HEADER TRANSFERASE 14-OCT-03 1R62 TITLE CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF THE TWO-COMPONENT SYSTEM TITLE 2 TRANSMITTER PROTEIN NRII (NTRB) COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITROGEN REGULATION PROTEIN NR(II); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL FRAGMENT (RESIDUES 190-349); COMPND 5 EC: 2.7.3.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: NTRB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET30A KEYWDS NRII, PII, HISTIDINE KINASE, TWO COMPONENT SYSTEM, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.SONG,D.PEISACH,A.A.PIOSZAK,Z.XU,A.J.NINFA REVDAT 4 14-FEB-24 1R62 1 DBREF REVDAT 3 13-JUL-11 1R62 1 VERSN REVDAT 2 24-FEB-09 1R62 1 VERSN REVDAT 1 15-JUN-04 1R62 0 JRNL AUTH Y.SONG,D.PEISACH,A.A.PIOSZAK,Z.XU,A.J.NINFA JRNL TITL CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF THE JRNL TITL 2 TWO-COMPONENT SYSTEM TRANSMITTER PROTEIN NITROGEN REGULATOR JRNL TITL 3 II (NRII; NTRB), REGULATOR OF NITROGEN ASSIMILATION IN JRNL TITL 4 ESCHERICHIA COLI. JRNL REF BIOCHEMISTRY V. 43 6670 2004 JRNL REFN ISSN 0006-2960 JRNL PMID 15157101 JRNL DOI 10.1021/BI049474R REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.61 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1487105.040 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 15907 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 SET) : 0.237 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1742 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.70 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2413 REMARK 3 BIN R VALUE (WORKING SET) : 0.2820 REMARK 3 BIN FREE R VALUE : 0.2950 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 260 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1073 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 109 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 0.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.66000 REMARK 3 B22 (A**2) : 1.92000 REMARK 3 B33 (A**2) : -0.26000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.31000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.18 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.22 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.800 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : OVERALL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.200 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.770 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.180 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.150 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.41 REMARK 3 BSOL : 68.33 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 1R62 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-OCT-03. REMARK 100 THE DEPOSITION ID IS D_1000020482. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-AUG-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 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 : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18060 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 4.050 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 35.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.15 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.19800 REMARK 200 FOR SHELL : 4.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5% PEG 20,000 AND 0.1M MES, PH 6.1, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 48.22000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.47000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 48.22000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 16.47000 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 300 REMARK: THE FULL LENGTH NRII IS A DIMER, BUT THE C-TERMINAL DOMAIN REMARK 300 IS A MONOMER IN SOLUTION 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 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 LEU A 190 REMARK 465 PRO A 191 REMARK 465 GLY A 192 REMARK 465 THR A 193 REMARK 465 PRO A 293 REMARK 465 PRO A 294 REMARK 465 HIS A 295 REMARK 465 LEU A 296 REMARK 465 GLN A 297 REMARK 465 ASP A 298 REMARK 465 THR A 299 REMARK 465 LEU A 300 REMARK 465 PHE A 301 REMARK 465 TYR A 302 REMARK 465 PRO A 303 REMARK 465 MET A 304 REMARK 465 VAL A 305 REMARK 465 SER A 306 REMARK 465 GLY A 307 REMARK 465 ARG A 308 REMARK 465 GLU A 309 REMARK 465 GLY A 310 REMARK 465 GLY A 311 REMARK 465 THR A 312 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 219 CD NE CZ NH1 NH2 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 GLU A 256 CG CD OE1 OE2 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 336 111.43 -34.62 REMARK 500 REMARK 500 REMARK: NULL DBREF 1R62 A 190 349 UNP P06712 NTRB_ECOLI 190 349 SEQRES 1 A 160 LEU PRO GLY THR ARG VAL THR GLU SER ILE HIS LYS VAL SEQRES 2 A 160 ALA GLU ARG VAL VAL THR LEU VAL SER MET GLU LEU PRO SEQRES 3 A 160 ASP ASN VAL ARG LEU ILE ARG ASP TYR ASP PRO SER LEU SEQRES 4 A 160 PRO GLU LEU ALA HIS ASP PRO ASP GLN ILE GLU GLN VAL SEQRES 5 A 160 LEU LEU ASN ILE VAL ARG ASN ALA LEU GLN ALA LEU GLY SEQRES 6 A 160 PRO GLU GLY GLY GLU ILE ILE LEU ARG THR ARG THR ALA SEQRES 7 A 160 PHE GLN LEU THR LEU HIS GLY GLU ARG TYR ARG LEU ALA SEQRES 8 A 160 ALA ARG ILE ASP VAL GLU ASP ASN GLY PRO GLY ILE PRO SEQRES 9 A 160 PRO HIS LEU GLN ASP THR LEU PHE TYR PRO MET VAL SER SEQRES 10 A 160 GLY ARG GLU GLY GLY THR GLY LEU GLY LEU SER ILE ALA SEQRES 11 A 160 ARG ASN LEU ILE ASP GLN HIS SER GLY LYS ILE GLU PHE SEQRES 12 A 160 THR SER TRP PRO GLY HIS THR GLU PHE SER VAL TYR LEU SEQRES 13 A 160 PRO ILE ARG LYS FORMUL 2 HOH *109(H2 O) HELIX 1 1 SER A 198 SER A 211 1 14 HELIX 2 2 ASP A 234 GLY A 254 1 21 HELIX 3 3 PRO A 255 GLY A 257 5 3 HELIX 4 4 GLY A 313 HIS A 326 1 14 SHEET 1 A 2 VAL A 195 GLU A 197 0 SHEET 2 A 2 LEU A 231 HIS A 233 -1 O LEU A 231 N GLU A 197 SHEET 1 B 5 VAL A 218 ASP A 223 0 SHEET 2 B 5 GLY A 258 LEU A 272 1 O ILE A 260 N ILE A 221 SHEET 3 B 5 GLU A 275 ASN A 288 -1 O GLU A 286 N ILE A 261 SHEET 4 B 5 HIS A 338 ARG A 348 -1 O VAL A 343 N ILE A 283 SHEET 5 B 5 LYS A 329 TRP A 335 -1 N TRP A 335 O HIS A 338 CRYST1 96.440 32.940 46.010 90.00 108.19 90.00 C 1 2 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 0.010369 0.000000 0.003407 0.00000 SCALE2 0.000000 0.030358 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022878 0.00000