HEADER ISOMERASE 28-SEP-05 2B5E TITLE CRYSTAL STRUCTURE OF YEAST PROTEIN DISULFIDE ISOMERASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN DISULFIDE-ISOMERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PDI, THIOREDOXIN-RELATED GLYCOPROTEIN 1; COMPND 5 EC: 5.3.4.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: PDI1, MFP1, TRG1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PTYB12 KEYWDS PROTEIN DISULFIDE ISOMERASE, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.SCHINDELIN,G.TIAN REVDAT 4 16-OCT-24 2B5E 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 2B5E 1 VERSN REVDAT 2 24-FEB-09 2B5E 1 VERSN REVDAT 1 24-JAN-06 2B5E 0 JRNL AUTH G.TIAN,S.XIANG,R.NOIVA,W.J.LENNARZ,H.SCHINDELIN JRNL TITL THE CRYSTAL STRUCTURE OF YEAST PROTEIN DISULFIDE ISOMERASE JRNL TITL 2 SUGGESTS COOPERATIVITY BETWEEN ITS ACTIVE SITES. JRNL REF CELL(CAMBRIDGE,MASS.) V. 124 61 2006 JRNL REFN ISSN 0092-8674 JRNL PMID 16413482 JRNL DOI 10.1016/J.CELL.2005.10.044 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 23557 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 + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1246 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1623 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.07 REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE SET COUNT : 89 REMARK 3 BIN FREE R VALUE : 0.3170 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3820 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 138 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 66.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.75000 REMARK 3 B22 (A**2) : -1.75000 REMARK 3 B33 (A**2) : 3.50000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.329 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.246 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.209 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 17.464 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3923 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3410 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5321 ; 1.624 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8008 ; 0.883 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 482 ; 8.219 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 198 ;37.729 ;26.111 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 656 ;18.080 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;19.371 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 579 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4405 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 751 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 872 ; 0.223 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3405 ; 0.186 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1884 ; 0.186 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2302 ; 0.091 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 151 ; 0.231 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.290 ; 0.200 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 14 ; 0.224 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 53 ; 0.234 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.264 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3079 ; 0.854 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 969 ; 0.145 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3896 ; 1.093 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1783 ; 1.758 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1425 ; 2.700 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 22 A 139 REMARK 3 ORIGIN FOR THE GROUP (A): -15.4561 -23.4264 -17.8324 REMARK 3 T TENSOR REMARK 3 T11: -0.1320 T22: -0.0167 REMARK 3 T33: -0.2907 T12: 0.1262 REMARK 3 T13: 0.2122 T23: 0.2893 REMARK 3 L TENSOR REMARK 3 L11: 8.8844 L22: 5.9632 REMARK 3 L33: 2.7540 L12: -2.0833 REMARK 3 L13: 1.0110 L23: -0.6568 REMARK 3 S TENSOR REMARK 3 S11: -0.4718 S12: -1.3245 S13: -0.8277 REMARK 3 S21: 0.8953 S22: 0.3606 S23: 0.3788 REMARK 3 S31: 0.0827 S32: 0.1385 S33: 0.1112 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 140 A 242 REMARK 3 ORIGIN FOR THE GROUP (A): 8.5068 -26.6276 -37.9761 REMARK 3 T TENSOR REMARK 3 T11: -0.4190 T22: -0.2782 REMARK 3 T33: -0.2974 T12: 0.0180 REMARK 3 T13: -0.0133 T23: 0.0291 REMARK 3 L TENSOR REMARK 3 L11: 8.9068 L22: 5.0050 REMARK 3 L33: 6.3504 L12: 2.5833 REMARK 3 L13: 1.9947 L23: 3.7088 REMARK 3 S TENSOR REMARK 3 S11: -0.0189 S12: 0.7753 S13: -0.7368 REMARK 3 S21: -0.1626 S22: 0.0198 S23: -0.4645 REMARK 3 S31: -0.0035 S32: 0.2078 S33: -0.0008 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 243 A 365 REMARK 3 ORIGIN FOR THE GROUP (A): -13.9766 -39.2351 -52.2311 REMARK 3 T TENSOR REMARK 3 T11: -0.3432 T22: -0.2007 REMARK 3 T33: -0.3170 T12: 0.0020 REMARK 3 T13: -0.0005 T23: -0.0344 REMARK 3 L TENSOR REMARK 3 L11: 16.8675 L22: 7.8991 REMARK 3 L33: 4.7174 L12: 6.5502 REMARK 3 L13: 5.7221 L23: 3.5607 REMARK 3 S TENSOR REMARK 3 S11: -0.0571 S12: 0.0053 S13: 0.0834 REMARK 3 S21: -0.1265 S22: 0.0654 S23: 0.5012 REMARK 3 S31: 0.1476 S32: -0.0960 S33: -0.0083 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 366 A 504 REMARK 3 ORIGIN FOR THE GROUP (A): -41.5684 -16.9173 -63.2922 REMARK 3 T TENSOR REMARK 3 T11: 0.0630 T22: -0.1283 REMARK 3 T33: 0.1547 T12: 0.0751 REMARK 3 T13: -0.1721 T23: -0.2744 REMARK 3 L TENSOR REMARK 3 L11: 6.4916 L22: 12.0971 REMARK 3 L33: 6.9523 L12: -0.8061 REMARK 3 L13: 2.8933 L23: 0.3148 REMARK 3 S TENSOR REMARK 3 S11: -0.1448 S12: 0.2168 S13: -0.1727 REMARK 3 S21: -0.1748 S22: 0.0102 S23: -1.0983 REMARK 3 S31: -0.9284 S32: -0.2737 S33: 0.1346 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2B5E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-OCT-05. REMARK 100 THE DEPOSITION ID IS D_1000034695. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JAN-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : 1.1 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24847 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 (%) : NULL 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CACODYLATE, MAGNESIUM CHLORIDE, REMARK 280 PEG 2000 MME, BARIUM CHLORIDE, PH 6.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,Z+1/2 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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 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 68.28000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 68.28000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 34.76200 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 68.28000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 68.28000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 34.76200 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 68.28000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 68.28000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 34.76200 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 68.28000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 68.28000 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 34.76200 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 ALA A 19 REMARK 465 GLY A 20 REMARK 465 HIS A 21 REMARK 465 ALA A 505 REMARK 465 ASP A 506 REMARK 465 ALA A 507 REMARK 465 ASP A 508 REMARK 465 ALA A 509 REMARK 465 GLU A 510 REMARK 465 LEU A 511 REMARK 465 ALA A 512 REMARK 465 ASP A 513 REMARK 465 GLU A 514 REMARK 465 GLU A 515 REMARK 465 ASP A 516 REMARK 465 ALA A 517 REMARK 465 ILE A 518 REMARK 465 HIS A 519 REMARK 465 ASP A 520 REMARK 465 GLU A 521 REMARK 465 LEU A 522 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 ND2 ASN A 373 O HOH A 644 1.67 REMARK 500 OH TYR A 467 O SER A 470 1.81 REMARK 500 O GLU A 463 N VAL A 465 2.02 REMARK 500 O HOH A 531 O HOH A 659 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 SER A 32 CB SER A 32 OG 0.097 REMARK 500 CYS A 97 CB CYS A 97 SG 0.146 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 471 NE - CZ - NH1 ANGL. DEV. = 4.2 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 196 -9.89 -56.45 REMARK 500 GLU A 212 79.39 -150.78 REMARK 500 LYS A 219 79.35 -101.51 REMARK 500 ALA A 237 60.13 -100.63 REMARK 500 PHE A 241 62.77 -150.88 REMARK 500 ARG A 300 -50.81 -29.26 REMARK 500 ASN A 306 50.18 37.94 REMARK 500 ALA A 361 132.36 157.23 REMARK 500 ASN A 373 143.90 75.12 REMARK 500 ASP A 375 73.91 -61.36 REMARK 500 TRP A 405 9.95 -69.83 REMARK 500 SER A 464 47.20 -31.99 REMARK 500 ARG A 471 36.12 -84.91 REMARK 500 GLU A 496 -71.63 -47.61 REMARK 500 ALA A 502 22.31 -70.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN A 217 GLY A 218 -144.89 REMARK 500 LYS A 395 ASP A 396 123.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BA A 1 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 123 OE2 REMARK 620 2 GLU A 194 OE1 152.6 REMARK 620 3 GLU A 194 OE2 124.6 36.7 REMARK 620 4 HOH A 555 O 143.7 63.0 89.6 REMARK 620 5 HOH A 599 O 128.0 47.8 81.4 62.4 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BA A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 523 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 524 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MEK RELATED DB: PDB REMARK 900 NMR STRUCTURE OF HUMAN PDI DOMAIN A REMARK 900 RELATED ID: 2BJX RELATED DB: PDB REMARK 900 NMR STRUCTURE OF HUMAN PDI DOMAIN B REMARK 900 RELATED ID: 2TRX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E.COLI THIOREDOXIN REMARK 900 RELATED ID: 1EEJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E.COLI PROTEIN DISULFIDE ISOMERASE DSBC REMARK 900 RELATED ID: 1V57 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E.COLI PROTEIN DISULFIDE ISOMERASE DSBG REMARK 900 RELATED ID: 1A8Y RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CALSEQUESTRIN DBREF 2B5E A 23 522 UNP P17967 PDI_YEAST 23 522 SEQADV 2B5E ALA A 19 UNP P17967 CLONING ARTIFACT SEQADV 2B5E GLY A 20 UNP P17967 CLONING ARTIFACT SEQADV 2B5E HIS A 21 UNP P17967 CLONING ARTIFACT SEQADV 2B5E MET A 22 UNP P17967 INITIATING METHIONINE SEQRES 1 A 504 ALA GLY HIS MET GLN GLN GLU ALA VAL ALA PRO GLU ASP SEQRES 2 A 504 SER ALA VAL VAL LYS LEU ALA THR ASP SER PHE ASN GLU SEQRES 3 A 504 TYR ILE GLN SER HIS ASP LEU VAL LEU ALA GLU PHE PHE SEQRES 4 A 504 ALA PRO TRP CYS GLY HIS CYS LYS ASN MET ALA PRO GLU SEQRES 5 A 504 TYR VAL LYS ALA ALA GLU THR LEU VAL GLU LYS ASN ILE SEQRES 6 A 504 THR LEU ALA GLN ILE ASP CYS THR GLU ASN GLN ASP LEU SEQRES 7 A 504 CYS MET GLU HIS ASN ILE PRO GLY PHE PRO SER LEU LYS SEQRES 8 A 504 ILE PHE LYS ASN SER ASP VAL ASN ASN SER ILE ASP TYR SEQRES 9 A 504 GLU GLY PRO ARG THR ALA GLU ALA ILE VAL GLN PHE MET SEQRES 10 A 504 ILE LYS GLN SER GLN PRO ALA VAL ALA VAL VAL ALA ASP SEQRES 11 A 504 LEU PRO ALA TYR LEU ALA ASN GLU THR PHE VAL THR PRO SEQRES 12 A 504 VAL ILE VAL GLN SER GLY LYS ILE ASP ALA ASP PHE ASN SEQRES 13 A 504 ALA THR PHE TYR SER MET ALA ASN LYS HIS PHE ASN ASP SEQRES 14 A 504 TYR ASP PHE VAL SER ALA GLU ASN ALA ASP ASP ASP PHE SEQRES 15 A 504 LYS LEU SER ILE TYR LEU PRO SER ALA MET ASP GLU PRO SEQRES 16 A 504 VAL VAL TYR ASN GLY LYS LYS ALA ASP ILE ALA ASP ALA SEQRES 17 A 504 ASP VAL PHE GLU LYS TRP LEU GLN VAL GLU ALA LEU PRO SEQRES 18 A 504 TYR PHE GLY GLU ILE ASP GLY SER VAL PHE ALA GLN TYR SEQRES 19 A 504 VAL GLU SER GLY LEU PRO LEU GLY TYR LEU PHE TYR ASN SEQRES 20 A 504 ASP GLU GLU GLU LEU GLU GLU TYR LYS PRO LEU PHE THR SEQRES 21 A 504 GLU LEU ALA LYS LYS ASN ARG GLY LEU MET ASN PHE VAL SEQRES 22 A 504 SER ILE ASP ALA ARG LYS PHE GLY ARG HIS ALA GLY ASN SEQRES 23 A 504 LEU ASN MET LYS GLU GLN PHE PRO LEU PHE ALA ILE HIS SEQRES 24 A 504 ASP MET THR GLU ASP LEU LYS TYR GLY LEU PRO GLN LEU SEQRES 25 A 504 SER GLU GLU ALA PHE ASP GLU LEU SER ASP LYS ILE VAL SEQRES 26 A 504 LEU GLU SER LYS ALA ILE GLU SER LEU VAL LYS ASP PHE SEQRES 27 A 504 LEU LYS GLY ASP ALA SER PRO ILE VAL LYS SER GLN GLU SEQRES 28 A 504 ILE PHE GLU ASN GLN ASP SER SER VAL PHE GLN LEU VAL SEQRES 29 A 504 GLY LYS ASN HIS ASP GLU ILE VAL ASN ASP PRO LYS LYS SEQRES 30 A 504 ASP VAL LEU VAL LEU TYR TYR ALA PRO TRP CYS GLY HIS SEQRES 31 A 504 CYS LYS ARG LEU ALA PRO THR TYR GLN GLU LEU ALA ASP SEQRES 32 A 504 THR TYR ALA ASN ALA THR SER ASP VAL LEU ILE ALA LYS SEQRES 33 A 504 LEU ASP HIS THR GLU ASN ASP VAL ARG GLY VAL VAL ILE SEQRES 34 A 504 GLU GLY TYR PRO THR ILE VAL LEU TYR PRO GLY GLY LYS SEQRES 35 A 504 LYS SER GLU SER VAL VAL TYR GLN GLY SER ARG SER LEU SEQRES 36 A 504 ASP SER LEU PHE ASP PHE ILE LYS GLU ASN GLY HIS PHE SEQRES 37 A 504 ASP VAL ASP GLY LYS ALA LEU TYR GLU GLU ALA GLN GLU SEQRES 38 A 504 LYS ALA ALA GLU GLU ALA ASP ALA ASP ALA GLU LEU ALA SEQRES 39 A 504 ASP GLU GLU ASP ALA ILE HIS ASP GLU LEU HET BA A 1 1 HET GOL A 523 6 HET GOL A 524 6 HETNAM BA BARIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 BA BA 2+ FORMUL 3 GOL 2(C3 H8 O3) FORMUL 5 HOH *138(H2 O) HELIX 1 1 SER A 41 GLN A 47 1 7 HELIX 2 2 CYS A 61 LEU A 78 1 18 HELIX 3 3 ASN A 93 HIS A 100 1 8 HELIX 4 4 THR A 127 SER A 139 1 13 HELIX 5 5 ASP A 148 GLU A 156 1 9 HELIX 6 6 ASP A 170 HIS A 184 1 15 HELIX 7 7 LYS A 219 ALA A 224 1 6 HELIX 8 8 ASP A 225 ALA A 237 1 13 HELIX 9 9 ASP A 245 SER A 255 1 11 HELIX 10 10 ASP A 266 ASN A 284 1 19 HELIX 11 11 ALA A 295 GLY A 299 1 5 HELIX 12 12 ARG A 300 LEU A 305 1 6 HELIX 13 13 SER A 331 GLU A 337 1 7 HELIX 14 14 GLU A 345 GLY A 359 1 15 HELIX 15 15 ASN A 385 ASP A 392 1 8 HELIX 16 16 CYS A 406 THR A 427 1 22 HELIX 17 17 THR A 438 ASN A 440 5 3 HELIX 18 18 SER A 472 GLY A 484 1 13 HELIX 19 19 ASP A 489 ALA A 502 1 14 SHEET 1 A 5 VAL A 35 LYS A 36 0 SHEET 2 A 5 THR A 84 ASP A 89 1 O GLN A 87 N VAL A 35 SHEET 3 A 5 LEU A 51 PHE A 57 1 N GLU A 55 O ILE A 88 SHEET 4 A 5 SER A 107 LYS A 112 -1 O LYS A 109 N ALA A 54 SHEET 5 A 5 SER A 119 ASP A 121 -1 O ILE A 120 N ILE A 110 SHEET 1 B 5 VAL A 143 VAL A 145 0 SHEET 2 B 5 ASP A 189 GLU A 194 1 O SER A 192 N ALA A 144 SHEET 3 B 5 VAL A 162 GLY A 167 1 N ILE A 163 O ASP A 189 SHEET 4 B 5 LYS A 201 LEU A 206 -1 O TYR A 205 N VAL A 162 SHEET 5 B 5 ALA A 209 VAL A 215 -1 O VAL A 214 N ILE A 204 SHEET 1 C 4 ASN A 289 ASP A 294 0 SHEET 2 C 4 LEU A 259 TYR A 264 1 N GLY A 260 O VAL A 291 SHEET 3 C 4 LEU A 313 ASP A 318 -1 O ALA A 315 N TYR A 261 SHEET 4 C 4 LEU A 323 GLY A 326 -1 O LEU A 323 N ASP A 318 SHEET 1 D 4 VAL A 378 LEU A 381 0 SHEET 2 D 4 LEU A 431 ASP A 436 1 O LYS A 434 N PHE A 379 SHEET 3 D 4 VAL A 397 TYR A 402 1 N LEU A 398 O LEU A 431 SHEET 4 D 4 THR A 452 TYR A 456 -1 O THR A 452 N TYR A 401 SSBOND 1 CYS A 61 CYS A 64 1555 1555 2.12 SSBOND 2 CYS A 90 CYS A 97 1555 1555 2.06 LINK BA BA A 1 OE2 GLU A 123 1555 3555 3.62 LINK BA BA A 1 OE1 GLU A 194 1555 1555 3.71 LINK BA BA A 1 OE2 GLU A 194 1555 1555 2.93 LINK BA BA A 1 O HOH A 555 1555 3555 2.68 LINK BA BA A 1 O HOH A 599 1555 3555 2.09 CISPEP 1 PHE A 105 PRO A 106 0 -5.08 CISPEP 2 PHE A 311 PRO A 312 0 5.66 CISPEP 3 TYR A 450 PRO A 451 0 -3.80 SITE 1 AC1 4 GLU A 123 GLU A 194 HOH A 555 HOH A 599 SITE 1 AC2 4 GLU A 272 LEU A 344 GLU A 345 SER A 346 SITE 1 AC3 3 GLU A 99 HIS A 100 SER A 119 CRYST1 136.560 136.560 69.524 90.00 90.00 90.00 I 4 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 0.007323 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007323 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014384 0.00000