PDB Short entry for 1JPE HEADER ELECTRON TRANSPORT 02-AUG-01 1JPE TITLE CRYSTAL STRUCTURE OF DSBD-ALPHA; THE N-TERMINAL DOMAIN OF TITLE 2 DSBD COMPND MOL_ID: 1; COMPND 2 MOLECULE: DSBD-ALPHA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DSBD-ALPHA; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_CELL_LINE: DH5ALPHA (Z1) CELLS; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PFK115 KEYWDS REDOX-ACTIVE CENTER, ELECTRON TRANSPORT, INNER MEMBRANE, KEYWDS 2 DISULFIDE BOND FORMATION EXPDTA X-RAY DIFFRACTION AUTHOR P.W.HAEBEL,D.GOLDSTONE,P.METCALF REVDAT 2 24-FEB-09 1JPE 1 VERSN REVDAT 1 25-SEP-02 1JPE 0 JRNL AUTH P.W.HAEBEL,D.GOLDSTONE,F.KATZEN,J.BECKWITH, JRNL AUTH 2 P.METCALF JRNL TITL THE DISULFIDE BOND ISOMERASE DSBC IS ACTIVATED BY JRNL TITL 2 AN IMMUNOGLOBULIN-FOLD THIOL OXIDOREDUCTASE: JRNL TITL 3 CRYSTAL STRUCTURE OF THE DSBC-DSBD ALPHA COMPLEX. JRNL REF EMBO J. V. 21 4774 2002 JRNL REFN ISSN 0261-4189 JRNL PMID 12234918 JRNL DOI 10.1093/EMBOJ/CDF489 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 457274.180 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 11540 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) : 0.216 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1192 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1503 REMARK 3 BIN R VALUE (WORKING SET) : 0.2440 REMARK 3 BIN FREE R VALUE : 0.2430 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 166 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.019 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 87 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.81000 REMARK 3 B22 (A**2) : 13.10000 REMARK 3 B33 (A**2) : -6.29000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.16 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) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.15 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.79 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 41.87 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: NULL REMARK 4 REMARK 4 1JPE COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-AUG-01. REMARK 100 THE RCSB ID CODE IS RCSB014031. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-FEB-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL 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 : 11606 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.890 REMARK 200 RESOLUTION RANGE LOW (A) : 30.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 5.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 1.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 51.23900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.23900 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 26.54100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.30150 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 26.54100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.30150 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 51.23900 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 26.54100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 27.30150 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 51.23900 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 26.54100 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 27.30150 REMARK 290 SMTRY3 8 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: 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 MET A -18 REMARK 465 ARG A -17 REMARK 465 GLY A -16 REMARK 465 SER A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 GLY A -8 REMARK 465 SER A -7 REMARK 465 GLU A -6 REMARK 465 ASN A -5 REMARK 465 LEU A -4 REMARK 465 TYR A -3 REMARK 465 PHE A -2 REMARK 465 GLN A -1 REMARK 465 SER A 0 REMARK 465 GLY A 1 REMARK 465 LEU A 2 REMARK 465 PHE A 3 REMARK 465 ASP A 4 REMARK 465 ALA A 5 REMARK 465 PRO A 6 REMARK 465 GLY A 7 REMARK 465 ARG A 8 REMARK 465 SER A 9 REMARK 465 ASN A 126 REMARK 465 ALA A 127 REMARK 465 ALA A 128 REMARK 465 PRO A 129 REMARK 465 GLN A 130 REMARK 465 PRO A 131 REMARK 465 VAL A 132 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 26 -119.62 60.72 REMARK 500 ASP A 79 -58.88 68.77 REMARK 500 ALA A 124 171.72 -48.58 REMARK 500 REMARK 500 REMARK: NULL DBREF 1JPE A 0 132 UNP P36655 DSBD_ECOLI 19 151 SEQADV 1JPE MET A -18 UNP P36655 EXPRESSION TAG SEQADV 1JPE ARG A -17 UNP P36655 EXPRESSION TAG SEQADV 1JPE GLY A -16 UNP P36655 EXPRESSION TAG SEQADV 1JPE SER A -15 UNP P36655 EXPRESSION TAG SEQADV 1JPE HIS A -14 UNP P36655 EXPRESSION TAG SEQADV 1JPE HIS A -13 UNP P36655 EXPRESSION TAG SEQADV 1JPE HIS A -12 UNP P36655 EXPRESSION TAG SEQADV 1JPE HIS A -11 UNP P36655 EXPRESSION TAG SEQADV 1JPE HIS A -10 UNP P36655 EXPRESSION TAG SEQADV 1JPE HIS A -9 UNP P36655 EXPRESSION TAG SEQADV 1JPE GLY A -8 UNP P36655 EXPRESSION TAG SEQADV 1JPE SER A -7 UNP P36655 EXPRESSION TAG SEQADV 1JPE GLU A -6 UNP P36655 EXPRESSION TAG SEQADV 1JPE ASN A -5 UNP P36655 EXPRESSION TAG SEQADV 1JPE LEU A -4 UNP P36655 EXPRESSION TAG SEQADV 1JPE TYR A -3 UNP P36655 EXPRESSION TAG SEQADV 1JPE PHE A -2 UNP P36655 EXPRESSION TAG SEQADV 1JPE GLN A -1 UNP P36655 EXPRESSION TAG SEQADV 1JPE SER A 0 UNP P36655 ALA 19 CONFLICT SEQRES 1 A 151 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER GLU SEQRES 2 A 151 ASN LEU TYR PHE GLN SER GLY LEU PHE ASP ALA PRO GLY SEQRES 3 A 151 ARG SER GLN PHE VAL PRO ALA ASP GLN ALA PHE ALA PHE SEQRES 4 A 151 ASP PHE GLN GLN ASN GLN HIS ASP LEU ASN LEU THR TRP SEQRES 5 A 151 GLN ILE LYS ASP GLY TYR TYR LEU TYR ARG LYS GLN ILE SEQRES 6 A 151 ARG ILE THR PRO GLU HIS ALA LYS ILE ALA ASP VAL GLN SEQRES 7 A 151 LEU PRO GLN GLY VAL TRP HIS GLU ASP GLU PHE TYR GLY SEQRES 8 A 151 LYS SER GLU ILE TYR ARG ASP ARG LEU THR LEU PRO VAL SEQRES 9 A 151 THR ILE ASN GLN ALA SER ALA GLY ALA THR LEU THR VAL SEQRES 10 A 151 THR TYR GLN GLY CYS ALA ASP ALA GLY PHE CYS TYR PRO SEQRES 11 A 151 PRO GLU THR LYS THR VAL PRO LEU SER GLU VAL VAL ALA SEQRES 12 A 151 ASN ASN ALA ALA PRO GLN PRO VAL FORMUL 2 HOH *87(H2 O) HELIX 1 1 PRO A 13 ALA A 17 1 5 HELIX 2 2 LYS A 44 ILE A 46 5 3 SHEET 1 A 4 ARG A 47 ILE A 55 0 SHEET 2 A 4 ARG A 80 TYR A 100 -1 O THR A 97 N THR A 49 SHEET 3 A 4 ASP A 28 ILE A 35 0 SHEET 4 A 4 PHE A 18 ASN A 25 -1 N ASN A 25 O ASP A 28 SHEET 1 B 3 ARG A 47 ILE A 55 0 SHEET 2 B 3 ARG A 80 TYR A 100 -1 O THR A 97 N THR A 49 SHEET 3 B 3 GLU A 113 PRO A 118 0 SHEET 1 C 5 VAL A 64 ASP A 68 0 SHEET 2 C 5 GLY A 72 TYR A 77 -1 O ILE A 76 N VAL A 64 SHEET 3 C 5 TYR A 39 TYR A 42 -1 N LEU A 41 O TYR A 77 SHEET 4 C 5 GLY A 102 ALA A 104 -1 O CYS A 103 N TYR A 40 SHEET 5 C 5 PHE A 108 CYS A 109 -1 O PHE A 108 N ALA A 104 SSBOND 1 CYS A 103 CYS A 109 1555 1555 2.04 CRYST1 53.082 54.603 102.478 90.00 90.00 90.00 C 2 2 21 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 0.018839 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018314 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009758 0.00000