HEADER TRANSFERASE 14-JAN-10 3LE3 TITLE CRYSTAL STRUCTURE OF APOHPR MONOMER FROM THERMOANAEROBACTER TITLE 2 TENGCONGENSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOTRANSFERASE SYSTEM, HPR-RELATED PROTEINS; COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOANAEROBACTER TENGCONGENSIS; SOURCE 3 ORGANISM_TAXID: 273068; SOURCE 4 STRAIN: MB4T; SOURCE 5 GENE: FRUB, TTE1820; 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: PET21B KEYWDS HPR PTS PHOSPHOTRANSFERASE, KINASE, PHOSPHOTRANSFERASE SYSTEM, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR T.M.FU,X.D.SU REVDAT 2 20-MAR-24 3LE3 1 REMARK REVDAT 1 15-DEC-10 3LE3 0 JRNL AUTH T.M.FU,X.D.SU JRNL TITL DIMERIZATION OF HPR BY REVERSIBLE DOMAIN SWAPPING JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 21995 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1116 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 30.2795 - 3.7193 1.00 2917 134 0.1706 0.1938 REMARK 3 2 3.7193 - 2.9529 1.00 2750 167 0.1957 0.2408 REMARK 3 3 2.9529 - 2.5799 1.00 2733 147 0.2120 0.2773 REMARK 3 4 2.5799 - 2.3441 0.97 2604 156 0.2048 0.2386 REMARK 3 5 2.3441 - 2.1761 0.92 2503 136 0.1889 0.2313 REMARK 3 6 2.1761 - 2.0479 0.91 2452 125 0.1761 0.2284 REMARK 3 7 2.0479 - 1.9453 0.91 2485 116 0.1802 0.2251 REMARK 3 8 1.9453 - 1.8607 0.91 2435 135 0.2032 0.2544 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.33 REMARK 3 B_SOL : 59.56 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.98 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.92 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.25800 REMARK 3 B22 (A**2) : -3.84900 REMARK 3 B33 (A**2) : 3.59100 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 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 : 0.007 2004 REMARK 3 ANGLE : 0.919 2691 REMARK 3 CHIRALITY : 0.062 320 REMARK 3 PLANARITY : 0.004 340 REMARK 3 DIHEDRAL : 13.899 752 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 3LE3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-FEB-10. REMARK 100 THE DEPOSITION ID IS D_1000057163. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-NOV-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 : BSRF REMARK 200 BEAMLINE : 3W1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9797 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22049 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03400 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 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: 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 (%): 46.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M MGCL2, 0.1M HEPES PH7.5, 30% PEG REMARK 280 MME 550, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 24.64800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.36300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.29950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.36300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.64800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.29950 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 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 350 REMARK 350 BIOMOLECULE: 3 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: 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 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 GLU C 88 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 LYS A 11 CD CE NZ REMARK 470 GLN A 32 CD OE1 NE2 REMARK 470 ASN A 39 CG OD1 ND2 REMARK 470 LYS A 40 CE NZ REMARK 470 GLU A 71 CG CD OE1 OE2 REMARK 470 LYS B 28 CE NZ REMARK 470 ASN B 39 CG OD1 ND2 REMARK 470 LYS B 40 CE NZ REMARK 470 LYS C 28 CE NZ REMARK 470 ASP C 38 CG OD1 OD2 REMARK 470 ASN C 39 CG OD1 ND2 REMARK 470 LYS C 40 CD CE NZ 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 ALA A 16 -139.95 57.17 REMARK 500 ALA B 16 -142.00 59.21 REMARK 500 ALA C 16 -137.28 52.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3LE1 RELATED DB: PDB REMARK 900 RELATED ID: 3LE5 RELATED DB: PDB REMARK 900 RELATED ID: 3LFG RELATED DB: PDB DBREF 3LE3 A 1 88 UNP Q8R910 Q8R910_THETN 1 88 DBREF 3LE3 B 1 88 UNP Q8R910 Q8R910_THETN 1 88 DBREF 3LE3 C 1 88 UNP Q8R910 Q8R910_THETN 1 88 SEQRES 1 A 88 MET LYS GLU VAL THR ILE GLU ILE LYS ASN LYS THR GLY SEQRES 2 A 88 LEU HIS ALA ARG PRO ALA ALA LEU PHE VAL GLN THR ALA SEQRES 3 A 88 SER LYS PHE SER SER GLN ILE TRP VAL GLU LYS ASP ASN SEQRES 4 A 88 LYS LYS VAL ASN ALA LYS SER ILE MET GLY ILE MET SER SEQRES 5 A 88 LEU GLY VAL SER GLN GLY ASN VAL VAL LYS LEU SER ALA SEQRES 6 A 88 GLU GLY ASP ASP GLU GLU GLU ALA ILE LYS ALA LEU VAL SEQRES 7 A 88 ASP LEU ILE GLU SER LYS PHE GLY GLU GLU SEQRES 1 B 88 MET LYS GLU VAL THR ILE GLU ILE LYS ASN LYS THR GLY SEQRES 2 B 88 LEU HIS ALA ARG PRO ALA ALA LEU PHE VAL GLN THR ALA SEQRES 3 B 88 SER LYS PHE SER SER GLN ILE TRP VAL GLU LYS ASP ASN SEQRES 4 B 88 LYS LYS VAL ASN ALA LYS SER ILE MET GLY ILE MET SER SEQRES 5 B 88 LEU GLY VAL SER GLN GLY ASN VAL VAL LYS LEU SER ALA SEQRES 6 B 88 GLU GLY ASP ASP GLU GLU GLU ALA ILE LYS ALA LEU VAL SEQRES 7 B 88 ASP LEU ILE GLU SER LYS PHE GLY GLU GLU SEQRES 1 C 88 MET LYS GLU VAL THR ILE GLU ILE LYS ASN LYS THR GLY SEQRES 2 C 88 LEU HIS ALA ARG PRO ALA ALA LEU PHE VAL GLN THR ALA SEQRES 3 C 88 SER LYS PHE SER SER GLN ILE TRP VAL GLU LYS ASP ASN SEQRES 4 C 88 LYS LYS VAL ASN ALA LYS SER ILE MET GLY ILE MET SER SEQRES 5 C 88 LEU GLY VAL SER GLN GLY ASN VAL VAL LYS LEU SER ALA SEQRES 6 C 88 GLU GLY ASP ASP GLU GLU GLU ALA ILE LYS ALA LEU VAL SEQRES 7 C 88 ASP LEU ILE GLU SER LYS PHE GLY GLU GLU FORMUL 4 HOH *275(H2 O) HELIX 1 1 HIS A 15 SER A 27 1 13 HELIX 2 2 SER A 46 GLY A 54 1 9 HELIX 3 3 ASP A 69 SER A 83 1 15 HELIX 4 4 HIS B 15 SER B 27 1 13 HELIX 5 5 SER B 46 GLY B 54 1 9 HELIX 6 6 ASP B 69 SER B 83 1 15 HELIX 7 7 HIS C 15 SER C 27 1 13 HELIX 8 8 SER C 46 GLY C 54 1 9 HELIX 9 9 ASP C 69 SER C 83 1 15 HELIX 10 10 LYS C 84 GLU C 87 5 4 SHEET 1 A 4 LYS A 2 GLU A 7 0 SHEET 2 A 4 VAL A 60 GLU A 66 -1 O LEU A 63 N VAL A 4 SHEET 3 A 4 GLN A 32 LYS A 37 -1 N TRP A 34 O SER A 64 SHEET 4 A 4 LYS A 40 ASN A 43 -1 O LYS A 40 N LYS A 37 SHEET 1 B 4 LYS B 2 GLU B 7 0 SHEET 2 B 4 VAL B 60 GLU B 66 -1 O LEU B 63 N VAL B 4 SHEET 3 B 4 GLN B 32 LYS B 37 -1 N TRP B 34 O SER B 64 SHEET 4 B 4 LYS B 40 ASN B 43 -1 O VAL B 42 N VAL B 35 SHEET 1 C 4 LYS C 2 GLU C 7 0 SHEET 2 C 4 VAL C 60 GLU C 66 -1 O LEU C 63 N VAL C 4 SHEET 3 C 4 GLN C 32 LYS C 37 -1 N TRP C 34 O SER C 64 SHEET 4 C 4 LYS C 40 ASN C 43 -1 O LYS C 40 N LYS C 37 CRYST1 49.296 70.599 76.726 90.00 90.00 90.00 P 21 21 21 12 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 0.020286 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014165 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013033 0.00000