PDB Short entry for 1IIB HEADER PHOSPHOTRANSFERASE 23-DEC-96 1IIB TITLE CRYSTAL STRUCTURE OF IIBCELLOBIOSE FROM ESCHERICHIA COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENZYME IIB OF THE CELLOBIOSE-SPECIFIC PHOSPHOTRANSFERASE COMPND 3 SYSTEM; COMPND 4 CHAIN: A, B; COMPND 5 FRAGMENT: ENZYME IIB; COMPND 6 EC: 2.7.1.69; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 CELLULAR_LOCATION: CYTOPLASM; SOURCE 6 GENE: CELA; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI STR. K12 SUBSTR. W3110; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 316407; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: W3110 KEYWDS PHOSPHOENOLPYRUVATE DEPENDENT PHOSPHOTRANSFERASE SYSTEM, IIB ENZYMES, KEYWDS 2 CYSTEINE PHOSPHORYLATION, PHOSPHOTRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.L.M.VAN MONTFORT,T.PIJNING,K.H.KALK,J.REIZER,M.H.SAIER, AUTHOR 2 M.M.G.M.THUNNISSEN,G.T.ROBILLARD,B.W.DIJKSTRA REVDAT 5 03-NOV-21 1IIB 1 REMARK SEQADV REVDAT 4 13-JUL-11 1IIB 1 VERSN REVDAT 3 24-FEB-09 1IIB 1 VERSN REVDAT 2 01-APR-03 1IIB 1 JRNL REVDAT 1 24-DEC-97 1IIB 0 JRNL AUTH R.L.VAN MONTFORT,T.PIJNING,K.H.KALK,J.REIZER,M.H.SAIER JR., JRNL AUTH 2 M.M.THUNNISSEN,G.T.ROBILLARD,B.W.DIJKSTRA JRNL TITL THE STRUCTURE OF AN ENERGY-COUPLING PROTEIN FROM BACTERIA, JRNL TITL 2 IIBCELLOBIOSE, REVEALS SIMILARITY TO EUKARYOTIC PROTEIN JRNL TITL 3 TYROSINE PHOSPHATASES. JRNL REF STRUCTURE V. 5 217 1997 JRNL REFN ISSN 0969-2126 JRNL PMID 9032081 JRNL DOI 10.1016/S0969-2126(97)00180-9 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 87.3 REMARK 3 NUMBER OF REFLECTIONS : 16419 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) : 0.187 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1550 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 128 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.90 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : 0.22 REMARK 3 LOW RESOLUTION CUTOFF (A) : 10.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.680 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.370 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.500 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.000 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 2.000 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.500 ; NULL 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 : PARHCSDX_1996.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NCS-RESTRAINTS RELEASED AT 1.8 ANGSTROM REMARK 3 RESOLUTION REMARK 4 REMARK 4 1IIB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000174166. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : MAY-95 REMARK 200 TEMPERATURE (KELVIN) : 293 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 : X31 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : BIOMOL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16165 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 82.8 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.12200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE NATIVE DATASET USED WAS OBTAINED BY MERGING OF A 2.6 REMARK 200 ANGSTROM IN HOUSE DATA SET WITH A 1.8 ANGSTROM X31 DATASET. THE REMARK 200 STATISTICS OF THE X-31 DATASET ARE GIVEN ABOVE. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 15.89100 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 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 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 GLU A 2 REMARK 465 ASN A 106 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 ASN B 106 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 B 104 -6.35 -56.69 REMARK 500 REMARK 500 REMARK: NULL DBREF 1IIB A 1 106 UNP P69795 PTQB_ECOLI 1 106 DBREF 1IIB B 1 106 UNP P69795 PTQB_ECOLI 1 106 SEQADV 1IIB SER A 10 UNP P69795 CYS 10 ENGINEERED MUTATION SEQADV 1IIB SER B 10 UNP P69795 CYS 10 ENGINEERED MUTATION SEQRES 1 A 106 MET GLU LYS LYS HIS ILE TYR LEU PHE SER SER ALA GLY SEQRES 2 A 106 MET SER THR SER LEU LEU VAL SER LYS MET ARG ALA GLN SEQRES 3 A 106 ALA GLU LYS TYR GLU VAL PRO VAL ILE ILE GLU ALA PHE SEQRES 4 A 106 PRO GLU THR LEU ALA GLY GLU LYS GLY GLN ASN ALA ASP SEQRES 5 A 106 VAL VAL LEU LEU GLY PRO GLN ILE ALA TYR MET LEU PRO SEQRES 6 A 106 GLU ILE GLN ARG LEU LEU PRO ASN LYS PRO VAL GLU VAL SEQRES 7 A 106 ILE ASP SER LEU LEU TYR GLY LYS VAL ASP GLY LEU GLY SEQRES 8 A 106 VAL LEU LYS ALA ALA VAL ALA ALA ILE LYS LYS ALA ALA SEQRES 9 A 106 ALA ASN SEQRES 1 B 106 MET GLU LYS LYS HIS ILE TYR LEU PHE SER SER ALA GLY SEQRES 2 B 106 MET SER THR SER LEU LEU VAL SER LYS MET ARG ALA GLN SEQRES 3 B 106 ALA GLU LYS TYR GLU VAL PRO VAL ILE ILE GLU ALA PHE SEQRES 4 B 106 PRO GLU THR LEU ALA GLY GLU LYS GLY GLN ASN ALA ASP SEQRES 5 B 106 VAL VAL LEU LEU GLY PRO GLN ILE ALA TYR MET LEU PRO SEQRES 6 B 106 GLU ILE GLN ARG LEU LEU PRO ASN LYS PRO VAL GLU VAL SEQRES 7 B 106 ILE ASP SER LEU LEU TYR GLY LYS VAL ASP GLY LEU GLY SEQRES 8 B 106 VAL LEU LYS ALA ALA VAL ALA ALA ILE LYS LYS ALA ALA SEQRES 9 B 106 ALA ASN FORMUL 3 HOH *128(H2 O) HELIX 1 1 GLY A 13 LYS A 29 1 17 HELIX 2 2 GLU A 41 ASN A 50 5 10 HELIX 3 3 PRO A 58 LEU A 70 5 13 HELIX 4 4 SER A 81 GLY A 85 1 5 HELIX 5 5 GLY A 89 ALA A 104 1 16 HELIX 6 6 GLY B 13 LYS B 29 1 17 HELIX 7 7 GLU B 41 LEU B 43 5 3 HELIX 8 8 GLY B 48 ASN B 50 5 3 HELIX 9 9 PRO B 58 LEU B 70 5 13 HELIX 10 10 SER B 81 GLY B 85 1 5 HELIX 11 11 GLY B 89 ALA B 103 1 15 SHEET 1 A 4 VAL A 34 PRO A 40 0 SHEET 2 A 4 LYS A 4 SER A 10 1 N LYS A 4 O ILE A 35 SHEET 3 A 4 VAL A 53 LEU A 56 1 N VAL A 53 O TYR A 7 SHEET 4 A 4 PRO A 75 VAL A 78 1 N PRO A 75 O VAL A 54 SHEET 1 B 4 VAL B 34 PRO B 40 0 SHEET 2 B 4 LYS B 4 SER B 10 1 N LYS B 4 O ILE B 35 SHEET 3 B 4 VAL B 53 LEU B 56 1 N VAL B 53 O TYR B 7 SHEET 4 B 4 PRO B 75 VAL B 78 1 N PRO B 75 O VAL B 54 CRYST1 53.791 31.782 60.253 90.00 101.70 90.00 P 1 21 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 0.018590 0.000000 0.003850 0.00000 SCALE2 0.000000 0.031464 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016949 0.00000 MTRIX1 1 0.995894 -0.002445 -0.090488 -30.02300 1 MTRIX2 1 -0.002788 -0.999989 -0.003668 50.23600 1 MTRIX3 1 -0.090478 0.003906 -0.995891 92.78100 1