HEADER TRANSFERASE 17-AUG-16 5T12 TITLE N-TERMINAL DOMAIN OF ENZYME 1 - NITROGEN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOENOLPYRUVATE--PROTEIN PHOSPHOTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 170-424; COMPND 5 SYNONYM: PHOSPHOENOLPYRUVATE-PROTEIN PHOSPHOTRANSFERASE, COMPND 6 PHOSPHOENOLPYRUVATE-PROTEIN PHOSPHOTRANSFERASE PTSP; COMPND 7 EC: 2.7.3.9; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: PTSP, AC789_1C31510, ACU90_23270, AML37_15090, AWH59_07225, SOURCE 5 WQ89_09920; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PTSNTR, PHOSPHOTRANSFER, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.M.STANLEY,I.BOTOS,S.K.BUCHANAN REVDAT 4 04-OCT-23 5T12 1 SEQADV REVDAT 3 14-DEC-16 5T12 1 JRNL REVDAT 2 30-NOV-16 5T12 1 JRNL REVDAT 1 23-NOV-16 5T12 0 JRNL AUTH M.STRICKLAND,A.M.STANLEY,G.WANG,I.BOTOS,C.D.SCHWIETERS, JRNL AUTH 2 S.K.BUCHANAN,A.PETERKOFSKY,N.TJANDRA JRNL TITL STRUCTURE OF THE NPR:EIN(NTR) COMPLEX: MECHANISM FOR JRNL TITL 2 SPECIFICITY IN PARALOGOUS PHOSPHOTRANSFERASE SYSTEMS. JRNL REF STRUCTURE V. 24 2127 2016 JRNL REFN ISSN 1878-4186 JRNL PMID 27839951 JRNL DOI 10.1016/J.STR.2016.10.007 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2155) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.9 REMARK 3 NUMBER OF REFLECTIONS : 11880 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 595 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 33.2249 - 3.6488 0.78 2462 122 0.1776 0.2003 REMARK 3 2 3.6488 - 2.8967 0.89 2776 149 0.2225 0.2448 REMARK 3 3 2.8967 - 2.5306 0.99 3067 161 0.2468 0.3371 REMARK 3 4 2.5306 - 2.2993 0.97 2980 163 0.2860 0.3346 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.310 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.002 1894 REMARK 3 ANGLE : 0.534 2569 REMARK 3 CHIRALITY : 0.039 294 REMARK 3 PLANARITY : 0.004 338 REMARK 3 DIHEDRAL : 19.032 1155 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5T12 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1000223417. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11880 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.299 REMARK 200 RESOLUTION RANGE LOW (A) : 33.221 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.11200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.50900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.480 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1ZYM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0M POTASSIUM/SODIUM TARTRATE 0.1M REMARK 280 IMIDAZOLE 8.0 0.2M NACL 1.0M SODIUM IODIDE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 82.46133 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 41.23067 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 61.84600 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 20.61533 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 103.07667 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 TOTAL BURIED SURFACE AREA: 730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 KCAL/MOL 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 ASN A 312A REMARK 465 GLN A 312B REMARK 465 GLY A 312C REMARK 465 PRO A 312D REMARK 465 GLU A 412 REMARK 465 ILE A 413 REMARK 465 GLU A 414 REMARK 465 LEU A 415 REMARK 465 SER A 416 REMARK 465 ARG A 417 REMARK 465 LEU A 418 REMARK 465 ALA A 419 REMARK 465 GLU A 420 REMARK 465 ASP A 421 REMARK 465 ASP A 422 REMARK 465 VAL A 423 REMARK 465 ASN A 424 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 GLN A 235 138.16 177.47 REMARK 500 ASP A 373 105.30 -56.68 REMARK 500 ASP A 396 61.56 70.38 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 IOD A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 505 DBREF1 5T12 A 170 424 UNP A0A0E1LBH7_ECOLX DBREF2 5T12 A A0A0E1LBH7 170 424 SEQADV 5T12 GLN A 356 UNP A0A0E1LBH HIS 356 ENGINEERED MUTATION SEQRES 1 A 255 ARG ILE ARG ALA LEU PRO ALA ALA PRO GLY VAL ALA ILE SEQRES 2 A 255 ALA GLU GLY TRP GLN ASP ALA THR LEU PRO LEU MET GLU SEQRES 3 A 255 GLN VAL TYR GLN ALA SER THR LEU ASP PRO ALA LEU GLU SEQRES 4 A 255 ARG GLU ARG LEU THR GLY ALA LEU GLU GLU ALA ALA ASN SEQRES 5 A 255 GLU PHE ARG ARG TYR SER LYS ARG PHE ALA ALA GLY ALA SEQRES 6 A 255 GLN LYS GLU THR ALA ALA ILE PHE ASP LEU TYR SER HIS SEQRES 7 A 255 LEU LEU SER ASP THR ARG LEU ARG ARG GLU LEU PHE ALA SEQRES 8 A 255 GLU VAL ASP LYS GLY SER VAL ALA GLU TRP ALA VAL LYS SEQRES 9 A 255 THR VAL ILE GLU LYS PHE ALA GLU GLN PHE ALA ALA LEU SEQRES 10 A 255 SER ASP ASN TYR LEU LYS GLU ARG ALA GLY ASP LEU ARG SEQRES 11 A 255 ALA LEU GLY GLN ARG LEU LEU PHE HIS LEU ASP ASP ALA SEQRES 12 A 255 ASN GLN GLY PRO ASN ALA TRP PRO GLU ARG PHE ILE LEU SEQRES 13 A 255 VAL ALA ASP GLU LEU SER ALA THR THR LEU ALA GLU LEU SEQRES 14 A 255 PRO GLN ASP ARG LEU VAL GLY VAL VAL VAL ARG ASP GLY SEQRES 15 A 255 ALA ALA ASN SER GLN ALA ALA ILE MET VAL ARG ALA LEU SEQRES 16 A 255 GLY ILE PRO THR VAL MET GLY ALA ASP ILE GLN PRO SER SEQRES 17 A 255 VAL LEU HIS ARG ARG THR LEU ILE VAL ASP GLY TYR ARG SEQRES 18 A 255 GLY GLU LEU LEU VAL ASP PRO GLU PRO VAL LEU LEU GLN SEQRES 19 A 255 GLU TYR GLN ARG LEU ILE SER GLU GLU ILE GLU LEU SER SEQRES 20 A 255 ARG LEU ALA GLU ASP ASP VAL ASN HET IOD A 501 1 HET IOD A 502 1 HET IOD A 503 1 HET IOD A 504 1 HET IOD A 505 1 HETNAM IOD IODIDE ION FORMUL 2 IOD 5(I 1-) FORMUL 7 HOH *41(H2 O) HELIX 1 AA1 ASP A 204 ALA A 231 1 28 HELIX 2 AA2 LYS A 236 SER A 250 1 15 HELIX 3 AA3 ASP A 251 LYS A 264 1 14 HELIX 4 AA4 VAL A 267 ALA A 285 1 19 HELIX 5 AA5 ASP A 288 GLU A 293 1 6 HELIX 6 AA6 ARG A 294 ASP A 310 1 17 HELIX 7 AA7 SER A 331 ALA A 336 1 6 HELIX 8 AA8 SER A 355 GLY A 365 1 11 HELIX 9 AA9 GLN A 375 HIS A 380 1 6 HELIX 10 AB1 ASP A 396 GLU A 411 1 16 SHEET 1 AA1 8 ILE A 171 ARG A 172 0 SHEET 2 AA1 8 GLU A 392 VAL A 395 -1 O LEU A 393 N ILE A 171 SHEET 3 AA1 8 THR A 383 ASP A 387 -1 N ASP A 387 O GLU A 392 SHEET 4 AA1 8 VAL A 180 GLN A 187 -1 N ALA A 183 O LEU A 384 SHEET 5 AA1 8 PHE A 323 ALA A 327 1 O ILE A 324 N GLU A 184 SHEET 6 AA1 8 LEU A 343 VAL A 348 1 O VAL A 347 N LEU A 325 SHEET 7 AA1 8 THR A 368 MET A 370 1 O VAL A 369 N VAL A 348 SHEET 8 AA1 8 LEU A 174 ALA A 177 -1 N LEU A 174 O MET A 370 SITE 1 AC1 2 GLN A 187 ASP A 328 SITE 1 AC2 1 GLN A 375 SITE 1 AC3 2 THR A 252 ARG A 256 SITE 1 AC4 2 GLN A 199 ASN A 354 CRYST1 64.770 64.770 123.692 90.00 90.00 120.00 P 65 6 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 0.015439 0.008914 0.000000 0.00000 SCALE2 0.000000 0.017828 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008085 0.00000