HEADER ISOMERASE 22-FEB-08 2K18
TITLE SOLUTION STRUCTURE OF BB' DOMAINS OF HUMAN PROTEIN DISULFIDE ISOMERASE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PROTEIN DISULFIDE-ISOMERASE;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: RESIDUES 135-357;
COMPND 5 SYNONYM: PDI, PROLYL 4- HYDROXYLASE SUBUNIT BETA, CELLULAR THYROID
COMPND 6 HORMONE-BINDING PROTEIN, P55;
COMPND 7 EC: 5.3.4.1;
COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: P4HB, ERBA2L, PDI, PDIA1, PO4DB;
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: PGEX-6P1
KEYWDS PDI, ENDOPLASMIC RETICULUM, DISULFIDE BONDS, PROTEIN FOLDING,
KEYWDS 2 CHAPERONE, ISOMERASE, MEMBRANE, REDOX-ACTIVE CENTER
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR A.Y.DENISOV,P.MAATTANEN,C.DABROWSKI,G.KOZLOV,D.Y.THOMAS,K.GEHRING
REVDAT 4 16-MAR-22 2K18 1 REMARK SEQADV
REVDAT 3 10-MAR-09 2K18 1 JRNL
REVDAT 2 24-FEB-09 2K18 1 VERSN
REVDAT 1 29-APR-08 2K18 0
JRNL AUTH A.Y.DENISOV,P.MAATTANEN,C.DABROWSKI,G.KOZLOV,D.Y.THOMAS,
JRNL AUTH 2 K.GEHRING
JRNL TITL SOLUTION STRUCTURE OF THE BB' DOMAINS OF HUMAN PROTEIN
JRNL TITL 2 DISULFIDE ISOMERASE.
JRNL REF FEBS J. V. 276 1440 2009
JRNL REFN ISSN 1742-464X
JRNL PMID 19187238
JRNL DOI 10.1111/J.1742-4658.2009.06884.X
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : NMRPIPE 2.0, CNS 1.1
REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX
REMARK 3 (NMRPIPE), BRUNGER, ADAMS, CLORE, GROS, NILGES AND
REMARK 3 READ (CNS)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE WAS REFINED BY USING STANDARD
REMARK 3 PROTOCOL IN CNS WITH RESTRAINTS FROM NOE DISTANCES, BACKBONE
REMARK 3 TORSIONS, HYDROGEN BONDS AND RESIDUAL DIPOLAR COUPLINGS
REMARK 4
REMARK 4 2K18 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-FEB-08.
REMARK 100 THE DEPOSITION ID IS D_1000100547.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 303
REMARK 210 PH : 7.0
REMARK 210 IONIC STRENGTH : 0.1
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : 2 MM [U-99% 13C; U-99% 15N] HPDI
REMARK 210 -BB, 25 MM SODIUM PHOSPHATE, 70
REMARK 210 MM SODIUM CHLORIDE, 0.5 MM EDTA,
REMARK 210 5 MM DTT, 90% H2O/10% D2O; 2 MM
REMARK 210 HPDI-BB, 25 MM SODIUM PHOSPHATE,
REMARK 210 70 MM SODIUM CHLORIDE, 0.5 MM
REMARK 210 EDTA, 5 MM DTT, 100% D2O; 0.5 MM
REMARK 210 [U-99% 15N] HPDI-BB, 25 MM
REMARK 210 SODIUM PHOSPHATE, 70 MM SODIUM
REMARK 210 CHLORIDE, 0.5 MM EDTA, 5 MM DTT,
REMARK 210 12 MG/ML PF1 PHAGES, 90% H2O/10%
REMARK 210 D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC;
REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY;
REMARK 210 IPAP-HSQC
REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : UNITY INOVA; DRX
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : XEASY 1.3.13, ARIA 1.1, TALOS
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 200
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST
REMARK 210 ENERGY AND THE LEAST RESTRAINT
REMARK 210 VIOLATIONS
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: STRUCTURE WAS DETERMINED USING MULTI-DIMENTIONAL NMR
REMARK 210 SPECTROSCOPY
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 205 H ARG A 209 1.59
REMARK 500 O VAL A 21 H SER A 24 1.59
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 PRO A 2 89.57 -68.86
REMARK 500 1 LEU A 3 148.18 -175.19
REMARK 500 1 ASP A 72 -178.92 -51.12
REMARK 500 1 ASP A 81 -127.40 71.96
REMARK 500 1 GLU A 123 80.82 72.09
REMARK 500 1 ILE A 124 92.40 43.26
REMARK 500 1 PRO A 133 -93.68 -62.00
REMARK 500 1 SER A 135 -34.37 83.47
REMARK 500 1 SER A 137 -46.59 91.14
REMARK 500 1 SER A 164 -46.70 -28.86
REMARK 500 1 ASP A 165 47.03 36.55
REMARK 500 1 HIS A 166 -5.62 -51.07
REMARK 500 1 THR A 167 -68.08 -104.86
REMARK 500 1 LYS A 179 -145.67 -131.08
REMARK 500 1 LYS A 180 -51.66 -18.77
REMARK 500 1 GLU A 181 19.30 -67.18
REMARK 500 1 GLU A 192 -75.47 -178.71
REMARK 500 1 PRO A 200 -179.46 -68.97
REMARK 500 1 GLU A 201 -76.97 -159.02
REMARK 500 1 GLU A 204 -110.54 -117.97
REMARK 500 1 THR A 206 -77.23 -33.71
REMARK 500 1 PRO A 224 -90.57 -68.72
REMARK 500 1 HIS A 225 -75.50 64.24
REMARK 500 2 LEU A 3 -167.93 -70.31
REMARK 500 2 SER A 59 -32.31 -135.27
REMARK 500 2 ASP A 70 29.64 -176.74
REMARK 500 2 ASP A 81 -126.23 70.20
REMARK 500 2 GLU A 88 -72.90 -42.90
REMARK 500 2 GLU A 123 82.87 71.36
REMARK 500 2 ILE A 124 96.08 45.99
REMARK 500 2 PRO A 133 -92.19 -58.69
REMARK 500 2 LYS A 134 -108.29 -74.50
REMARK 500 2 SER A 135 -40.25 165.40
REMARK 500 2 SER A 137 -56.40 78.57
REMARK 500 2 SER A 164 -47.60 -29.59
REMARK 500 2 ASP A 165 49.04 34.54
REMARK 500 2 HIS A 166 -5.01 -50.88
REMARK 500 2 THR A 167 -68.80 -107.46
REMARK 500 2 LYS A 179 -146.28 -131.09
REMARK 500 2 LYS A 180 -57.94 -16.10
REMARK 500 2 GLU A 181 19.67 -66.58
REMARK 500 2 GLU A 192 -78.38 -168.01
REMARK 500 2 GLU A 194 -178.70 -173.46
REMARK 500 2 PRO A 200 -174.37 -68.73
REMARK 500 2 GLU A 201 -46.88 -140.68
REMARK 500 2 GLU A 204 -109.16 -134.67
REMARK 500 2 THR A 206 -70.88 -26.19
REMARK 500 2 LYS A 221 -171.73 -57.27
REMARK 500 2 PRO A 224 -152.69 -67.64
REMARK 500 2 HIS A 225 -171.87 -59.40
REMARK 500
REMARK 500 THIS ENTRY HAS 233 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 15303 RELATED DB: BMRB
REMARK 900 BB' DOMAINS OF HUMAN PDI
REMARK 900 RELATED ID: 1BJX RELATED DB: PDB
REMARK 900 B DOMAIN OF HUMAN PDI
DBREF 2K18 A 6 228 UNP P07237 PDIA1_HUMAN 135 357
SEQADV 2K18 GLY A 1 UNP P07237 EXPRESSION TAG
SEQADV 2K18 PRO A 2 UNP P07237 EXPRESSION TAG
SEQADV 2K18 LEU A 3 UNP P07237 EXPRESSION TAG
SEQADV 2K18 GLY A 4 UNP P07237 EXPRESSION TAG
SEQADV 2K18 SER A 5 UNP P07237 EXPRESSION TAG
SEQRES 1 A 228 GLY PRO LEU GLY SER PRO ALA ALA THR THR LEU PRO ASP
SEQRES 2 A 228 GLY ALA ALA ALA GLU SER LEU VAL GLU SER SER GLU VAL
SEQRES 3 A 228 ALA VAL ILE GLY PHE PHE LYS ASP VAL GLU SER ASP SER
SEQRES 4 A 228 ALA LYS GLN PHE LEU GLN ALA ALA GLU ALA ILE ASP ASP
SEQRES 5 A 228 ILE PRO PHE GLY ILE THR SER ASN SER ASP VAL PHE SER
SEQRES 6 A 228 LYS TYR GLN LEU ASP LYS ASP GLY VAL VAL LEU PHE LYS
SEQRES 7 A 228 LYS PHE ASP GLU GLY ARG ASN ASN PHE GLU GLY GLU VAL
SEQRES 8 A 228 THR LYS GLU ASN LEU LEU ASP PHE ILE LYS HIS ASN GLN
SEQRES 9 A 228 LEU PRO LEU VAL ILE GLU PHE THR GLU GLN THR ALA PRO
SEQRES 10 A 228 LYS ILE PHE GLY GLY GLU ILE LYS THR HIS ILE LEU LEU
SEQRES 11 A 228 PHE LEU PRO LYS SER VAL SER ASP TYR ASP GLY LYS LEU
SEQRES 12 A 228 SER ASN PHE LYS THR ALA ALA GLU SER PHE LYS GLY LYS
SEQRES 13 A 228 ILE LEU PHE ILE PHE ILE ASP SER ASP HIS THR ASP ASN
SEQRES 14 A 228 GLN ARG ILE LEU GLU PHE PHE GLY LEU LYS LYS GLU GLU
SEQRES 15 A 228 CYS PRO ALA VAL ARG LEU ILE THR LEU GLU GLU GLU MET
SEQRES 16 A 228 THR LYS TYR LYS PRO GLU SER GLU GLU LEU THR ALA GLU
SEQRES 17 A 228 ARG ILE THR GLU PHE CYS HIS ARG PHE LEU GLU GLY LYS
SEQRES 18 A 228 ILE LYS PRO HIS LEU MET SER
HELIX 1 1 ASP A 13 SER A 23 1 11
HELIX 2 2 SER A 37 ILE A 50 1 14
HELIX 3 3 ASN A 60 TYR A 67 1 8
HELIX 4 4 THR A 92 GLN A 104 1 13
HELIX 5 5 GLN A 114 GLY A 121 1 8
HELIX 6 6 ASP A 138 PHE A 153 1 16
HELIX 7 7 ASN A 169 GLY A 177 1 9
HELIX 8 8 LEU A 205 GLU A 219 1 15
SHEET 1 A 5 ALA A 8 THR A 10 0
SHEET 2 A 5 PHE A 55 THR A 58 1 O PHE A 55 N THR A 9
SHEET 3 A 5 ALA A 27 PHE A 31 1 N GLY A 30 O GLY A 56
SHEET 4 A 5 GLY A 73 PHE A 77 -1 O VAL A 75 N ILE A 29
SHEET 5 A 5 ARG A 84 ASN A 86 -1 O ASN A 85 N LEU A 76
SHEET 1 B 5 GLU A 110 PHE A 111 0
SHEET 2 B 5 ILE A 157 ASP A 163 1 O PHE A 161 N PHE A 111
SHEET 3 B 5 THR A 126 LEU A 132 1 N ILE A 128 O ILE A 160
SHEET 4 B 5 ALA A 185 LEU A 191 -1 O ARG A 187 N LEU A 129
SHEET 5 B 5 MET A 195 TYR A 198 -1 O TYR A 198 N LEU A 188
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
(ATOM LINES ARE NOT SHOWN.)
END
