PDB Short entry for 2KFW HEADER ISOMERASE 28-FEB-09 2KFW TITLE SOLUTION STRUCTURE OF FULL-LENGTH SLYD FROM E.COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: FKBP-TYPE PEPTIDYL-PROLYL CIS-TRANS ISOMERASE SLYD; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PPIASE, ROTAMASE, HISTIDINE-RICH PROTEIN, WHP; COMPND 5 EC: 5.2.1.8; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: SLYD, B3349, JW3311; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: M15; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PQE60 KEYWDS PROTEIN, SLYD, COBALT, COPPER, CYTOPLASM, ISOMERASE, METAL-BINDING, KEYWDS 2 NICKEL, ROTAMASE, ZINC EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR L.MARTINO,Y.HE,K.L.HANDS-TAYLOR,E.R.VALENTINE,G.KELLY,C.GIANCOLA, AUTHOR 2 M.R.CONTE REVDAT 3 01-MAY-24 2KFW 1 REMARK REVDAT 2 26-FEB-20 2KFW 1 REMARK REVDAT 1 15-SEP-09 2KFW 0 JRNL AUTH L.MARTINO,Y.HE,K.L.HANDS-TAYLOR,E.R.VALENTINE,G.KELLY, JRNL AUTH 2 C.GIANCOLA,M.R.CONTE JRNL TITL THE INTERACTION OF THE ESCHERICHIA COLI PROTEIN SLYD WITH JRNL TITL 2 NICKEL IONS ILLUMINATES THE MECHANISM OF REGULATION OF ITS JRNL TITL 3 PEPTIDYL-PROLYL ISOMERASE ACTIVITY. JRNL REF FEBS J. V. 276 4529 2009 JRNL REFN ISSN 1742-464X JRNL PMID 19645725 JRNL DOI 10.1111/J.1742-4658.2009.07159.X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR, X-PLOR REMARK 3 AUTHORS : BRUNGER (X-PLOR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KFW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000101070. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.25 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 20 MM TRIS, 100 MM POTASSIUM REMARK 210 CHLORIDE, 1 MM DTT, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCA; 3D HN(CO)CA; 3D HNCACB; REMARK 210 3D CBCA(CO)NH; 3D HCCH-TOCSY; 3D REMARK 210 HNCO; 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; 3D HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, TALOS, MOLMOL, XEASY, REMARK 210 PROCHECKNMR, VNMR, TOPSPIN, REMARK 210 NMRDRAW REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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 H ASP A 161 OD2 ASP A 163 1.54 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 SER A 40 -63.42 177.78 REMARK 500 1 HIS A 52 -88.95 -155.17 REMARK 500 1 GLU A 53 143.45 167.31 REMARK 500 1 ASP A 66 73.57 170.57 REMARK 500 1 ALA A 67 -83.74 -171.85 REMARK 500 1 PHE A 84 115.21 -177.51 REMARK 500 1 MET A 85 22.31 -141.33 REMARK 500 1 VAL A 87 32.36 -90.27 REMARK 500 1 GLU A 89 104.54 166.64 REMARK 500 1 MET A 94 155.39 -46.54 REMARK 500 1 ALA A 111 112.16 179.28 REMARK 500 1 ASP A 114 157.26 -47.12 REMARK 500 1 ASP A 115 -56.62 73.49 REMARK 500 1 ALA A 126 -166.55 -129.94 REMARK 500 1 ALA A 155 -89.49 52.33 REMARK 500 1 HIS A 159 -164.12 -60.46 REMARK 500 1 HIS A 160 -165.53 -58.14 REMARK 500 1 ASP A 161 80.97 -162.98 REMARK 500 1 CYS A 168 -81.50 -117.29 REMARK 500 1 HIS A 173 -73.10 -68.89 REMARK 500 1 HIS A 177 -65.71 -103.27 REMARK 500 1 HIS A 179 -74.50 64.08 REMARK 500 1 GLU A 182 172.11 -53.86 REMARK 500 1 CYS A 184 148.52 64.13 REMARK 500 1 ASN A 190 -179.51 -57.54 REMARK 500 2 ALA A 30 57.27 -144.66 REMARK 500 2 SER A 40 -43.71 169.56 REMARK 500 2 LEU A 41 168.52 -43.68 REMARK 500 2 HIS A 52 -111.06 -59.30 REMARK 500 2 ASP A 66 66.52 -175.22 REMARK 500 2 ALA A 67 96.89 175.56 REMARK 500 2 TYR A 68 -61.57 65.91 REMARK 500 2 GLN A 70 -143.70 65.83 REMARK 500 2 PHE A 84 -79.20 -75.84 REMARK 500 2 MET A 85 89.66 53.29 REMARK 500 2 GLU A 89 107.37 170.94 REMARK 500 2 LEU A 125 -70.10 -73.41 REMARK 500 2 ALA A 126 -167.30 -109.31 REMARK 500 2 HIS A 153 23.11 49.30 REMARK 500 2 ALA A 155 -61.27 -95.38 REMARK 500 2 HIS A 159 38.62 -95.03 REMARK 500 2 ASP A 161 -107.92 -139.35 REMARK 500 2 HIS A 162 56.63 176.22 REMARK 500 2 HIS A 164 35.90 -99.16 REMARK 500 2 HIS A 173 106.13 57.26 REMARK 500 2 HIS A 175 -161.56 -102.01 REMARK 500 2 HIS A 177 82.36 -150.69 REMARK 500 2 CYS A 184 94.23 48.74 REMARK 500 2 CYS A 185 -38.58 -143.74 REMARK 500 2 ASN A 190 -161.63 49.49 REMARK 500 REMARK 500 THIS ENTRY HAS 551 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 16 0.32 SIDE CHAIN REMARK 500 1 ARG A 78 0.26 SIDE CHAIN REMARK 500 1 ARG A 95 0.32 SIDE CHAIN REMARK 500 1 ARG A 140 0.20 SIDE CHAIN REMARK 500 2 ARG A 16 0.21 SIDE CHAIN REMARK 500 2 ARG A 78 0.10 SIDE CHAIN REMARK 500 2 ARG A 95 0.17 SIDE CHAIN REMARK 500 2 ARG A 140 0.29 SIDE CHAIN REMARK 500 3 ARG A 16 0.20 SIDE CHAIN REMARK 500 3 ARG A 78 0.32 SIDE CHAIN REMARK 500 3 ARG A 95 0.25 SIDE CHAIN REMARK 500 3 ARG A 140 0.31 SIDE CHAIN REMARK 500 4 ARG A 78 0.15 SIDE CHAIN REMARK 500 4 ARG A 95 0.31 SIDE CHAIN REMARK 500 4 ARG A 140 0.11 SIDE CHAIN REMARK 500 5 ARG A 16 0.31 SIDE CHAIN REMARK 500 5 ARG A 95 0.23 SIDE CHAIN REMARK 500 5 ARG A 140 0.14 SIDE CHAIN REMARK 500 6 ARG A 16 0.29 SIDE CHAIN REMARK 500 6 ARG A 78 0.29 SIDE CHAIN REMARK 500 6 ARG A 95 0.30 SIDE CHAIN REMARK 500 7 ARG A 16 0.15 SIDE CHAIN REMARK 500 7 ARG A 78 0.25 SIDE CHAIN REMARK 500 7 ARG A 95 0.19 SIDE CHAIN REMARK 500 7 ARG A 140 0.28 SIDE CHAIN REMARK 500 8 ARG A 16 0.20 SIDE CHAIN REMARK 500 8 ARG A 78 0.25 SIDE CHAIN REMARK 500 8 ARG A 95 0.27 SIDE CHAIN REMARK 500 8 ARG A 140 0.20 SIDE CHAIN REMARK 500 9 ARG A 16 0.20 SIDE CHAIN REMARK 500 9 ARG A 78 0.22 SIDE CHAIN REMARK 500 9 ARG A 95 0.31 SIDE CHAIN REMARK 500 9 ARG A 140 0.24 SIDE CHAIN REMARK 500 10 ARG A 16 0.31 SIDE CHAIN REMARK 500 10 ARG A 78 0.14 SIDE CHAIN REMARK 500 10 ARG A 95 0.23 SIDE CHAIN REMARK 500 10 ARG A 140 0.31 SIDE CHAIN REMARK 500 11 ARG A 16 0.32 SIDE CHAIN REMARK 500 11 ARG A 78 0.31 SIDE CHAIN REMARK 500 11 ARG A 95 0.24 SIDE CHAIN REMARK 500 11 ARG A 140 0.30 SIDE CHAIN REMARK 500 12 ARG A 16 0.32 SIDE CHAIN REMARK 500 12 ARG A 78 0.30 SIDE CHAIN REMARK 500 12 ARG A 95 0.30 SIDE CHAIN REMARK 500 12 ARG A 140 0.28 SIDE CHAIN REMARK 500 13 ARG A 16 0.23 SIDE CHAIN REMARK 500 13 ARG A 78 0.28 SIDE CHAIN REMARK 500 13 ARG A 95 0.20 SIDE CHAIN REMARK 500 13 ARG A 140 0.31 SIDE CHAIN REMARK 500 14 ARG A 16 0.32 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 76 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16240 RELATED DB: BMRB DBREF 2KFW A 1 196 UNP P0A9K9 SLYD_ECOLI 1 196 SEQRES 1 A 196 MET LYS VAL ALA LYS ASP LEU VAL VAL SER LEU ALA TYR SEQRES 2 A 196 GLN VAL ARG THR GLU ASP GLY VAL LEU VAL ASP GLU SER SEQRES 3 A 196 PRO VAL SER ALA PRO LEU ASP TYR LEU HIS GLY HIS GLY SEQRES 4 A 196 SER LEU ILE SER GLY LEU GLU THR ALA LEU GLU GLY HIS SEQRES 5 A 196 GLU VAL GLY ASP LYS PHE ASP VAL ALA VAL GLY ALA ASN SEQRES 6 A 196 ASP ALA TYR GLY GLN TYR ASP GLU ASN LEU VAL GLN ARG SEQRES 7 A 196 VAL PRO LYS ASP VAL PHE MET GLY VAL ASP GLU LEU GLN SEQRES 8 A 196 VAL GLY MET ARG PHE LEU ALA GLU THR ASP GLN GLY PRO SEQRES 9 A 196 VAL PRO VAL GLU ILE THR ALA VAL GLU ASP ASP HIS VAL SEQRES 10 A 196 VAL VAL ASP GLY ASN HIS MET LEU ALA GLY GLN ASN LEU SEQRES 11 A 196 LYS PHE ASN VAL GLU VAL VAL ALA ILE ARG GLU ALA THR SEQRES 12 A 196 GLU GLU GLU LEU ALA HIS GLY HIS VAL HIS GLY ALA HIS SEQRES 13 A 196 ASP HIS HIS HIS ASP HIS ASP HIS ASP GLY CYS CYS GLY SEQRES 14 A 196 GLY HIS GLY HIS ASP HIS GLY HIS GLU HIS GLY GLY GLU SEQRES 15 A 196 GLY CYS CYS GLY GLY LYS GLY ASN GLY GLY CYS GLY CYS SEQRES 16 A 196 HIS HELIX 1 1 ILE A 42 GLU A 50 1 9 HELIX 2 2 PRO A 80 PHE A 84 5 5 HELIX 3 3 THR A 143 GLY A 150 1 8 SHEET 1 A 3 VAL A 21 GLU A 25 0 SHEET 2 A 3 VAL A 8 THR A 17 -1 N THR A 17 O VAL A 21 SHEET 3 A 3 ASP A 33 LEU A 35 -1 O TYR A 34 N VAL A 9 SHEET 1 B 4 VAL A 21 GLU A 25 0 SHEET 2 B 4 VAL A 8 THR A 17 -1 N THR A 17 O VAL A 21 SHEET 3 B 4 LYS A 131 VAL A 136 -1 O LYS A 131 N ARG A 16 SHEET 4 B 4 LYS A 57 ALA A 61 -1 N PHE A 58 O VAL A 134 SHEET 1 C 2 GLN A 77 VAL A 79 0 SHEET 2 C 2 VAL A 117 VAL A 119 -1 O VAL A 119 N GLN A 77 SHEET 1 D 2 ARG A 95 THR A 100 0 SHEET 2 D 2 GLY A 103 GLU A 108 -1 O VAL A 105 N ALA A 98 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