLY SEQRES 3 B 233 LEU ARG LEU SER GLY PHE GLU VAL ALA THR ALA VAL ASP SEQRES 4 B 233 GLY ALA GLU ALA LEU ARG SER ALA THR GLU ASN ARG PRO SEQRES 5 B 233 ASP ALA ILE VAL LEU ASP ILE ASN MET PRO VAL LEU ASP SEQRES 6 B 233 GLY VAL SER VAL VAL THR ALA LEU ARG ALA MET ASP ASN SEQRES 7 B 233 ASP VAL PRO VAL CYS VAL LEU SER ALA ARG SER SER VAL SEQRES 8 B 233 ASP ASP ARG VAL ALA GLY LEU GLU ALA GLY ALA ASP ASP SEQRES 9 B 233 TYR LEU VAL LYS PRO PHE VAL LEU ALA GLU LEU VAL ALA SEQRES 10 B 233 ARG VAL LYS ALA LEU LEU ARG ARG ARG GLY SER THR ALA SEQRES 11 B 233 THR SER SER SER GLU THR ILE THR VAL GLY PRO LEU GLU SEQRES 12 B 233 VAL ASP ILE PRO GLY ARG ARG ALA ARG VAL ASN GLY VAL SEQRES 13 B 233 ASP VAL ASP LEU THR LYS ARG GLU PHE ASP LEU LEU ALA SEQRES 14 B 233 VAL LEU ALA GLU HIS LYS THR ALA VAL LEU SER ARG ALA SEQRES 15 B 233 GLN LEU LEU GLU LEU VAL TRP GLY TYR ASP PHE ALA ALA SEQRES 16 B 233 ASP THR ASN VAL VAL ASP VAL PHE ILE GLY TYR LEU ARG SEQRES 17 B 233 ARG LYS LEU GLU ALA GLY GLY GLY PRO ARG LEU LEU HIS SEQRES 18 B 233 THR VAL ARG GLY VAL GLY PHE VAL LEU ARG MET GLN HET CA A1001 1 HET CA B1002 1 HET GOL B2001 6 HETNAM CA CALCIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 CA 2(CA 2+) FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *340(H2 O) HELIX 1 1 ASP A 16 SER A 30 1 15 HELIX 2 2 ASP A 39 ARG A 51 1 13 HELIX 3 3 ASP A 65 MET A 76 1 12 HELIX 4 4 VAL A 95 GLY A 101 1 7 HELIX 5 5 VAL A 111 SER A 128 1 18 HELIX 6 6 THR A 161 HIS A 174 1 14 HELIX 7 7 SER A 180 VAL A 188 1 9 HELIX 8 8 ASN A 198 GLU A 212 1 15 HELIX 9 9 ASP B 16 SER B 30 1 15 HELIX 10 10 ASP B 39 ARG B 51 1 13 HELIX 11 11 ASP B 65 MET B 76 1 12 HELIX 12 12 SER B 90 GLY B 101 1 12 HELIX 13 13 VAL B 111 ARG B 125 1 15 HELIX 14 14 THR B 161 HIS B 174 1 14 HELIX 15 15 SER B 180 VAL B 188 1 9 HELIX 16 16 ASN B 198 ALA B 213 1 16 SHEET 1 A 5 GLU A 33 ALA A 37 0 SHEET 2 A 5 ARG A 9 VAL A 13 1 N VAL A 12 O ALA A 35 SHEET 3 A 5 ALA A 54 ASP A 58 1 O VAL A 56 N VAL A 13 SHEET 4 A 5 VAL A 82 SER A 86 1 O CYS A 83 N LEU A 57 SHEET 5 A 5 ASP A 104 VAL A 107 1 O LEU A 106 N VAL A 84 SHEET 1 B 4 THR A 136 VAL A 139 0 SHEET 2 B 4 LEU A 142 ASP A 145 -1 O VAL A 144 N ILE A 137 SHEET 3 B 4 ARG A 150 VAL A 153 -1 O ARG A 150 N ASP A 145 SHEET 4 B 4 VAL A 156 VAL A 158 -1 O VAL A 156 N VAL A 153 SHEET 1 C 3 VAL A 178 LEU A 179 0 SHEET 2 C 3 GLY A 227 LEU A 230 -1 O PHE A 228 N LEU A 179 SHEET 3 C 3 LEU A 220 VAL A 223 -1 N VAL A 223 O GLY A 227 SHEET 1 D 5 GLU B 33 ALA B 37 0 SHEET 2 D 5 ARG B 9 VAL B 13 1 N VAL B 12 O ALA B 35 SHEET 3 D 5 ALA B 54 ASP B 58 1 O VAL B 56 N VAL B 13 SHEET 4 D 5 VAL B 82 ALA B 87 1 O CYS B 83 N LEU B 57 SHEET 5 D 5 ASP B 104 LYS B 108 1 O LYS B 108 N SER B 86 SHEET 1 E 4 ILE B 137 VAL B 139 0 SHEET 2 E 4 LEU B 142 ASP B 145 -1 O VAL B 144 N ILE B 137 SHEET 3 E 4 ARG B 150 VAL B 153 -1 O ARG B 150 N ASP B 145 SHEET 4 E 4 VAL B 156 ASP B 157 -1 O VAL B 156 N VAL B 153 SHEET 1 F 2 LEU B 220 VAL B 223 0 SHEET 2 F 2 GLY B 227 LEU B 230 -1 O VAL B 229 N HIS B 221 LINK OD1 ASP A 15 CA CA A1001 1555 1555 2.22 LINK OD2 ASP A 58 CA CA A1001 1555 1555 2.25 LINK O ASN A 60 CA CA A1001 1555 1555 2.28 LINK CA CA A1001 O HOH A1058 1555 1555 2.54 LINK CA CA A1001 O HOH A1074 1555 1555 2.20 LINK CA CA A1001 O HOH A1075 1555 1555 2.42 LINK OD1 ASP B 15 CA CA B1002 1555 1555 2.24 LINK OD2 ASP B 58 CA CA B1002 1555 1555 2.17 LINK O ASN B 60 CA CA B1002 1555 1555 2.36 LINK CA CA B1002 O HOH B2011 1555 1555 2.39 LINK CA CA B1002 O HOH B2064 1555 1555 2.42 LINK CA CA B1002 O HOH B2067 1555 1555 2.43 CISPEP 1 LYS A 108 PRO A 109 0 0.34 CISPEP 2 LYS B 108 PRO B 109 0 -9.36 SITE 1 AC1 6 ASP A 15 ASP A 58 ASN A 60 HOH A1058 SITE 2 AC1 6 HOH A1074 HOH A1075 SITE 1 AC2 6 ASP B 15 ASP B 58 ASN B 60 HOH B2011 SITE 2 AC2 6 HOH B2064 HOH B2067 SITE 1 AC3 6 ARG B 149 ARG B 150 ALA B 151 VAL B 158 SITE 2 AC3 6 LEU B 160 HOH B2063 CRYST1 37.222 46.538 65.660 100.29 101.68 92.52 P 1 2 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 0.026866 0.001182 0.005892 0.00000 SCALE2 0.000000 0.021509 0.004202 0.00000 SCALE3 0.000000 0.000000 0.015846 0.00000