HEADER RIBOSOMAL PROTEIN 18-NOV-13 4NNG TITLE STRUCTURAL BASIS FOR TARGETING THE RIBOSOMAL PROTEIN S1 OF TITLE 2 MYCOBACTERIUM TUBERCULOSIS BY PYRAZINAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 30S RIBOSOMAL PROTEIN S1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 285-435; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: ATCC 25618 / H37RV; SOURCE 5 GENE: MT1666, MTCY01B2.22, RPSA, RV1630; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-28A KEYWDS BETA BARREL, RIBOSOMAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.YANG,Y.LIU,Q.CAI,D.LIN REVDAT 4 20-MAR-24 4NNG 1 SEQADV REVDAT 3 22-NOV-17 4NNG 1 REMARK REVDAT 2 09-SEP-15 4NNG 1 JRNL REVDAT 1 24-DEC-14 4NNG 0 JRNL AUTH J.YANG,Y.LIU,J.BI,Q.CAI,X.LIAO,W.LI,C.GUO,Q.ZHANG,T.LIN, JRNL AUTH 2 Y.ZHAO,H.WANG,J.LIU,X.ZHANG,D.LIN JRNL TITL STRUCTURAL BASIS FOR TARGETING THE RIBOSOMAL PROTEIN S1 OF JRNL TITL 2 MYCOBACTERIUM TUBERCULOSIS BY PYRAZINAMIDE. JRNL REF MOL.MICROBIOL. V. 95 791 2015 JRNL REFN ISSN 0950-382X JRNL PMID 25430994 JRNL DOI 10.1111/MMI.12892 REMARK 2 REMARK 2 RESOLUTION. 2.02 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) : 2.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 12228 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) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 624 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) : 2.02 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 890 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.36 REMARK 3 BIN R VALUE (WORKING SET) : 0.2090 REMARK 3 BIN FREE R VALUE SET COUNT : 48 REMARK 3 BIN FREE R VALUE : 0.2290 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1281 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 116 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.30000 REMARK 3 B22 (A**2) : 0.60000 REMARK 3 B33 (A**2) : -1.90000 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): 0.196 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.181 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.131 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.658 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.918 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1309 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1213 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1764 ; 1.699 ; 1.929 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2784 ; 0.806 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 156 ; 4.844 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 76 ;36.989 ;24.079 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 227 ;15.950 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;21.645 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 181 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1507 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 322 ; 0.001 ; 0.020 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 4NNG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-DEC-13. REMARK 100 THE DEPOSITION ID IS D_1000083421. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-APR-13 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 : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 2.020 REMARK 200 RESOLUTION RANGE LOW (A) : 38.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: PHASER 2.5.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NACL, AMMONIUM SULFATE, PH 7.5, REMARK 280 HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 26.06650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.67100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.01550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.67100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.06650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.01550 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 PHE A 435 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NNH RELATED DB: PDB REMARK 900 RELATED ID: 4NNI RELATED DB: PDB REMARK 900 RELATED ID: 4NNK RELATED DB: PDB DBREF 4NNG A 285 435 UNP P9WH43 RS1_MYCTU 285 435 SEQADV 4NNG ASN A 278 UNP P9WH43 EXPRESSION TAG SEQADV 4NNG LEU A 279 UNP P9WH43 EXPRESSION TAG SEQADV 4NNG TYR A 280 UNP P9WH43 EXPRESSION TAG SEQADV 4NNG PHE A 281 UNP P9WH43 EXPRESSION TAG SEQADV 4NNG GLN A 282 UNP P9WH43 EXPRESSION TAG SEQADV 4NNG HIS A 283 UNP P9WH43 EXPRESSION TAG SEQADV 4NNG MET A 284 UNP P9WH43 EXPRESSION TAG SEQADV 4NNG ALA A 298 UNP P9WH43 PRO 298 ENGINEERED MUTATION SEQRES 1 A 158 ASN LEU TYR PHE GLN HIS MET ARG HIS PHE ALA ARG THR SEQRES 2 A 158 HIS ALA ILE GLY GLN ILE VAL ALA GLY LYS VAL THR LYS SEQRES 3 A 158 LEU VAL PRO PHE GLY ALA PHE VAL ARG VAL GLU GLU GLY SEQRES 4 A 158 ILE GLU GLY LEU VAL HIS ILE SER GLU LEU ALA GLU ARG SEQRES 5 A 158 HIS VAL GLU VAL PRO ASP GLN VAL VAL ALA VAL GLY ASP SEQRES 6 A 158 ASP ALA MET VAL LYS VAL ILE ASP ILE ASP LEU GLU ARG SEQRES 7 A 158 ARG ARG ILE SER LEU SER LEU LYS GLN ALA ASN GLU ASP SEQRES 8 A 158 TYR THR GLU GLU PHE ASP PRO ALA LYS TYR GLY MET ALA SEQRES 9 A 158 ASP SER TYR ASP GLU GLN GLY ASN TYR ILE PHE PRO GLU SEQRES 10 A 158 GLY PHE ASP ALA GLU THR ASN GLU TRP LEU GLU GLY PHE SEQRES 11 A 158 GLU LYS GLN ARG ALA GLU TRP GLU ALA ARG TYR ALA GLU SEQRES 12 A 158 ALA GLU ARG ARG HIS LYS MET HIS THR ALA GLN MET GLU SEQRES 13 A 158 LYS PHE FORMUL 2 HOH *116(H2 O) HELIX 1 1 TYR A 280 HIS A 291 1 12 HELIX 2 2 SER A 324 LEU A 326 5 3 HELIX 3 3 VAL A 333 VAL A 337 5 5 HELIX 4 4 LEU A 362 TYR A 369 1 8 HELIX 5 5 ASP A 374 TYR A 378 5 5 HELIX 6 6 MET A 380 TYR A 384 5 5 HELIX 7 7 PHE A 407 LYS A 434 1 28 SHEET 1 A 6 ILE A 296 VAL A 305 0 SHEET 2 A 6 GLY A 308 GLU A 314 -1 O ARG A 312 N LYS A 300 SHEET 3 A 6 ILE A 317 HIS A 322 -1 O ILE A 317 N GLU A 314 SHEET 4 A 6 ARG A 357 SER A 361 1 O LEU A 360 N LEU A 320 SHEET 5 A 6 ASP A 343 ASP A 352 -1 N ASP A 350 O SER A 359 SHEET 6 A 6 ILE A 296 VAL A 305 -1 N VAL A 297 O VAL A 346 SHEET 1 B 2 PHE A 396 ASP A 397 0 SHEET 2 B 2 GLU A 402 TRP A 403 -1 O GLU A 402 N ASP A 397 CRYST1 52.133 56.031 65.342 90.00 90.00 90.00 P 21 21 21 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 0.019182 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017847 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015304 0.00000