10 20 30 40 50 60 70 80 1L6P - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER ELECTRON TRANSPORT 12-MAR-02 1L6P
TITLE N-TERMINAL OF DSBD (RESIDUES 20-144) FROM E. COLI.
COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOL:DISULFIDE INTERCHANGE PROTEIN DSBD; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 20-143; COMPND 5 SYNONYM: C-TYPE CYTOCHROME BIOGENESIS PROTEIN CYCZ, INNER COMPND 6 MEMBRANE COPPER TOLERANCE PROTEIN; COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI K12; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: K12; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: DH5ALPHA CELLS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGEX-2T
KEYWDS DISULFIDE BOND ISOMERASE PROTEIN, IMMUNOGLOBULIN-LIKE FOLD, KEYWDS 2 ELECTRON TRANSPORT
EXPDTA X-RAY DIFFRACTION
AUTHOR C.W.GOULDING,M.R.SAWAYA,A.PARSEGHIAN
REVDAT 3 24-FEB-09 1L6P 1 VERSN REVDAT 2 01-APR-03 1L6P 1 JRNL REVDAT 1 12-JUN-02 1L6P 0
JRNL AUTH C.W.GOULDING,M.R.SAWAYA,A.PARSEGHIAN,V.LIM, JRNL AUTH 2 D.EISENBERG,D.MISSIAKAS JRNL TITL THIOL-DISULFIDE EXCHANGE IN AN IMMUNOGLOBULIN-LIKE JRNL TITL 2 FOLD: STRUCTURE OF THE N-TERMINAL DOMAIN OF DSBD. JRNL REF BIOCHEMISTRY V. 41 6920 2002 JRNL REFN ISSN 0006-2960 JRNL PMID 12033924 JRNL DOI 10.1021/BI016038L
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.65 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.5 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) : 0.141 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.139 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 925 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 17500 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.131 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.129 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 783 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 14579 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 958 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 245 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1202.50 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 10826 REMARK 3 NUMBER OF RESTRAINTS : 12742 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 ANGLE DISTANCES (A) : 0.027 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.025 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.038 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.060 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.010 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.003 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.065 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.084 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL 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 1L6P COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAR-02. REMARK 100 THE RCSB ID CODE IS RCSB015693.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-01 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-D REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18609 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 26.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 28.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.38200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.110 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM ACTETATE, AMMONIUM REMARK 280 SULFATE, PH 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 300K
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 51.02600 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 51.02600 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 26.60300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.81500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 26.60300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.81500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 51.02600 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 26.60300 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 27.81500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 51.02600 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 26.60300 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 27.81500 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 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 218 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 GLY A 1 REMARK 465 LEU A 2 REMARK 465 PHE A 3 REMARK 465 ASN A 125
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 ARG A 8 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 73 CG CD CE NZ
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 ASP A 21 CB - CG - OD1 ANGL. DEV. = 8.0 DEGREES REMARK 500 ARG A 43 NE - CZ - NH1 ANGL. DEV. = -3.9 DEGREES REMARK 500 ASP A 68 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 80 NE - CZ - NH2 ANGL. DEV. = -4.1 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 A 5 157.68 -45.49 REMARK 500 GLN A 26 -115.35 54.50 REMARK 500 ASP A 79 -63.34 72.39 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 A 268 DISTANCE = 5.54 ANGSTROMS REMARK 525 HOH A 274 DISTANCE = 6.59 ANGSTROMS REMARK 525 HOH A 319 DISTANCE = 5.49 ANGSTROMS REMARK 525 HOH A 333 DISTANCE = 5.53 ANGSTROMS REMARK 525 HOH A 339 DISTANCE = 7.45 ANGSTROMS REMARK 525 HOH A 354 DISTANCE = 6.27 ANGSTROMS REMARK 525 HOH A 357 DISTANCE = 5.05 ANGSTROMS
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JPE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DSBD-ALPHA; THE N-TERMINAL DOMAIN OF REMARK 900 DSBD
DBREF 1L6P A 1 125 UNP P36655 DSBD_ECOLI 20 144
SEQRES 1 A 125 GLY LEU PHE ASP ALA PRO GLY ARG SER GLN PHE VAL PRO SEQRES 2 A 125 ALA ASP GLN ALA PHE ALA PHE ASP PHE GLN GLN ASN GLN SEQRES 3 A 125 HIS ASP LEU ASN LEU THR TRP GLN ILE LYS ASP GLY TYR SEQRES 4 A 125 TYR LEU TYR ARG LYS GLN ILE ARG ILE THR PRO GLU HIS SEQRES 5 A 125 ALA LYS ILE ALA ASP VAL GLN LEU PRO GLN GLY VAL TRP SEQRES 6 A 125 HIS GLU ASP GLU PHE TYR GLY LYS SER GLU ILE TYR ARG SEQRES 7 A 125 ASP ARG LEU THR LEU PRO VAL THR ILE ASN GLN ALA SER SEQRES 8 A 125 ALA GLY ALA THR LEU THR VAL THR TYR GLN GLY CYS ALA SEQRES 9 A 125 ASP ALA GLY PHE CYS TYR PRO PRO GLU THR LYS THR VAL SEQRES 10 A 125 PRO LEU SER GLU VAL VAL ALA ASN
FORMUL 2 HOH *245(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 -1 N LEU A 29 O VAL A 85 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 -1 O VAL A 117 N LEU A 96 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 53.206 55.630 102.052 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 0.018795 0.000000 0.000000 0.00000
SCALE2 0.000000 0.017976 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009799 0.00000