10 20 30 40 50 60 70 80 1IHR - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER PROTEIN TRANSPORT 20-APR-01 1IHR
TITLE CRYSTAL STRUCTURE OF THE DIMERIC C-TERMINAL DOMAIN OF TONB
COMPND MOL_ID: 1; COMPND 2 MOLECULE: TONB PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN RESIDUES 164-239; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: JM83; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: XLI-BLUE; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PAT37
KEYWDS NOVEL FOLD, INTERTWINED DIMER, PROTEIN TRANSPORT
EXPDTA X-RAY DIFFRACTION
AUTHOR C.CHANG,A.MOOSER,A.PLUCKTHUN,A.WLODAWER
REVDAT 2 24-FEB-09 1IHR 1 VERSN REVDAT 1 01-AUG-01 1IHR 0
JRNL AUTH C.CHANG,A.MOOSER,A.PLUCKTHUN,A.WLODAWER JRNL TITL CRYSTAL STRUCTURE OF THE DIMERIC C-TERMINAL DOMAIN JRNL TITL 2 OF TONB REVEALS A NOVEL FOLD. JRNL REF J.BIOL.CHEM. V. 276 27535 2001 JRNL REFN ISSN 0021-9258 JRNL PMID 11328822 JRNL DOI 10.1074/JBC.M102778200
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.3 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.166 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.160 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1076 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 20365 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.163 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.158 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1023 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 19525 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1174 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 219 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1384.50 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 4 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 12576 REMARK 3 NUMBER OF RESTRAINTS : 14847 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 ANGLE DISTANCES (A) : 0.028 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.024 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.041 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.054 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.011 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.003 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.067 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.079 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1IHR COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-APR-01. REMARK 100 THE RCSB ID CODE IS RCSB013279.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-NOV-00 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 : NSLS REMARK 200 BEAMLINE : X9B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9800, 0.9163, 0.9196, 0.9199 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL REMARK 200 OPTICS : FOCUSSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21518 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.02700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 40.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.11000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, TRIS, CACL2, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 31.88500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.16500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.88500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.16500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 336 LIES ON A SPECIAL POSITION.
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 PRO A 164 REMARK 465 ILE A 238 REMARK 465 GLN A 239 REMARK 465 PRO B 164 REMARK 465 GLN B 239
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 170 CA - CB - CG ANGL. DEV. = 15.8 DEGREES REMARK 500 ARG A 187 CD - NE - CZ ANGL. DEV. = 8.8 DEGREES REMARK 500 ARG A 187 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 211 CD - NE - CZ ANGL. DEV. = 14.5 DEGREES REMARK 500 ARG A 212 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 ARG A 214 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 187 NH1 - CZ - NH2 ANGL. DEV. = -9.7 DEGREES REMARK 500 ARG B 187 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 187 NE - CZ - NH1 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG B 187 NE - CZ - NH2 ANGL. DEV. = 15.5 DEGREES REMARK 500 ARG B 211 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 199 166.53 -34.72 REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 384 DISTANCE = 6.31 ANGSTROMS
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR A 301 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR A 302 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR B 303 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR B 304
DBREF 1IHR A 164 239 UNP P02929 TONB_ECOLI 164 239 DBREF 1IHR B 164 239 UNP P02929 TONB_ECOLI 164 239
SEQRES 1 A 76 PRO ALA ARG ALA GLN ALA LEU ARG ILE GLU GLY GLN VAL SEQRES 2 A 76 LYS VAL LYS PHE ASP VAL THR PRO ASP GLY ARG VAL ASP SEQRES 3 A 76 ASN VAL GLN ILE LEU SER ALA LYS PRO ALA ASN MET PHE SEQRES 4 A 76 GLU ARG GLU VAL LYS ASN ALA MET ARG ARG TRP ARG TYR SEQRES 5 A 76 GLU PRO GLY LYS PRO GLY SER GLY ILE VAL VAL ASN ILE SEQRES 6 A 76 LEU PHE LYS ILE ASN GLY THR THR GLU ILE GLN SEQRES 1 B 76 PRO ALA ARG ALA GLN ALA LEU ARG ILE GLU GLY GLN VAL SEQRES 2 B 76 LYS VAL LYS PHE ASP VAL THR PRO ASP GLY ARG VAL ASP SEQRES 3 B 76 ASN VAL GLN ILE LEU SER ALA LYS PRO ALA ASN MET PHE SEQRES 4 B 76 GLU ARG GLU VAL LYS ASN ALA MET ARG ARG TRP ARG TYR SEQRES 5 B 76 GLU PRO GLY LYS PRO GLY SER GLY ILE VAL VAL ASN ILE SEQRES 6 B 76 LEU PHE LYS ILE ASN GLY THR THR GLU ILE GLN
HET BR A 301 1 HET BR A 302 1 HET BR B 303 1 HET BR B 304 1
HETNAM BR BROMIDE ION
FORMUL 3 BR 4(BR 1-) FORMUL 7 HOH *219(H2 O)
HELIX 1 1 ASN A 200 MET A 210 1 11 HELIX 2 2 ARG A 211 TRP A 213 5 3 HELIX 3 3 ASN B 200 ARG B 211 1 12
SHEET 1 A 6 VAL A 188 LEU A 194 0 SHEET 2 A 6 ALA A 169 VAL A 182 -1 O LYS A 177 N LEU A 194 SHEET 3 A 6 GLY B 221 THR B 236 -1 O GLY B 221 N VAL A 182 SHEET 4 A 6 GLY A 221 THR A 236 -1 N LEU A 229 O THR B 235 SHEET 5 A 6 ALA B 169 VAL B 182 -1 O LEU B 170 N GLY A 234 SHEET 6 A 6 VAL B 188 LEU B 194 -1 O ASP B 189 N ASP B 181
SITE 1 AC1 3 ARG A 166 GLU A 216 HOH A 365 SITE 1 AC2 2 ARG A 212 HOH A 334 SITE 1 AC3 3 GLY A 174 GLN A 175 HOH B 356 SITE 1 AC4 3 ARG B 166 TYR B 215 GLU B 216
CRYST1 63.770 86.330 26.550 90.00 90.00 90.00 P 21 21 2 8
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 0.015681 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011583 0.000000 0.00000
SCALE3 0.000000 0.000000 0.037665 0.00000