HEADER ELECTRON TRANSPORT 16-APR-96 1MEK TITLE HUMAN PROTEIN DISULFIDE ISOMERASE, NMR, 40 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN DISULFIDE ISOMERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PROLYL 4-HYDROXYLASE BETA SUBUNIT; COMPND 5 EC: 5.3.4.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET-12 KEYWDS ELECTRON TRANSPORT, REDOX-ACTIVE CENTER, ISOMERASE, ENDOPLASMIC KEYWDS 2 RETICULUM EXPDTA SOLUTION NMR NUMMDL 40 AUTHOR J.KEMMINK,N.J.DARBY,K.DIJKSTRA,M.NILGES,T.E.CREIGHTON REVDAT 4 16-OCT-24 1MEK 1 REMARK REVDAT 3 23-FEB-22 1MEK 1 REMARK REVDAT 2 24-FEB-09 1MEK 1 VERSN REVDAT 1 21-APR-97 1MEK 0 JRNL AUTH J.KEMMINK,N.J.DARBY,K.DIJKSTRA,M.NILGES,T.E.CREIGHTON JRNL TITL STRUCTURE DETERMINATION OF THE N-TERMINAL THIOREDOXIN-LIKE JRNL TITL 2 DOMAIN OF PROTEIN DISULFIDE ISOMERASE USING MULTIDIMENSIONAL JRNL TITL 3 HETERONUCLEAR 13C/15N NMR SPECTROSCOPY. JRNL REF BIOCHEMISTRY V. 35 7684 1996 JRNL REFN ISSN 0006-2960 JRNL PMID 8672469 JRNL DOI 10.1021/BI960335M REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.KEMMINK,N.J.DARBY,K.DIJKSTRA,R.M.SCHEEK,T.E.CREIGHTON REMARK 1 TITL NUCLEAR MAGNETIC RESONANCE CHARACTERIZATION OF THE REMARK 1 TITL 2 N-TERMINAL THIOREDOXIN-LIKE DOMAIN OF PROTEIN DISULFIDE REMARK 1 TITL 3 ISOMERASE REMARK 1 REF PROTEIN SCI. V. 4 2587 1995 REMARK 1 REFN ISSN 0961-8368 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES WERE DETERMINED USING A REMARK 3 HYBRID DISTANCE GEOMETRY/SIMULATED ANNEALING APPROACH (M. NILGES, REMARK 3 G.M. CLORE, A.M. GRONENBORN, FEBS LETT. 229, 317, 1988). THE REMARK 3 STRUCTURES ARE BASED ON 1270 INTERPROTON DISTANCE RESTRAINTS REMARK 3 DERIVED FROM NOE MEASUREMENTS; 34 HYDROGEN BOND DISTANCE REMARK 3 RESTRAINTS DERIVED FROM 17 SLOWLY EXCHANGING AMIDE PROTONS AND REMARK 3 OBSERVED NOE PATTERNS; AND 5 DISTANCE RESTRAINTS WHICH DEFINE REMARK 3 THE DISULFIDE BOND BETWEEN CYS 36 AND CYS 39. REMARK 4 REMARK 4 1MEK COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000174975. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 40 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 O LEU A 42 H TYR A 46 1.60 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 2 PHE A 87 CE1 PHE A 87 CZ 0.128 REMARK 500 10 TYR A 26 CE1 TYR A 26 CZ 0.125 REMARK 500 10 TYR A 26 CZ TYR A 26 CE2 -0.086 REMARK 500 27 TYR A 26 CE1 TYR A 26 CZ 0.078 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 1 ASP A 7 -88.28 56.99 REMARK 500 1 GLU A 19 -63.06 -91.06 REMARK 500 1 SER A 71 17.82 57.42 REMARK 500 1 ALA A 94 -54.99 -175.33 REMARK 500 1 ALA A 101 -154.29 -116.50 REMARK 500 1 ARG A 103 -42.47 -143.49 REMARK 500 1 THR A 116 -71.08 -109.73 REMARK 500 2 ALA A 2 101.26 55.38 REMARK 500 2 GLU A 6 -82.40 -113.80 REMARK 500 2 HIS A 8 16.11 57.88 REMARK 500 2 LYS A 25 -73.72 -90.84 REMARK 500 2 HIS A 38 18.19 57.72 REMARK 500 2 SER A 58 177.82 -57.57 REMARK 500 2 GLU A 69 -49.00 -146.88 REMARK 500 2 GLU A 70 44.18 -103.10 REMARK 500 2 ALA A 94 -49.07 -162.94 REMARK 500 2 SER A 95 75.37 -150.36 REMARK 500 2 THR A 100 89.72 -150.76 REMARK 500 2 ALA A 101 -82.13 -134.22 REMARK 500 2 ARG A 103 43.34 -166.63 REMARK 500 3 ALA A 2 95.74 53.73 REMARK 500 3 GLU A 6 -82.48 -99.85 REMARK 500 3 HIS A 24 -155.04 -122.44 REMARK 500 3 SER A 58 72.50 54.00 REMARK 500 3 GLU A 69 -53.14 -136.02 REMARK 500 3 VAL A 79 95.74 51.33 REMARK 500 3 THR A 93 -159.68 44.32 REMARK 500 3 ALA A 94 96.92 55.71 REMARK 500 3 SER A 95 77.23 53.97 REMARK 500 3 ALA A 101 -161.67 -108.75 REMARK 500 4 ALA A 2 100.50 55.31 REMARK 500 4 LYS A 25 -74.66 -73.62 REMARK 500 4 SER A 58 47.03 -90.42 REMARK 500 4 GLU A 59 36.12 34.88 REMARK 500 4 GLU A 69 -41.81 -141.12 REMARK 500 4 GLU A 70 34.33 -92.74 REMARK 500 4 VAL A 79 86.75 48.30 REMARK 500 4 ASP A 92 -66.05 -99.65 REMARK 500 4 ALA A 94 -43.71 -158.09 REMARK 500 4 ALA A 101 -152.28 -69.67 REMARK 500 4 ARG A 103 -57.60 -154.48 REMARK 500 4 THR A 116 30.73 -142.21 REMARK 500 5 GLU A 4 130.48 59.37 REMARK 500 5 GLU A 5 127.45 58.80 REMARK 500 5 ASP A 7 -88.25 56.23 REMARK 500 5 ALA A 23 -70.09 -67.08 REMARK 500 5 LYS A 25 -77.99 -49.04 REMARK 500 5 GLU A 69 -50.73 -125.25 REMARK 500 5 THR A 93 28.23 43.10 REMARK 500 5 ALA A 94 -81.42 -150.07 REMARK 500 REMARK 500 THIS ENTRY HAS 467 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 13 0.16 SIDE CHAIN REMARK 500 1 ARG A 61 0.31 SIDE CHAIN REMARK 500 1 ARG A 80 0.31 SIDE CHAIN REMARK 500 1 ARG A 89 0.28 SIDE CHAIN REMARK 500 1 ARG A 103 0.30 SIDE CHAIN REMARK 500 1 ARG A 115 0.18 SIDE CHAIN REMARK 500 2 ARG A 13 0.29 SIDE CHAIN REMARK 500 2 ARG A 61 0.32 SIDE CHAIN REMARK 500 2 ARG A 80 0.22 SIDE CHAIN REMARK 500 2 ARG A 89 0.23 SIDE CHAIN REMARK 500 2 ARG A 103 0.31 SIDE CHAIN REMARK 500 2 ARG A 115 0.31 SIDE CHAIN REMARK 500 3 ARG A 13 0.15 SIDE CHAIN REMARK 500 3 ARG A 61 0.32 SIDE CHAIN REMARK 500 3 ARG A 80 0.31 SIDE CHAIN REMARK 500 3 ARG A 89 0.27 SIDE CHAIN REMARK 500 3 ARG A 103 0.22 SIDE CHAIN REMARK 500 3 ARG A 115 0.24 SIDE CHAIN REMARK 500 4 ARG A 13 0.26 SIDE CHAIN REMARK 500 4 ARG A 61 0.26 SIDE CHAIN REMARK 500 4 ARG A 80 0.25 SIDE CHAIN REMARK 500 4 ARG A 89 0.22 SIDE CHAIN REMARK 500 4 ARG A 103 0.18 SIDE CHAIN REMARK 500 4 ARG A 115 0.28 SIDE CHAIN REMARK 500 5 ARG A 13 0.27 SIDE CHAIN REMARK 500 5 ARG A 61 0.18 SIDE CHAIN REMARK 500 5 ARG A 80 0.26 SIDE CHAIN REMARK 500 5 ARG A 89 0.30 SIDE CHAIN REMARK 500 5 ARG A 103 0.23 SIDE CHAIN REMARK 500 5 ARG A 115 0.26 SIDE CHAIN REMARK 500 6 ARG A 13 0.21 SIDE CHAIN REMARK 500 6 ARG A 61 0.31 SIDE CHAIN REMARK 500 6 ARG A 80 0.24 SIDE CHAIN REMARK 500 6 ARG A 89 0.22 SIDE CHAIN REMARK 500 6 ARG A 103 0.30 SIDE CHAIN REMARK 500 6 ARG A 115 0.28 SIDE CHAIN REMARK 500 7 ARG A 13 0.22 SIDE CHAIN REMARK 500 7 ARG A 61 0.17 SIDE CHAIN REMARK 500 7 ARG A 80 0.31 SIDE CHAIN REMARK 500 7 ARG A 89 0.26 SIDE CHAIN REMARK 500 7 ARG A 103 0.30 SIDE CHAIN REMARK 500 7 ARG A 115 0.32 SIDE CHAIN REMARK 500 8 ARG A 13 0.22 SIDE CHAIN REMARK 500 8 ARG A 61 0.17 SIDE CHAIN REMARK 500 8 ARG A 80 0.19 SIDE CHAIN REMARK 500 8 ARG A 89 0.28 SIDE CHAIN REMARK 500 8 ARG A 103 0.17 SIDE CHAIN REMARK 500 8 ARG A 115 0.27 SIDE CHAIN REMARK 500 9 ARG A 13 0.32 SIDE CHAIN REMARK 500 9 ARG A 61 0.27 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 240 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1MEK A 1 120 UNP P07237 PDIA1_HUMAN 18 137 SEQRES 1 A 120 ASP ALA PRO GLU GLU GLU ASP HIS VAL LEU VAL LEU ARG SEQRES 2 A 120 LYS SER ASN PHE ALA GLU ALA LEU ALA ALA HIS LYS TYR SEQRES 3 A 120 LEU LEU VAL GLU PHE TYR ALA PRO TRP CYS GLY HIS CYS SEQRES 4 A 120 LYS ALA LEU ALA PRO GLU TYR ALA LYS ALA ALA GLY LYS SEQRES 5 A 120 LEU LYS ALA GLU GLY SER GLU ILE ARG LEU ALA LYS VAL SEQRES 6 A 120 ASP ALA THR GLU GLU SER ASP LEU ALA GLN GLN TYR GLY SEQRES 7 A 120 VAL ARG GLY TYR PRO THR ILE LYS PHE PHE ARG ASN GLY SEQRES 8 A 120 ASP THR ALA SER PRO LYS GLU TYR THR ALA GLY ARG GLU SEQRES 9 A 120 ALA ASP ASP ILE VAL ASN TRP LEU LYS LYS ARG THR GLY SEQRES 10 A 120 PRO ALA ALA HELIX 1 1 PHE A 17 ALA A 23 1 7 HELIX 2 2 ALA A 43 GLY A 51 1 9 HELIX 3 3 ALA A 74 TYR A 77 1 4 HELIX 4 4 ALA A 105 LYS A 113 1 9 SHEET 1 A 3 THR A 84 ARG A 89 0 SHEET 2 A 3 TYR A 26 TYR A 32 -1 N PHE A 31 O THR A 84 SHEET 3 A 3 LYS A 64 ASP A 66 1 N VAL A 65 O GLU A 30 SSBOND 1 CYS A 36 CYS A 39 1555 1555 2.02 CISPEP 1 TYR A 82 PRO A 83 1 0.25 CISPEP 2 TYR A 82 PRO A 83 2 -0.06 CISPEP 3 TYR A 82 PRO A 83 3 0.19 CISPEP 4 TYR A 82 PRO A 83 4 0.04 CISPEP 5 TYR A 82 PRO A 83 5 0.38 CISPEP 6 TYR A 82 PRO A 83 6 0.39 CISPEP 7 TYR A 82 PRO A 83 7 0.07 CISPEP 8 TYR A 82 PRO A 83 8 -0.08 CISPEP 9 TYR A 82 PRO A 83 9 0.08 CISPEP 10 TYR A 82 PRO A 83 10 0.24 CISPEP 11 TYR A 82 PRO A 83 11 -0.04 CISPEP 12 TYR A 82 PRO A 83 12 0.15 CISPEP 13 TYR A 82 PRO A 83 13 0.16 CISPEP 14 TYR A 82 PRO A 83 14 0.00 CISPEP 15 TYR A 82 PRO A 83 15 -0.24 CISPEP 16 TYR A 82 PRO A 83 16 0.07 CISPEP 17 TYR A 82 PRO A 83 17 0.00 CISPEP 18 TYR A 82 PRO A 83 18 0.21 CISPEP 19 TYR A 82 PRO A 83 19 0.12 CISPEP 20 TYR A 82 PRO A 83 20 0.13 CISPEP 21 TYR A 82 PRO A 83 21 0.12 CISPEP 22 TYR A 82 PRO A 83 22 -0.06 CISPEP 23 TYR A 82 PRO A 83 23 0.17 CISPEP 24 TYR A 82 PRO A 83 24 0.03 CISPEP 25 TYR A 82 PRO A 83 25 0.03 CISPEP 26 TYR A 82 PRO A 83 26 0.24 CISPEP 27 TYR A 82 PRO A 83 27 0.22 CISPEP 28 TYR A 82 PRO A 83 28 0.01 CISPEP 29 TYR A 82 PRO A 83 29 0.21 CISPEP 30 TYR A 82 PRO A 83 30 0.38 CISPEP 31 TYR A 82 PRO A 83 31 0.18 CISPEP 32 TYR A 82 PRO A 83 32 0.10 CISPEP 33 TYR A 82 PRO A 83 33 0.13 CISPEP 34 TYR A 82 PRO A 83 34 0.41 CISPEP 35 TYR A 82 PRO A 83 35 0.07 CISPEP 36 TYR A 82 PRO A 83 36 0.16 CISPEP 37 TYR A 82 PRO A 83 37 0.30 CISPEP 38 TYR A 82 PRO A 83 38 0.18 CISPEP 39 TYR A 82 PRO A 83 39 -0.22 CISPEP 40 TYR A 82 PRO A 83 40 -0.01 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1